From 111b74963cb3b5a6afcedb7f1925af5da369e5e4 Mon Sep 17 00:00:00 2001 From: geoffreyweal Date: Wed, 12 Aug 2026 07:58:44 +1200 Subject: [PATCH 1/3] Initial information about openfold3, including downloading parameters and databases --- .../Available_Applications/OpenFold3.md | 205 ++++++++++++++++++ 1 file changed, 205 insertions(+) create mode 100644 docs/Software/Available_Applications/OpenFold3.md diff --git a/docs/Software/Available_Applications/OpenFold3.md b/docs/Software/Available_Applications/OpenFold3.md new file mode 100644 index 000000000..7408b139d --- /dev/null +++ b/docs/Software/Available_Applications/OpenFold3.md @@ -0,0 +1,205 @@ +--- +title: OpenFold3 +tags: +- biology +- machine_learning +- gpu +description: Predicting protein structures from amino acid sequences with OpenFold3 +--- + +[//]: <> (APPS PAGE BOILERPLATE START) +{% set app_name = page.title | trim %} +{% set app = applications[app_name] %} +{% include "partials/app_header.html" %} +[//]: <> (APPS PAGE BOILERPLATE END) + +## Description + + +## Referencing + + +## Setting up OpenFold3 + +### Downloading the parameters files + +If you are using OpenFold3 for the first time on Mahuika, you will need to download the OpenFold3 model parameters to your directory. + +1. Load OpenFold3: + + ```bash + module load OpenFold3 + ``` + +2. Run `setup_openfold` in the terminal: + + ```bash + setup_openfold + ``` + + * You will need to write out in full the direct path to where you want to store OpenFold3 files. + * `Please specify the OpenFold cache directory`: Best idea to change this to your project folder. Example: `/nesi/project///openfold3` + * `Please specify the directory for parameter download`: This should default to your cache directory. Example `/nesi/project///openfold3` + * `Select parameters to download`: Download whatever parameters you would like. + * `Force re-download parameters even if they already exist?`: Set this to `yes` + * `Run integration tests?`: `no` + + The setup should look something like this + + ```bash + user.name@login03:~$ setup_openfold + [2026-08-11 17:54:31,291] [WARNING] [real_accelerator.py:199:get_accelerator] Setting accelerator to CPU. If you have GPU or other accelerator, we were unable to detect it. + Setting up OpenFold3... + Please specify the OpenFold cache directory (default: /home/user.name/.openfold3): /nesi/project/nesi12345/user.name/openfold3 + Please specify the directory for parameter download (default: /nesi/project/nesi12345/user.name/openfold3): + Select parameters to download: + 1) Download only the default checkpoint (openfold3-p2-155k) + 2) Download all parameters (openfold3-p2-145k, openfold3-p2-155k) + 3) Download a specific parameter by name + Enter your choice (1/2/3, default: 1): 2 + Force re-download parameters even if they already exist? (yes/no, default: no) yes + Run integration tests? (yes/no) no + Parameters directory set to: /nesi/project/nesi12345/user.name/openfold3 + Starting parameter download... + Downloading s3://openfold3-data/openfold3-parameters/of3-p2-145k.pt (2.13 GB) to /nesi/project/nesi12345/user.name/openfold3/of3-p2-145k.pt... + of3-p2-145k.pt: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.29G/2.29G [00:19<00:00, 115MB/s] + Download complete. + Downloading s3://openfold3-data/openfold3-parameters/of3-p2-155k.pt (2.13 GB) to /nesi/project/nesi12345/user.name/openfold3/of3-p2-155k.pt... + of3-p2-155k.pt: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.29G/2.29G [00:19<00:00, 116MB/s] + Download complete. + Download completed successfully. + Starting Biotite CCD setup... + Biotite CCD file at /opt/nesi/zen3/OpenFold3/0.4.4-foss-2026-CUDA-13.2.1/lib/python3.14/site-packages/biotite/structure/info/components.bcif is up-to-date with s3://openfold3-data/components.bcif, skipping. + Skipping integration tests. + Setup configuration saved to /nesi/project/nesi12345/user.name/openfold3/setup_config.json + ``` + + !!! warning + + If you get an error message relating to Biotite CCD, get in touch with support. + +3. Add the following line to your `.bashrc` and source it: + + ```bash + printf '\n# Path to your OpenFold3 Cache\nexport OPENFOLD_CACHE=/nesi/project///openfold3\n' >> ~/.bashrc + source ~/.bashrc + ``` + + Check that your `OPENFOLD_CACHE` path is correct: + + ```bash + echo $OPENFOLD_CACHE + ``` + + If this doesn't look right, you will need to change your `~/.bashrc` file by using `nano` or `vim` + +4. Test that your setup was successful. In the terminal, copy the following json file from [openfold3](from https://github.com/aqlaboratory/openfold-3/blob/main/examples/example_inference_inputs/query_ubiquitin.json): + + ```bash + cat > query_ubiquitin.json << 'EOF' + { + "queries": { + "ubiquitin": { + "chains": [ + { + "molecule_type": "protein", + "chain_ids": ["A"], + "sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG" + } + ] + } + } + } + EOF + ``` + + Then run the following in your terminal: + + ```bash + python - <<'EOF' + import os, pathlib, zipfile + + import openfold3 + from openfold3.projects.of3_all_atom.config.inference_query_format import InferenceQuerySet + print("[ok] openfold3 imports") + + import biotite.structure.info as info + print(f"[ok] CCD: {len(info.all_residues())} components, " + f"ALA={info.residue('ALA').array_length()} atoms") + + cache = pathlib.Path(os.environ.get("OPENFOLD_CACHE", pathlib.Path.home() / ".openfold3")) + ckpts = sorted(cache.glob("*.pt")) + assert ckpts, f"no checkpoint in {cache}" + for c in ckpts: + print(f"[ok] checkpoint {c.name}: {c.stat().st_size/1e9:.2f} GB, " + f"intact={zipfile.is_zipfile(c)}") + + InferenceQuerySet.from_json("query_ubiquitin.json") + print("[ok] query JSON validates against this version's schema") + EOF + ``` + + If successful, you will get the following output: + + ```bash + [2026-08-11 18:03:24,289] [WARNING] [real_accelerator.py:199:get_accelerator] Setting accelerator to CPU. If you have GPU or other accelerator, we were unable to detect it. + [ok] openfold3 imports + [ok] CCD: 49282 components, ALA=13 atoms + [ok] checkpoint of3-p2-145k.pt: 2.29 GB, intact=True + [ok] checkpoint of3-p2-155k.pt: 2.29 GB, intact=True + [ok] query JSON validates against this version's schema + ``` + +### Downloading the database files + +1. `cd` into the path where you would like to store your OpenFold3 databases. Ideally, this should be in your project directory: + + ```bash + mkdir -p /nesi/project//openfold3_databases + cd /nesi/project//openfold3_databases + ``` + +2. Load OpenFold3: + + ```bash + module load OpenFold3 + ``` + +3. Download the desired databases from the list below: + + ```bash + aws s3 ls --no-sign-request --human-readable s3://openfold/alignment_databases/ + ``` + + For example, the following will download and uncompress your desired databases: + + ```bash + aws s3 cp --no-sign-request s3://openfold/alignment_databases/rfam.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/pdb_seqres.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/rnacentral.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/nucleotide_collection.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniref90.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniprot.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/mgnify.fasta.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/uniref30.tar.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/cfdb.tar.gz . + aws s3 cp --no-sign-request s3://openfold/alignment_databases/bfd.tar.gz . + ``` + + Be mindful of the amount of space you will need before you download the databases: + + | # | Database | Format | Size | Type | + |----|----------------------|------------|--------|--------------------| + | 1 | pdb_seqres | .fasta.gz | 55 MB | protein | + | 2 | rfam | .fasta.gz | 61 MB | RNA | + | 3 | nucleotide_collection | .fasta.gz | 2.3 GB | RNA | + | 4 | rnacentral | .fasta.gz | 4.2 GB | RNA | + | 5 | uniref90 | .fasta.gz | 47 GB | protein | + | 6 | uniprot | .fasta.gz | 61 GB | protein | + | 7 | mgnify | .fasta.gz | 79 GB | protein | + | 8 | uniref30 | .tar.gz | 141 GB | protein (HHblits) | + | 9 | cfdb | .tar.gz | 290 GB | protein (HHblits) | + | 10 | bfd | .tar.gz | 292 GB | protein (HHblits) | + + **Total download:** ~918 GB — budget ~3–4 TB of filesystem for the decompressed set. + From 36ca050599b5c607294c2b086b00af0a19a7ba5a Mon Sep 17 00:00:00 2001 From: geoffreyweal Date: Wed, 12 Aug 2026 08:22:20 +1200 Subject: [PATCH 2/3] update module list --- docs/assets/module-list.json | 2716 ++++++++++++---------------------- 1 file changed, 923 insertions(+), 1793 deletions(-) diff --git a/docs/assets/module-list.json b/docs/assets/module-list.json index 18b69faa8..23168e301 100644 --- a/docs/assets/module-list.json +++ b/docs/assets/module-list.json @@ -1,12 +1,9 @@ { "ABAQUS": { "description": "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.", - "domains": [ - "engineering", - "gpu" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "http://www.simulia.com/products/abaqus_fea.html", "support": "", "versions": [ @@ -47,7 +44,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "gpgpu", - "hourly_average": 0.87, + "hourly_average": 0.86, "slurm_block": false, "slurm_soak": true, "slurm_token_name": "gpgpu@uoa_foe", @@ -61,7 +58,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "parallel_teaching", - "hourly_average": 0.48, + "hourly_average": 0.46, "slurm_block": false, "slurm_soak": true, "slurm_token_name": "parallel_teaching@uoa_foe", @@ -75,7 +72,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "abaqus", - "hourly_average": 0.6, + "hourly_average": 0.59, "slurm_block": false, "slurm_soak": true, "slurm_token_name": "abaqus@uoa_foe", @@ -136,9 +133,7 @@ }, "ABRicate": { "description": "Mass screening of contigs for antimicrobial and virulence genes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/tseemann/abricate", @@ -158,9 +153,7 @@ }, "abritamr": { "description": "AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "abritamr-1.0.14" ], @@ -203,9 +196,7 @@ }, "ABySS": { "description": "Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.bcgsc.ca/platform/bioinfo/software/abyss", @@ -245,9 +236,7 @@ }, "AdapterRemoval": { "description": "Ssearches for and removes remnant adapter sequences\nfrom High-Throughput Sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/%/(github_account)s/adapterremoval", @@ -267,9 +256,7 @@ }, "AdaptiveCpp": { "description": "AdaptiveCpp (formerly hipSYCL) is a SYCL implementation targeting CPUs and\nGPUs, with a focus on leveraging existing toolchains such as CUDA or HIP", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/illuhad/hipSYCL", @@ -309,9 +296,7 @@ }, "AGAT": { "description": "Suite of tools to handle gene annotations in any GTF/GFF format.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "AGAT-1.0.0", "Carp-1.50", @@ -343,9 +328,7 @@ }, "AGE": { "description": "Alignment of sequences with structural variants.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/abyzovlab/AGE", @@ -369,11 +352,7 @@ }, "AlphaFold": { "description": "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known", - "domains": [ - "biology", - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/deepmind/alphafold", @@ -396,10 +375,7 @@ }, "AlphaFold2DB": { "description": "AlphaFold2 databases", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -420,10 +396,7 @@ }, "AlphaFold3DB": { "description": "AlphaFold3 databases", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -463,11 +436,9 @@ }, "Amber": { "description": "Amber (originally Assisted Model Building with Energy Refinement) is software for performing\n molecular dynamics and structure prediction.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "https://ambermd.org/amber.html", "support": "", "versions": [ @@ -485,9 +456,7 @@ }, "AMOS": { "description": "Collection of tools for genome assembly", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://amos.sourceforge.net", @@ -507,9 +476,7 @@ }, "AMRFinderPlus": { "description": "NCBI Antimicrobial Resistance Gene Finder Plus", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ncbi/amr/wiki", @@ -530,9 +497,7 @@ }, "Anaconda3": { "description": "Built to complement the rich, open source Python community,\nthe Anaconda platform provides an enterprise-ready data analytics platform \nthat empowers companies to adopt a modern open data science analytics architecture.\n\nIMPORTANT: This version of Anaconda Python comes with Intel MKL support to speed up\n certain types of mathematical computations, such as linear algebra or FFT.\n The module sets\n\n MKL_NUM_THREADS=1\n\n to run MKL on a single thread by default, avoiding accidental oversubscription\n of cores. The number of threads can be increased for large problems, please\n refer to the Intel MKL documentation for guidance.", - "domains": [ - "machine_learning" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.continuum.io/anaconda-overview", @@ -556,9 +521,7 @@ }, "angsd": { "description": "Program for analysing NGS data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.popgen.dk/angsd", @@ -578,9 +541,7 @@ }, "ANIcalculator": { "description": "Calculate the bidirectional average nucleotide identity (gANI) and \nAlignment Fraction (AF) between two genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ani.jgi.doe.gov/html/home.php", @@ -600,9 +561,7 @@ }, "ANNOVAR": { "description": "Efficient software tool to utilize update-to-date information to functionally \nannotate genetic variants detected from diverse genomes .", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://annovar.openbioinformatics.org/en/latest/", @@ -622,12 +581,9 @@ }, "ANSYS": { "description": "A bundle of computer-aided engineering software including Fluent and CFX.", - "domains": [ - "engineering", - "visualisation" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "https://www.ansys.com", "support": "", "versions": [ @@ -684,7 +640,7 @@ "server": "ANSYS@orbis", "server_polling": true, "server_type": "FLEXlm", - "server_uptime": 0.98, + "server_uptime": 0.97, "server_version": "", "features": [ { @@ -845,9 +801,7 @@ }, "antiSMASH": { "description": "antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary\n metabolite biosynthesis gene clusters in bacterial and fungal genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "antiSMASH-6.0.1", "bcbio-gff-0.6.6", @@ -895,9 +849,7 @@ }, "any2fasta": { "description": "Convert various sequence formats to FASTA", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/tseemann/any2fasta", @@ -1154,9 +1106,7 @@ }, "ARIBA": { "description": "Antimicrobial Resistance Identification By Assembly", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "ariba-2.14.6", "BeautifulSoup-4.11.1", @@ -1186,9 +1136,7 @@ }, "Armadillo": { "description": "C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://arma.sourceforge.net/", @@ -1255,9 +1203,7 @@ }, "ASAGI": { "description": "a pArallel Server for Adaptive GeoInformation", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://tum-i5.github.io/ASAGI/index.xhtml", @@ -1381,9 +1327,7 @@ }, "AUGUSTUS": { "description": "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bioinf.uni-greifswald.de/augustus/", @@ -1410,9 +1354,7 @@ }, "AutoDock-GPU": { "description": "OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly\nparallelizable LGA by processing ligand-receptor poses in parallel over\nmultiple compute units.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ccsb-scripps/AutoDock-GPU", @@ -1470,6 +1412,33 @@ "force_hide": "False", "force_show": "False" }, + "awscli": { + "description": "Universal Command Line Environment for AWS", + "domains": [], + "extensions": [ + "awscli-2.36.14", + "awscrt-0.36.0", + "colorama-0.4.6", + "distro-1.8.0", + "ruamel.yaml-0.19.1", + "ruamel.yaml.clib-0.2.15" + ], + "licence_type": "", + "homepage": "https://github.com/aws/aws-cli/", + "support": "", + "versions": [ + "2.36.14-GCCcore-15.2.0" + ], + "admin_list": [], + "network_licences": [], + "default": "2.36.14-GCCcore-15.2.0", + "default_type": "latest", + "last_updated": 1786052902, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/awscli/2.36.14-GCCcore-15.2.0.lua", + "force_hide": "False", + "force_show": "False" + }, "azul-zulu": { "description": "Java Development Kit (JDK), and a compliant implementation of the Java Standard Edition (SE) specification.", "domains": [], @@ -1523,9 +1492,7 @@ }, "BamTools": { "description": "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/pezmaster31/bamtools", @@ -1548,9 +1515,7 @@ }, "bamUtil": { "description": "Repository that contains several programs\n that perform operations on SAM/BAM files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://genome.sph.umich.edu/wiki/BamUtil", @@ -1570,9 +1535,7 @@ }, "Bandage": { "description": "Bandage is a program for visualising de novo assembly graphs", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://rrwick.github.io/Bandage/", @@ -1592,9 +1555,7 @@ }, "barrnap": { "description": "Barrnap predicts the location of ribosomal RNA genes in genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/tseemann/barrnap", @@ -1614,9 +1575,7 @@ }, "Basilisk": { "description": "Basilisk is a Free Software program for the solution of partial differential equations on adaptive Cartesian meshes.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "basilisk.fr", @@ -1637,9 +1596,7 @@ }, "BayesAss": { "description": "Program for inference of recent immigration rates between populations using unlinked multilocus genotypes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.rannala.org/?page_id=245", @@ -1659,9 +1616,7 @@ }, "BayeScan": { "description": "Identify candidate loci under natural selection from genetic data,\n using differences in allele frequencies between populations.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://cmpg.unibe.ch/software/BayeScan/", @@ -1681,9 +1636,7 @@ }, "BayPass": { "description": "Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://forge.inrae.fr/mathieu.gautier/baypass_public", @@ -1706,9 +1659,7 @@ }, "BBMap": { "description": "BBMap short read aligner, and other bioinformatic tools.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sourceforge.net/projects/bbmap/", @@ -1732,9 +1683,7 @@ }, "BCFtools": { "description": "Manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.htslib.org", @@ -1765,9 +1714,7 @@ }, "BCL-Convert": { "description": "Converts per cycle binary data output by Illumina sequencers containing basecall\nfiles and quality scores to per read FASTQ files", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html", @@ -1787,9 +1734,7 @@ }, "bcl2fastq2": { "description": "bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by\n Illumina sequencing systems to standard FASTQ file formats for downstream analysis.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html", @@ -1809,9 +1754,7 @@ }, "Beagle": { "description": "Package for phasing genotypes and for imputing ungenotyped markers.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://faculty.washington.edu/browning/beagle/beagle.html", @@ -1833,10 +1776,7 @@ }, "beagle-lib": { "description": "beagle-lib is a high-performance library that can perform the core\ncalculations at the heart of most Bayesian and Maximum Likelihood\nphylogenetics packages.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/beagle-dev/beagle-lib", @@ -1858,10 +1798,7 @@ }, "BEAST": { "description": "Bayesian MCMC phylogenetic analysis of molecular sequences for reconstructing \n phylogenies and testing evolutionary hypotheses.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://beast2.org/", @@ -1888,9 +1825,7 @@ }, "BEDOPS": { "description": "BEDOPS is an open-source command-line toolkit that performs highly \n efficient and scalable Boolean and other set operations, statistical calculations, \n archiving, conversion and other management of genomic data of arbitrary scale.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bedops/bedops", @@ -1910,9 +1845,7 @@ }, "BEDTools": { "description": "The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps\n and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF,\n and SAM/BAM.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/arq5x/bedtools2", @@ -1936,9 +1869,7 @@ }, "BEEF": { "description": "BEEF is a library implementing the Bayesian Error\nEstimation Functional, a description of which can be found here:\n\nhttp://dx.doi.org/10.1103/PhysRevB.85.235149", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://suncat.stanford.edu/facility/software/functional", @@ -1962,9 +1893,7 @@ }, "best": { "description": "Bam Error Stats Tool (best): analysis of error types in aligned reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/google/best", @@ -1984,9 +1913,7 @@ }, "BGC-Bayesian-genomic-clines": { "description": "Collection of code for Bayesian genomic cline analyses.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/zgompert/BGC-Bayesian-genomic-clines", @@ -2006,9 +1933,7 @@ }, "Bifrost": { "description": "Highly parallel construction, indexing and querying of colored and compacted de Bruijn graphs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/pmelsted/bifrost", @@ -2028,9 +1953,7 @@ }, "BiG-SCAPE": { "description": "Constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://bigscape-corason.secondarymetabolites.org/index.html", @@ -2084,9 +2007,7 @@ }, "Bio-DB-BigFile": { "description": "Read BigWig and BigBed genome feature databases", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://metacpan.org/release/Bio-BigFile", @@ -2107,9 +2028,7 @@ }, "Bio-DB-HTS": { "description": "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://metacpan.org/release/Bio-DB-HTS", @@ -2132,9 +2051,7 @@ }, "bioawk": { "description": "An extension to awk, adding the support of several common biological data formats", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/bioawk", @@ -2154,9 +2071,7 @@ }, "BioPP": { "description": "Bio++ is a set of C++ libraries for Bioinformatics, including sequence\nanalysis, phylogenetics, molecular evolution and population genetics. Bio++ is\nObject Oriented and is designed to be both easy to use and computer efficient.\nBio++ intends to help programmers to write computer expensive programs, by\nproviding them a set of re-usable tools.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/BioPP/bpp-core", @@ -2176,9 +2091,7 @@ }, "Bismark": { "description": "A tool to map bisulfite converted sequence reads and\ndetermine cytosine methylation states", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.bioinformatics.babraham.ac.uk/projects/bismark/", @@ -2199,9 +2112,7 @@ }, "Bison": { "description": "Bison is a general-purpose parser generator that converts an annotated context-free grammar\n into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.", - "domains": [ - "social_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.gnu.org/software/bison", @@ -2227,11 +2138,31 @@ "force_hide": "False", "force_show": "False" }, + "bitsandbytes": { + "description": "bitsandbytes enables accessible large language models via k-bit quantization for PyTorch.\n\nThis build ships both the CUDA and the CPU native library, so the module works on GPU nodes\nand on nodes without a usable GPU. Note that it still depends on a CUDA-enabled PyTorch; if\nyou need a genuinely CUDA-free stack, build a separate easyconfig with COMPUTE_BACKEND=cpu,\nno CUDA dependency and no versionsuffix.", + "domains": [], + "extensions": [ + "bitsandbytes-0.50.0" + ], + "licence_type": "", + "homepage": "https://huggingface.co/docs/bitsandbytes/main/en/index", + "support": "", + "versions": [ + "0.50.0-foss-2026-CUDA-13.2.1" + ], + "admin_list": [], + "network_licences": [], + "default": "0.50.0-foss-2026-CUDA-13.2.1", + "default_type": "latest", + "last_updated": 1786047845, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/bitsandbytes/0.50.0-foss-2026-CUDA-13.2.1.lua", + "force_hide": "False", + "force_show": "False" + }, "BLAST": { "description": "Basic Local Alignment Search Tool, or BLAST, is an algorithm\n for comparing primary biological sequence information, such as the amino-acid\n sequences of different proteins or the nucleotides of DNA sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://blast.ncbi.nlm.nih.gov/", @@ -2258,9 +2189,7 @@ }, "BLASTDB": { "description": "BLAST databases downloaded from NCBI.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -2268,7 +2197,8 @@ "versions": [ "2025-08", "2026-01", - "2026-04" + "2026-04", + "2026-08" ], "admin_list": [ { @@ -2276,19 +2206,17 @@ } ], "network_licences": [], - "default": "2026-01", + "default": "2026-08", "default_type": "latest", - "last_updated": 1768561678, + "last_updated": 1785801827, "modulefile_text": "", - "module_path": "/opt/nesi/lmod/generic/BLASTDB/2026-01.lua", + "module_path": "/opt/nesi/lmod/generic/BLASTDB/2026-08.lua", "force_hide": "False", "force_show": "False" }, "BLAT": { "description": "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://genome.ucsc.edu/FAQ/FAQblat.html", @@ -2318,9 +2246,7 @@ }, "BLIS": { "description": "BLIS is a portable software framework for instantiating high-performance\nBLAS-like dense linear algebra libraries.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.amd.com/amd-cpu-libraries/blas-library/", @@ -2344,9 +2270,7 @@ }, "BOLT-LMM": { "description": "The BOLT-LMM algorithm computes statistics for testing association between phenotype\n and genotypes using a linear mixed model (LMM) [1]. By default, BOLT-LMM assumes a Bayesian\n mixture-of-normals prior for the random effect attributed to SNPs other than the one being tested.\n This model generalizes the standard \"infinitesimal\" mixed model used by previous mixed model\n association methods (e.g., EMMAX, FaST-LMM, GEMMA, GRAMMAR-Gamma, GCTA-LOCO), providing an\n opportunity for increased power to detect associations while controlling false\n positives. Additionally, BOLT-LMM applies algorithmic advances to compute mixed model association\n statistics much faster than eigendecomposition-based methods, both when using the Bayesian mixture\n model and when specialized to standard mixed model association.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://storage.googleapis.com/broad-alkesgroup-public/BOLT-LMM/BOLT-LMM_manual.html", @@ -2402,11 +2326,54 @@ "force_hide": "False", "force_show": "False" }, + "Boost.Python-NumPy": { + "description": "Boost.Python is a C++ library which enables seamless interoperability between C++\n and the Python programming language.", + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://boostorg.github.io/python", + "support": "", + "versions": [ + "1.91.0-gfbf-2026" + ], + "admin_list": [], + "network_licences": [], + "default": "1.91.0-gfbf-2026", + "default_type": "latest", + "last_updated": 1786049870, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/Boost.Python-NumPy/1.91.0-gfbf-2026.lua", + "force_hide": "False", + "force_show": "False" + }, + "boto3": { + "description": "Boto3 is the Amazon Web Services (AWS) Software Development Kit\n(SDK) for Python, which allows Python developers to write software that makes\nuse of services like Amazon S3 and Amazon EC2.", + "domains": [], + "extensions": [ + "boto3-1.43.62", + "botocore-1.43.62", + "jmespath-1.1.0", + "s3transfer-0.19.2" + ], + "licence_type": "", + "homepage": "https://github.com/boto/boto3", + "support": "", + "versions": [ + "1.43.62-GCCcore-15.2.0" + ], + "admin_list": [], + "network_licences": [], + "default": "1.43.62-GCCcore-15.2.0", + "default_type": "latest", + "last_updated": 1786052394, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/boto3/1.43.62-GCCcore-15.2.0.lua", + "force_hide": "False", + "force_show": "False" + }, "Bowtie": { "description": "Ultrafast, memory-efficient short read aligner.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bowtie-bio.sourceforge.net/index.shtml", @@ -2433,9 +2400,7 @@ }, "Bowtie2": { "description": "Ultrafast and memory-efficient tool for aligning\nsequencing reads to long reference sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", @@ -2458,9 +2423,7 @@ }, "Bracken": { "description": "Hghly accurate statistical method that computes the abundance of \nspecies in DNA sequences from a metagenomics sample.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ccb.jhu.edu/software/bracken/", @@ -2485,9 +2448,7 @@ }, "BRAKER": { "description": "Pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET\n and AUGUSTUS in novel eukaryotic genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Sub::Quote-2.006008", "YAML::XS-0.86" @@ -2514,9 +2475,7 @@ }, "breseq": { "description": "breseq is a computational pipeline for the analysis of short-read re-sequencing data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://barricklab.org/breseq", @@ -2563,9 +2522,7 @@ }, "BUSCO": { "description": "Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://busco.ezlab.org", @@ -2592,9 +2549,7 @@ }, "BWA": { "description": "Burrows-Wheeler Aligner (BWA) is an efficient program that aligns\n relatively short nucleotide sequences against a long reference sequence such as the human genome.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bio-bwa.sourceforge.net/", @@ -2680,9 +2635,7 @@ }, "cairo": { "description": "Cairo is a 2D graphics library with support for multiple output devices.\n Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,\n PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://cairographics.org", @@ -2705,9 +2658,7 @@ }, "Canu": { "description": "Sequence assembler designed for high-noise single-molecule sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://canu.readthedocs.io", @@ -2751,11 +2702,29 @@ "force_hide": "False", "force_show": "False" }, + "Catch2": { + "description": "A modern, C++-native, header-only,\n test framework for unit-tests, TDD and BDD\n - using C++11, C++14, C++17 and later", + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://github.com/catchorg/Catch2", + "support": "", + "versions": [ + "3.15.3-GCCcore-15.2.0" + ], + "admin_list": [], + "network_licences": [], + "default": "3.15.3-GCCcore-15.2.0", + "default_type": "latest", + "last_updated": 1786048389, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/Catch2/3.15.3-GCCcore-15.2.0.lua", + "force_hide": "False", + "force_show": "False" + }, "CD-HIT": { "description": "CD-HIT is a very widely used program for clustering and\n comparing protein or nucleotide sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://weizhong-lab.ucsd.edu/cd-hit/", @@ -2776,9 +2745,7 @@ }, "cdbfasta": { "description": "Fasta file indexing and retrival tool", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sourceforge.net/projects/cdbfasta", @@ -2799,9 +2766,7 @@ }, "CDO": { "description": "CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.", - "domains": [ - "climate_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://code.zmaw.de/projects/cdo", @@ -2823,9 +2788,7 @@ }, "CellRanger": { "description": "Cell Ranger is a set of analysis pipelines that process Chromium\n single-cell RNA-seq output to align reads, generate gene-cell matrices and perform\n clustering and gene expression analysis.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger", @@ -2850,9 +2813,7 @@ }, "Centrifuge": { "description": "Classifier for metagenomic sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ccb.jhu.edu/software/centrifuge/", @@ -2984,9 +2945,7 @@ }, "CheckM": { "description": "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates,\n single cells, or metagenomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Ecogenomics/CheckM", @@ -3012,9 +2971,7 @@ }, "CheckM2": { "description": "Rapid assessment of genome bin quality using machine learning", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/chklovski/CheckM2", @@ -3034,9 +2991,7 @@ }, "CheckV": { "description": "Assess the quality of metagenome-assembled viral genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "archspec-0.2.6", "checkv-1.1.1", @@ -3071,9 +3026,7 @@ }, "chewBBACA": { "description": "A complete suite for gene-by-gene schema creation and strain identification..", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "chewBBACA-3.1.2", "isodate-0.6.1", @@ -3098,9 +3051,7 @@ }, "chopper": { "description": "Rust implementation of NanoFilt+NanoLyse", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wdecoster/chopper", @@ -3143,9 +3094,7 @@ }, "Circlator": { "description": "A tool to circularize genome assemblies", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "circlator-1.5.5", "pyfastaq-3.17.0", @@ -3190,9 +3139,7 @@ }, "Clair3": { "description": "Syumphonizing pileup and full-alignment for high-performance long-read variant calling.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/HKU-BAL/Clair3", @@ -3214,9 +3161,7 @@ }, "Clang": { "description": "C, C++, Objective-C compiler, based on LLVM. Does not\n include C++ standard library -- use libstdc++ from GCC.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://clang.llvm.org/", @@ -3236,9 +3181,7 @@ }, "Clustal-Omega": { "description": "Clustal Omega is a multiple sequence alignment\n program for proteins. It produces biologically meaningful multiple\n sequence alignments of divergent sequences. Evolutionary relationships\n can be seen via viewing Cladograms or Phylograms", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.clustal.org/omega/", @@ -3259,9 +3202,7 @@ }, "ClustalW2": { "description": "ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ebi.ac.uk/Tools/msa/clustalw2/", @@ -3309,9 +3250,7 @@ }, "CNVnator": { "description": "Copy Number Variation discovery and genotyping from depth of read mapping.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://sv.gersteinlab.org", @@ -3331,9 +3270,7 @@ }, "CNVpytor": { "description": "Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped read", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "CNVpytor-1.3.1", "gnureadline-8.1.2", @@ -3379,9 +3316,7 @@ }, "compleasm": { "description": "faster and more accurate reimplementation of BUSCO.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/huangnengCSU/compleasm", @@ -3405,13 +3340,9 @@ }, "COMSOL": { "description": "COMSOL is a multiphysics solver that provides a unified workflow for electrical, mechanical, fluid, and chemical applications.", - "domains": [ - "chemistry", - "engineering", - "physics" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "https://www.comsol.com/", "support": "", "versions": [ @@ -3442,7 +3373,7 @@ "server": "COMSOL@uoa_physics", "server_polling": true, "server_type": "FLEXlm", - "server_uptime": 0.99, + "server_uptime": 1.0, "server_version": "11.16.2", "features": [ { @@ -3484,7 +3415,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "comsol", - "hourly_average": 0.84, + "hourly_average": 0.83, "slurm_block": false, "slurm_soak": false, "slurm_token_name": "comsol@uoa_idg", @@ -3552,7 +3483,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "comsol", - "hourly_average": 0.91, + "hourly_average": 0.9, "slurm_block": false, "slurm_soak": false, "slurm_token_name": "comsol@uoa_foes", @@ -3586,7 +3517,7 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "comsol", - "hourly_average": 0.68, + "hourly_average": 0.7, "slurm_block": false, "slurm_soak": true, "slurm_token_name": "comsol@uoa_foe_des_rc", @@ -3654,12 +3585,12 @@ "buffer_constant": 1, "buffer_constant_other": 0, "feature_name": "comsol", - "hourly_average": 0.52, + "hourly_average": 0.55, "slurm_block": false, "slurm_soak": false, "slurm_token_name": "comsol@uc", "slurm_track": true, - "total": 5, + "total": 10, "usage_formula": "{node}", "use_conditions": "Version not greater than 6.3", "visible_on_docs": true @@ -3677,9 +3608,7 @@ }, "CONCOCT": { "description": "Program for unsupervised binning of metagenomic contigs by using nucleotide composition,\ncoverage data in multiple samples and linkage data from paired end reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://concoct.readthedocs.io", @@ -3702,11 +3631,29 @@ "force_hide": "False", "force_show": "False" }, + "CoordgenLibs": { + "description": "Schrodinger-developed 2D Coordinate Generation", + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://github.com/schrodinger/coordgenlibs", + "support": "", + "versions": [ + "3.0.2-gompi-2026" + ], + "admin_list": [], + "network_licences": [], + "default": "3.0.2-gompi-2026", + "default_type": "latest", + "last_updated": 1786048548, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/CoordgenLibs/3.0.2-gompi-2026.lua", + "force_hide": "False", + "force_show": "False" + }, "CoverM": { "description": "DNA read coverage and relative abundance calculator focused on metagenomics applications", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wwood/CoverM", @@ -3726,10 +3673,7 @@ }, "CP2K": { "description": "CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular\n simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different\n methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and\n classical pair and many-body potentials.", - "domains": [ - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.cp2k.org/", @@ -3752,9 +3696,7 @@ }, "CPMD": { "description": "The CPMD code is a parallelized plane wave / pseudopotential implementation of DFT,\n particularly designed for ab-initio molecular dynamics.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/CPMD-code", @@ -3798,9 +3740,7 @@ }, "CRABS": { "description": "Creating Reference databases for Amplicon-Based Sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/gjeunen/reference_database_creator", @@ -3820,9 +3760,7 @@ }, "CRAMINO": { "description": "A tool for quick quality assessment of cram and bam files, intended for long read sequencing", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wdecoster/cramino", @@ -3842,9 +3780,7 @@ }, "CREST": { "description": "CREST is an utility/driver program for the xtb program. Originally it was designed\n as conformer sampling program, hence the abbreviation Conformer\u2013Rotamer Ensemble Sampling Tool,\n but now offers also some utility functions for calculations with the GFNn\u2013xTB methods. Generally\n the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb\n program) and tool for the creation and analysation of structure ensembles.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://xtb-docs.readthedocs.io/en/latest/crest.html", @@ -3864,9 +3800,7 @@ }, "cromwell": { "description": "Workflow Management System geared towards scientific workflows.", - "domains": [ - "workflow_management" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://cromwell.readthedocs.io/en/stable/", @@ -3933,9 +3867,7 @@ }, "ctffind": { "description": "ctffind is a program for finding CTFs of electron micrographs", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://grigoriefflab.janelia.org/ctf", @@ -3995,9 +3927,7 @@ }, "CUDA": { "description": "CUDA (formerly Compute Unified Device Architecture) is a parallel\n computing platform and programming model created by NVIDIA and implemented by the\n graphics processing units (GPUs) that they produce. CUDA gives developers access\n to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.nvidia.com/cuda-toolkit", @@ -4038,9 +3968,7 @@ }, "cuDNN": { "description": "The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.nvidia.com/cudnn", @@ -4058,6 +3986,7 @@ "8.8.0.121-CUDA-12.0.0", "8.9.7.29-CUDA-12.2.2", "8.9.7.29-CUDA-12.3.0", + "9.24.0.43-CUDA-13.2.1", "9.3.0.75-CUDA-12.5.0", "9.5.1.17-CUDA-12.6.3" ], @@ -4096,9 +4025,7 @@ }, "cutadapt": { "description": "cutadapt removes adapter sequences\n from high-throughput sequencing data. This is usually\n necessary when the read length of the sequencing machine\n is longer than the molecule that is sequenced, for\n example when sequencing microRNAs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "cachetools-6.2.5", "cutadapt-5.2", @@ -4140,9 +4067,7 @@ }, "cuteSV": { "description": "Fast and scalable long-read-based SV detection", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "beautifulsoup4-4.12.0", "bs4-0.0.1", @@ -4171,10 +4096,7 @@ }, "Cytoscape": { "description": "Cytoscape is an open source software platform for visualizing molecular interaction networks and\n biological pathways and integrating these networks with annotations, gene expression profiles and other state data.", - "domains": [ - "biology", - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://cytoscape.org/", @@ -4194,9 +4116,7 @@ }, "cyvcf2": { "description": "cython + htslib == fast VCF and BCF processing", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "cigar-0.1.3", "coloredlogs-15.0.1", @@ -4225,9 +4145,7 @@ }, "D-Genies": { "description": "D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "argparse-1.4.0", "crontab-1.0.1", @@ -4270,10 +4188,7 @@ }, "dadi": { "description": "Diffusion Approximation for Demographic Inference", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [ "appdirs-1.4.4", "dadi-2.3.0", @@ -4302,9 +4217,7 @@ }, "DAS_Tool": { "description": "DAS Tool is an automated method that integrates the results of a flexible number of binning\n algorithms to calculate an optimized, non-redundant set of bins from a single assembly.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/cmks/DAS_Tool", @@ -4325,9 +4238,7 @@ }, "datasets": { "description": "Tool to gather data from across NCBI databases", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/", @@ -4432,9 +4343,7 @@ }, "DeconSeq": { "description": "A tool that can be used to automatically detect and efficiently remove sequence contaminations \n from genomic and metagenomic datasets.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://deconseq.sourceforge.net/", @@ -4454,10 +4363,7 @@ }, "DeepLabCut": { "description": "Efficient method for 3D markerless pose estimation based on transfer learning with deep neural networks.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.mackenziemathislab.org/deeplabcut", @@ -4478,9 +4384,7 @@ }, "DeePMD-kit": { "description": "Package written in Python/C++, designed to minimize the effort required to build deep learning-based models of interatomic potential energy and force field and to perform molecular dynamics.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://docs.deepmodeling.com/projects/deepmd/en/master/", @@ -4500,9 +4404,7 @@ }, "DeePMD-plugin": { "description": "Deep learning-based models of interatomic potential energy and force field, as a LAMMPS plugin.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://docs.deepmodeling.com/projects/deepmd", @@ -4522,9 +4424,7 @@ }, "deepTools": { "description": "deepTools is a suite of python tools particularly developed for the efficient analysis of\n high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "deepTools-3.2.1", "deeptoolsintervals-0.1.8", @@ -4549,9 +4449,7 @@ }, "Delft3D": { "description": "Integrated simulation of sediment transport and morphology, waves, water quality and ecology.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://oss.deltares.nl/web/delft3d", @@ -4573,9 +4471,7 @@ }, "Delft3D_FM": { "description": "3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://oss.deltares.nl/web/delft3d", @@ -4599,9 +4495,7 @@ }, "Delly": { "description": "Structural variant discovery by integrated paired-end and split-read analysis", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/dellytools/delly", @@ -4665,9 +4559,7 @@ }, "DFT-D4": { "description": "Generally Applicable Atomic-Charge Dependent London Dispersion Correction.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/dftd4/dftd4", @@ -4689,9 +4581,7 @@ }, "DIAMOND": { "description": "Sequence aligner for protein and translated DNA searches", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bbuchfink/diamond", @@ -4722,10 +4612,7 @@ }, "Dorado": { "description": "High-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nanoporetech.com/products/minit", @@ -4815,9 +4702,7 @@ }, "DRAM": { "description": "Tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs..", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://pypi.org/project/DRAM-bio/", @@ -4837,9 +4722,7 @@ }, "drep": { "description": "Rapid and accurate comparison and de-replication of microbial genomes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "drep-3.4.2" ], @@ -4862,9 +4745,7 @@ }, "Dsuite": { "description": "Fast calculation of the ABBA-BABA statistics across many populations/species", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/millanek/Dsuite", @@ -4908,9 +4789,7 @@ }, "duphold": { "description": "uphold your DUP and DEL calls", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/brentp/duphold", @@ -4930,9 +4809,7 @@ }, "duplex-tools": { "description": "Range of tools to support operations on Duplex Sequencing read pairs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "duplex_tools-0.2.20", "edlib-1.3.9", @@ -4962,9 +4839,7 @@ }, "easi": { "description": "easi is a library for the Easy Initialization of models in three (or less or more) dimensional domains.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://easyinit.readthedocs.io/en/latest/", @@ -5031,9 +4906,7 @@ }, "edlib": { "description": "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://martinsos.github.io/edlib", @@ -5053,9 +4926,7 @@ }, "eDNA": { "description": "A suite of tools to conduct metabarcoding analyses targeting any group of organisms. Includes utilities \nfor preprocessing raw data and building your own custom reference database.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "tqdm-4.59.0" ], @@ -5077,9 +4948,7 @@ }, "EDTA": { "description": "Automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/oushujun/EDTA", @@ -5116,7 +4985,7 @@ "network_licences": [], "default": "2025.06", "default_type": "latest", - "last_updated": 1779521581, + "last_updated": 1785446377, "modulefile_text": "", "module_path": "/opt/nesi/lmod/generic/EESSI/2025.06.lua", "force_hide": "False", @@ -5124,9 +4993,7 @@ }, "eggnog-mapper": { "description": "Tool for fast functional annotation of novel sequences (genes or proteins)\n using precomputed eggNOG-based orthology assignments", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "XlsxWriter-3.1.8" ], @@ -5149,9 +5016,7 @@ }, "Eigen": { "description": "Eigen is a C++ template library for linear algebra:\n matrices, vectors, numerical solvers, and related algorithms.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://eigen.tuxfamily.org/index.php?title=Main_Page", @@ -5175,9 +5040,7 @@ }, "EIGENSOFT": { "description": "The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. \n2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal \ncomponents analysis to explicitly model ancestry differences between cases and controls along continuous axes of \nvariation; the resulting correction is specific to a candidate marker\u2019s variation in frequency across ancestral \npopulations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT \npackage has a built-in plotting script and supports multiple file formats and quantitative phenotypes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.hsph.harvard.edu/alkes-price/software/", @@ -5197,9 +5060,7 @@ }, "ELPA": { "description": "Eigenvalue SoLvers for Petaflop-Applications.", - "domains": [ - "astronomy" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://elpa.mpcdf.mpg.de/", @@ -5222,11 +5083,7 @@ }, "EMAN2": { "description": "Greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes", - "domains": [ - "biology", - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://blake.bcm.edu/emanwiki/EMAN2/", @@ -5247,9 +5104,7 @@ }, "EMBOSS": { "description": "EMBOSS is 'The European Molecular Biology Open Software Suite'.\n EMBOSS is a free Open Source software analysis package specially developed for\n the needs of the molecular biology (e.g. EMBnet) user community.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://emboss.sourceforge.net/", @@ -5269,9 +5124,7 @@ }, "Embree": { "description": "Embree is a collection of high-performance ray tracing kernels, developed at Intel.\nThe target users of Embree are graphics application engineers who want to improve\nthe performance of their photo-realistic rendering application by leveraging Embree's\nperformance-optimized ray tracing kernels.", - "domains": [ - "engineering" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://embree.github.io/", @@ -5292,9 +5145,7 @@ }, "emmtyper": { "description": "Tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "emmtyper-0.2.0", "ispcr-0.9.1" @@ -5317,9 +5168,7 @@ }, "Emu": { "description": "species-level taxonomic abundance for full-length 16S reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gitlab.com/treangenlab/emu", @@ -5340,9 +5189,7 @@ }, "ensmallen": { "description": "C++ header-only library for numerical optimization", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/mlpack/ensmallen", @@ -5366,9 +5213,7 @@ }, "entrez-direct": { "description": "an advanced method for accessing the NCBI's set of interconnected databases \nsuch as publication, sequence, structure, gene, variation, expression, etc.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://dataguide.nlm.nih.gov/edirect/documentation.html", @@ -5388,10 +5233,7 @@ }, "ESMF": { "description": "The Earth System Modeling Framework (ESMF) is a suite of software tools for developing\n high-performance, multi-component Earth science modeling applications.", - "domains": [ - "climate_science", - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.earthsystemcog.org/projects/esmf/", @@ -5411,9 +5253,7 @@ }, "ETE": { "description": "A Python framework for the analysis and visualization of phylogenetic trees", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://etetoolkit.org", @@ -5436,9 +5276,7 @@ }, "EukRep-EukCC": { "description": "Completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.\nAlso condatains smetana, carveme and memote .", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.repeatmasker.org/", @@ -5458,9 +5296,7 @@ }, "ExaBayes": { "description": "Bayesian tree inference, particularly suitable for large-scale analyses.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sco.h-its.org/exelixis/web/software/exabayes/", @@ -5480,9 +5316,7 @@ }, "ExaML": { "description": "Exascale Maximum Likelihood for phylogenetic inference using MPI.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sco.h-its.org/exelixis/web/software/examl/index.html", @@ -5522,9 +5356,7 @@ }, "exonerate": { "description": "Generic tool for pairwise sequence comparison", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ebi.ac.uk/~guy/exonerate/", @@ -5547,9 +5379,7 @@ }, "ExpansionHunter": { "description": "Tool for estimating repeat sizes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Illumina/ExpansionHunter", @@ -5612,9 +5442,7 @@ }, "Faiss": { "description": "Faiss is a library for efficient similarity search and clustering of dense\n vectors. It contains algorithms that search in sets of vectors of any size, up\n to ones that possibly do not fit in RAM. It also contains supporting code for\n evaluation and parameter tuning. Faiss is written in C++ with complete\n wrappers for Python/numpy. Some of the most useful algorithms are implemented\n on the GPU. It is developed primarily at Meta's Fundamental AI Research group.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/facebookresearch/faiss", @@ -5634,9 +5462,7 @@ }, "FastANI": { "description": "Tool for fast alignment-free computation of\n whole-genome Average Nucleotide Identity (ANI).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.iodbc.org/", @@ -5664,9 +5490,7 @@ }, "FastME": { "description": "FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.atgc-montpellier.fr/fastme/", @@ -5688,9 +5512,7 @@ }, "fastp": { "description": "A tool designed to provide fast all-in-one preprocessing for FastQ files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/OpenGene/fastp", @@ -5713,9 +5535,7 @@ }, "FastQ_Screen": { "description": "FastQ Screen allows you to screen a library of sequences in FastQ\n format against a set of sequence databases so you can see if the composition of the\n library matches with what you expect.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "GD::Graph-1.54", "GD::Text-0.86" @@ -5738,9 +5558,7 @@ }, "FastQC": { "description": "A set of tools (in Java) for working with next generation sequencing data in the BAM format.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/", @@ -5762,9 +5580,7 @@ }, "Fastsimcoal2": { "description": "While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure.\n fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://cmpg.unibe.ch/software/fastsimcoal2/", @@ -5784,9 +5600,7 @@ }, "fastStructure": { "description": "fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://rajanil.github.io/fastStructure/", @@ -5806,9 +5620,7 @@ }, "FastTree": { "description": "FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide\n or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of\n time and memory.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.microbesonline.org/fasttree/", @@ -5831,9 +5643,7 @@ }, "FASTX-Toolkit": { "description": "Tools for Short-Reads FASTA/FASTQ files preprocessing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://hannonlab.cshl.edu/fastx_toolkit/", @@ -5878,10 +5688,7 @@ }, "FDS": { "description": "Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows,\n with an emphasis on smoke and heat transport from fires.", - "domains": [ - "engineering", - "physics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://pages.nist.gov/fds-smv/", @@ -5901,9 +5708,7 @@ }, "FFmpeg": { "description": "A complete, cross-platform solution to record, convert and stream audio and video.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ffmpeg.org/", @@ -5926,9 +5731,7 @@ }, "FFTW": { "description": "FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)\nin one or more dimensions, of arbitrary input size, and of both real and complex data.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.fftw.org", @@ -5954,9 +5757,7 @@ }, "FFTW.MPI": { "description": "FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)\nin one or more dimensions, of arbitrary input size, and of both real and complex data.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.fftw.org", @@ -5979,9 +5780,7 @@ }, "fgbio": { "description": "A set of tools to analyze genomic data with a focus on Next Generation Sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://fulcrumgenomics.github.io/fgbio", @@ -6005,9 +5804,7 @@ }, "FIGARO": { "description": "An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Zymo-Research/figaro", @@ -6068,9 +5865,7 @@ }, "Filtlong": { "description": "Tool for filtering long reads by quality.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rrwick/Filtlong", @@ -6090,9 +5885,7 @@ }, "FimTyper": { "description": "Identifies the FimH type in total or partial sequenced isolates of E. coli..", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Bio::SeqIO-1.7.8", "Try::Tiny-0.31", @@ -6120,9 +5913,7 @@ }, "fineRADstructure": { "description": "A package for population structure inference from RAD-seq data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html", @@ -6142,9 +5933,7 @@ }, "fineSTRUCTURE": { "description": "Population assignment using large numbers of densely sampled genomes, including both SNP chips and sequence dat", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "paran-1.5.2", "psych-2.3.6" @@ -6187,9 +5976,7 @@ }, "flex": { "description": "Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, \n sometimes called a tokenizer, is a program which recognizes lexical patterns\n in text.", - "domains": [ - "social_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://flex.sourceforge.net/", @@ -6257,9 +6044,7 @@ }, "Flye": { "description": "Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio\n and Oxford Nanopore Technologies.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/fenderglass/Flye", @@ -6305,10 +6090,7 @@ }, "Foldseek": { "description": "Foldseek enables fast and sensitive comparisons of large protein structure sets, \nsupporting monomer and multimer searches, as well as clustering.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/steineggerlab/foldseek", @@ -6373,9 +6155,7 @@ }, "FragGeneScan": { "description": "FragGeneScan is an application for finding (fragmented) genes in short reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://omics.informatics.indiana.edu/FragGeneScan/", @@ -6397,9 +6177,7 @@ }, "FreeBayes": { "description": "Genetic variant detector designed to find polymorphisms smaller than the length of a short-read sequencing alignment.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ekg/freebayes/blob/master/README.md", @@ -6425,9 +6203,7 @@ }, "FreeFEM": { "description": "FreeFEM offers a fast interpolation algorithm and a language for the manipulation\n of data on multiple meshes.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://freefem.org", @@ -6447,9 +6223,7 @@ }, "FreeSurfer": { "description": "FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.\nFreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://surfer.nmr.mgh.harvard.edu/", @@ -6469,9 +6243,7 @@ }, "freetype": { "description": "FreeType 2 is a software font engine that is designed to be small, efficient,\n highly customizable, and portable while capable of producing high-quality\n output (glyph images). It can be used in graphics libraries, display servers,\n font conversion tools, text image generation tools, and many other products\n as well.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://freetype.org", @@ -6607,9 +6379,7 @@ }, "GATK": { "description": "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute\n to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,\n with a primary focus on variant discovery and genotyping as well as strong emphasis on\n data quality assurance. Its robust architecture, powerful processing engine and\n high-performance computing features make it capable of taking on projects of any size.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.broadinstitute.org/gatk/", @@ -6641,11 +6411,9 @@ }, "Gaussian": { "description": "", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "", "support": "", "versions": [ @@ -6738,9 +6506,7 @@ }, "GD": { "description": "Interface to Gd Graphics Library", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [ "ExtUtils::PkgConfig-1.16", "GD-2.76", @@ -6767,9 +6533,7 @@ }, "GDAL": { "description": "GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style\n Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model\n to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for\n data translation and processing.\n NOTE: The GDAL IO cache by default uses 5% of total memory. This seems not necessary. This module sets GDAL_CACHEMAX=256 (256MB), \n which should have no performance impact. Feel free to change if necessary, using 'export GDAL_CACHEMAX=xxx' (in your job script) \n after loading the GDAL module.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.gdal.org/", @@ -6819,9 +6583,7 @@ }, "GEMMA": { "description": "Genome-wide Efficient Mixed Model Association", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/genetics-statistics/GEMMA", @@ -6861,9 +6623,7 @@ }, "GeneMark-ES": { "description": "Eukaryotic gene prediction suite with automatic training", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Clone::Choose-0.010", "Sub::Quote-2.006008", @@ -6908,9 +6668,7 @@ }, "GenomeThreader": { "description": "GenomeThreader is a software tool to compute gene structure predictions.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://genomethreader.org", @@ -6930,9 +6688,7 @@ }, "genometools": { "description": "GenomeTools: A Comprehensive Software Library for Efficient Processing of\n Structured Genome Annotations.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://genometools.org", @@ -6953,9 +6709,7 @@ }, "GenoVi": { "description": "Generates circular genome representations for complete, draft, and multiple bacterial and archaeal genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.repeatmasker.org/", @@ -6975,9 +6729,7 @@ }, "GEOS": { "description": "GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://trac.osgeo.org/geos", @@ -7002,9 +6754,7 @@ }, "GetOrganelle": { "description": "Toolkit to assemble organelle genome from genomic skimming data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Kinggerm/GetOrganelle", @@ -7046,9 +6796,7 @@ }, "gfastats": { "description": "single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/vgl-hub/gfastats", @@ -7068,9 +6816,7 @@ }, "gfatools": { "description": "Tools for manipulating sequence graphs in the GFA and rGFA formats", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/gfatools", @@ -7110,9 +6856,7 @@ }, "gffread": { "description": "GFF/GTF parsing utility providing format conversions,\nregion filtering, FASTA sequence extraction and more.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread", @@ -7133,9 +6877,7 @@ }, "giflib": { "description": "giflib is a library for reading and writing gif images.\nIt is API and ABI compatible with libungif which was in wide use while\nthe LZW compression algorithm was patented.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://giflib.sourceforge.net/", @@ -7242,9 +6984,7 @@ }, "GlimmerHMM": { "description": "Gene finder based on a Generalized Hidden Markov Model.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ccb.jhu.edu/software/glimmerhmm", @@ -7382,9 +7122,7 @@ }, "GMAP-GSNAP": { "description": "GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences\n GSNAP: Genomic Short-read Nucleotide Alignment Program", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://research-pub.gene.com/gmap/", @@ -7404,9 +7142,7 @@ }, "GMP": { "description": "GMP is a free library for arbitrary precision arithmetic, operating on signed\n integers, rational numbers, and floating point numbers.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gmplib.org/", @@ -7432,9 +7168,7 @@ }, "gmsh": { "description": "Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor..", - "domains": [ - "engineering" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://gmsh.info/", @@ -7454,9 +7188,7 @@ }, "GMT": { "description": "GMT is an open source collection of about 80 command-line tools for manipulating\n geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting,\n etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps\n to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another\n 40 more specialized and discipline-specific tools.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.generic-mapping-tools.org/", @@ -7477,9 +7209,7 @@ }, "gnuplot": { "description": "", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -7499,9 +7229,7 @@ }, "Go": { "description": "An open source programming language", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.golang.org", @@ -7522,12 +7250,9 @@ }, "GOLD": { "description": "A genetic algorithm for docking flexible ligands into protein binding sites", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "https://www.ccdc.cam.ac.uk/solutions/csd-discovery/Components/Gold/", "support": "", "versions": [ @@ -7610,9 +7335,7 @@ }, "GPAW": { "description": "GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW)\n method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or\n atom-centered basis-functions.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://wiki.fysik.dtu.dk/gpaw/", @@ -7653,10 +7376,7 @@ }, "GPUMD": { "description": "GPUMD stands for Graphics Processing Units Molecular Dynamics.\nIt is a general-purpose molecular dynamics (MD) package fully implemented on graphics processing units.", - "domains": [ - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gpumd.org/", @@ -7676,9 +7396,7 @@ }, "Graphviz": { "description": "Graphviz is open source graph visualization software. Graph visualization\n is a way of representing structural information as diagrams of\n abstract graphs and networks. It has important applications in networking,\n bioinformatics, software engineering, database and web design, machine learning,\n and in visual interfaces for other technical domains.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.graphviz.org/", @@ -7698,10 +7416,7 @@ }, "GRASS": { "description": "The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization", - "domains": [ - "earth_science", - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://grass.osgeo.org", @@ -7727,9 +7442,7 @@ }, "GRIDSS": { "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "argparse-2.1.3", "argparser-0.7.1", @@ -7755,10 +7468,7 @@ }, "GROMACS": { "description": "GROMACS is a versatile package to perform molecular dynamics,\n i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.\n\nThis is a GPU enabled build, containing both MPI and threadMPI binaries.", - "domains": [ - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.gromacs.org", @@ -7805,9 +7515,7 @@ }, "GSL": { "description": "The GNU Scientific Library (GSL) is a numerical library for C and C++\n programmers. The library provides a wide range of mathematical routines\n such as random number generators, special functions and least-squares fitting.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.gnu.org/software/gsl/", @@ -7839,9 +7547,7 @@ }, "GST-plugins-base": { "description": "GStreamer plug-ins and elements.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gstreamer.freedesktop.org/", @@ -7861,9 +7567,7 @@ }, "GStreamer": { "description": "library for constructing graphs of media-handling components..", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gstreamer.freedesktop.org/", @@ -7883,9 +7587,7 @@ }, "GTDB-Tk": { "description": "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "annotated-types-0.5.0", "pydantic-1.10.13", @@ -7963,9 +7665,7 @@ }, "Gubbins": { "description": "Genealogies Unbiased By recomBinations In Nucleotide Sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sanger-pathogens.github.io/gubbins/", @@ -7985,9 +7685,7 @@ }, "GUSHR": { "description": "Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Gaius-Augustus/GUSHR", @@ -8049,9 +7747,7 @@ }, "HAL": { "description": "HAL is a structure to efficiently store and index multiple genome alignments\nand ancestral reconstructions. HAL is a graph-based representation which\nprovides several advantages over matrix/block-based formats such as MAF, such as\nimproved scalability and the ability to perform queries with respect to an\narbitrary reference or subtree.\n\nThis package includes the HAL API and several analysis and conversion tools\nwhich are described below. HAL files are presently stored in either HDF5 or mmap\nformat, but we note that the tools and most of the API are format-independent,\nso other databases could be implemented in the future.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ComparativeGenomicsToolkit/hal", @@ -8071,9 +7767,7 @@ }, "haplocheck": { "description": "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/genepi/haplocheck", @@ -8168,9 +7862,7 @@ }, "hifiasm": { "description": "Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/chhylp123/hifiasm", @@ -8194,9 +7886,7 @@ }, "HISAT2": { "description": "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads\n (both DNA and RNA) against the general human population (as well as against a single reference genome).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://daehwankimlab.github.io/hisat2", @@ -8224,10 +7914,7 @@ }, "HMMER": { "description": "HMMER is used for searching sequence databases for homologs of protein sequences,\n and for making protein sequence alignments. It implements methods using probabilistic models\n called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other\n sequence alignment and database search tools based on older scoring methodology,\n HMMER aims to be significantly more accurate and more able to detect remote homologs\n because of the strength of its underlying mathematical models. In the past, this strength\n came at significant computational expense, but in the new HMMER3 project, HMMER is now\n essentially as fast as BLAST.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://hmmer.org/", @@ -8255,10 +7942,7 @@ }, "HMMER2": { "description": "HMMER is used for searching sequence databases for homologs of protein sequences,\n and for making protein sequence alignments. It implements methods using probabilistic models\n called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other\n sequence alignment and database search tools based on older scoring methodology,\n HMMER aims to be significantly more accurate and more able to detect remote homologs\n because of the strength of its underlying mathematical models. In the past, this strength\n came at significant computational expense, but in the new HMMER3 project, HMMER is now\n essentially as fast as BLAST.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://hmmer.org", @@ -8300,9 +7984,7 @@ }, "HTSeq": { "description": "HTSeq is a Python library to facilitate processing and analysis\n of data from high-throughput sequencing (HTS) experiments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/simon-anders/htseq", @@ -8322,9 +8004,7 @@ }, "HTSlib": { "description": "A C library for reading/writing high-throughput sequencing data.\n This package includes the utilities bgzip and tabix", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.htslib.org/", @@ -8358,9 +8038,7 @@ }, "Humann": { "description": "Pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://huttenhower.sph.harvard.edu/humann", @@ -8404,9 +8082,7 @@ }, "HybPiper": { "description": "Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/mossmatters/HybPiper", @@ -8424,6 +8100,38 @@ "force_hide": "False", "force_show": "False" }, + "Hydra": { + "description": "Hydra is an open-source Python framework that simplifies the development of\nresearch and other complex applications. The key feature is the ability to\ndynamically create a hierarchical configuration by composition and override it\nthrough config files and the command line. The name Hydra comes from its\nability to run multiple similar jobs - much like a Hydra with multiple heads.", + "domains": [], + "extensions": [ + "alembic-1.18.5", + "antlr4-python3-runtime-4.9.3", + "cmaes-0.13.0", + "colorlog-6.12.0", + "hydra-core-1.3.4", + "hydra-optuna-sweeper-1.4.0.dev7", + "hydra-submitit-launcher-1.2.0", + "omegaconf-2.3.1", + "optuna-4.9.0", + "read_version-0.3.2", + "submitit-1.5.4" + ], + "licence_type": "", + "homepage": "https://hydra.cc/", + "support": "", + "versions": [ + "1.3.4-foss-2026-with-plugins" + ], + "admin_list": [], + "network_licences": [], + "default": "1.3.4-foss-2026-with-plugins", + "default_type": "latest", + "last_updated": 1786048146, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/Hydra/1.3.4-foss-2026-with-plugins.lua", + "force_hide": "False", + "force_show": "False" + }, "Hypre": { "description": "Hypre is a library for solving large, sparse linear systems of equations on massively\n parallel computers. The problems of interest arise in the simulation codes being developed at LLNL\n and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.", "domains": [], @@ -8492,9 +8200,7 @@ }, "IDBA-UD": { "description": "IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads\n Sequencing data with Highly Uneven Sequencing Depth.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/", @@ -8555,10 +8261,7 @@ }, "IGV": { "description": "The Integrative Genomics Viewer (IGV) is a high-performance visualization \n tool for interactive exploration of large, integrated genomic datasets. It supports a wide \n variety of data types, including array-based and next-generation sequence data", - "domains": [ - "biology", - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.broadinstitute.org/software/igv/", @@ -8603,9 +8306,7 @@ }, "ImageMagick": { "description": "Create, edit, compose, or convert bitmap images", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.imagemagick.org/", @@ -8625,9 +8326,7 @@ }, "imkl": { "description": "Intel oneAPI Math Kernel Library", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html", @@ -8691,9 +8390,7 @@ }, "impi": { "description": "Intel MPI Library, compatible with MPICH ABI", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html", @@ -8718,9 +8415,7 @@ }, "Infernal": { "description": "Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases\nfor RNA structure and sequence similarities.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://eddylab.org/infernal/", @@ -8787,10 +8482,7 @@ }, "InterProScan": { "description": "Sequence analysis application (nucleotide and protein sequences) that combines\n different protein signature recognition methods into one resource.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ebi.ac.uk/interpro/", @@ -8873,9 +8565,7 @@ }, "ipyrad": { "description": "ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic\n data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "cython-3.2.4", "editables-0.5", @@ -8914,9 +8604,7 @@ }, "IQ-TREE": { "description": "Efficient phylogenomic software by maximum likelihood", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.iqtree.org/", @@ -8991,9 +8679,7 @@ }, "JAGS": { "description": "Just Another Gibbs Sampler - a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://mcmc-jags.sourceforge.net", @@ -9037,9 +8723,7 @@ }, "Java": { "description": "Java Platform, Standard Edition (Java SE) lets you develop and deploy\n Java applications on desktops and servers.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://java.com/", @@ -9086,9 +8770,7 @@ }, "jcvi": { "description": "Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "deap-1.3.1", "jcvi-1.0.6" @@ -9115,9 +8797,7 @@ }, "Jellyfish": { "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.genome.umd.edu/jellyfish.html", @@ -9234,9 +8914,7 @@ }, "Julia": { "description": "A high-level, high-performance dynamic language for technical computing.\n\nThis version was compiled from source with USE_INTEL_JITEVENTS=1 to enable profiling with VTune.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://julialang.org/", @@ -9409,9 +9087,7 @@ }, "jvarkit": { "description": "Java utilities for Bioinformatics", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://lindenb.github.io/jvarkit/JvarkitCentral.html", @@ -9431,9 +9107,7 @@ }, "Kaiju": { "description": "Kaiju is a program for sensitive taxonomic classification of high-throughput\nsequencing reads from metagenomic whole genome sequencing experiments", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://kaiju.binf.ku.dk/", @@ -9451,11 +9125,29 @@ "force_hide": "False", "force_show": "False" }, - "kalign2": { + "Kalign": { "description": "Kalign is a fast multiple sequence alignment program for biological sequences.", - "domains": [ - "biology" + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://github.com/TimoLassmann/kalign", + "support": "", + "versions": [ + "3.5.1-GCCcore-15.2.0" ], + "admin_list": [], + "network_licences": [], + "default": "3.5.1-GCCcore-15.2.0", + "default_type": "latest", + "last_updated": 1786048604, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/Kalign/3.5.1-GCCcore-15.2.0.lua", + "force_hide": "False", + "force_show": "False" + }, + "kalign2": { + "description": "Kalign is a fast multiple sequence alignment program for biological sequences.", + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/TimoLassmann/kalign", @@ -9475,9 +9167,7 @@ }, "kallisto": { "description": "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally\n of target sequences using high-throughput sequencing reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://pachterlab.github.io/kallisto/", @@ -9497,9 +9187,7 @@ }, "KAT": { "description": "The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.earlham.ac.uk/kat-tools", @@ -9565,9 +9253,7 @@ }, "Kent_tools": { "description": "Collection of tools used by the UCSC genome browser.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://genome.cse.ucsc.edu/", @@ -9607,9 +9293,7 @@ }, "kma": { "description": "KMA is a mapping method designed to map raw reads directly against redundant databases, \nin an ultra-fast manner using seed and extend.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://bitbucket.org/genomicepidemiology/kma", @@ -9630,9 +9314,7 @@ }, "KMC": { "description": "Disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://sun.aei.polsl.pl/kmc", @@ -9652,9 +9334,7 @@ }, "KmerGenie": { "description": "KmerGenie estimates the best k-mer length for genome de novo assembly.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://kmergenie.bx.psu.edu/", @@ -9674,9 +9354,7 @@ }, "KorfSNAP": { "description": "Semi-HMM-based Nucleic Acid Parser", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://korflab.ucdavis.edu/software.html", @@ -9697,9 +9375,7 @@ }, "Kraken2": { "description": "Taxonomic sequence classifier.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://ccb.jhu.edu/software/kraken/MANUAL.html", @@ -9725,9 +9401,7 @@ }, "KronaTools": { "description": "Krona Tools is a set of scripts to create Krona charts from \nseveral Bioinformatics tools as well as from text and XML files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/marbl/Krona/wiki/KronaTools", @@ -9769,11 +9443,7 @@ }, "LAMMPS": { "description": "LAMMPS is a classical molecular dynamics code, and an acronym\nfor Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has\npotentials for solid-state materials (metals, semiconductors) and soft matter\n(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be\nused to model atoms or, more generically, as a parallel particle simulator at\nthe atomic, meso, or continuum scale. LAMMPS runs on single processors or in\nparallel using message-passing techniques and a spatial-decomposition of the\nsimulation domain. The code is designed to be easy to modify or extend with new\nfunctionality.", - "domains": [ - "biology", - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://lammps.sandia.gov/", @@ -9798,9 +9468,7 @@ }, "LAST": { "description": "LAST finds similar regions between sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://last.cbrc.jp/", @@ -9824,9 +9492,7 @@ }, "LASTZ": { "description": "LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to\n handle sequences the size of human chromosomes and from different species, it is also useful for sequences\n produced by NGS sequencing technologies such as Roche 454.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.bx.psu.edu/~rsharris/lastz/", @@ -9848,9 +9514,7 @@ }, "LDC": { "description": "D programming language compiler", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://wiki.dlang.org/LDC", @@ -9874,9 +9538,7 @@ }, "LEfSe": { "description": "Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance \n\t\twith additional tests encoding biological consistency and effect relevance", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "coin-1.4-2", "libcoin-1.0-9", @@ -10010,9 +9672,7 @@ }, "libcuda-stub": { "description": "Dummy libcuda and libnvidia libraries for compiling CUDA programs on non-GPU nodes", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -10241,9 +9901,7 @@ }, "libgeotiff": { "description": "Library for reading and writing coordinate system information from/to GeoTIFF files", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/OSGeo/libgeotiff/", @@ -10358,10 +10016,7 @@ }, "libgpuarray": { "description": "Arrays on GPU device memory, for Theano", - "domains": [ - "gpu", - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://deeplearning.net/software/libgpuarray", @@ -10423,9 +10078,7 @@ }, "Libint": { "description": "Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body\n matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/evaleev/libint", @@ -10446,9 +10099,7 @@ }, "libjpeg-turbo": { "description": "libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG\ncompression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://libjpeg-turbo.org/", @@ -10557,9 +10208,7 @@ }, "libpng": { "description": "libpng is the official PNG reference library", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.libpng.org/pub/png/libpng.html", @@ -10668,9 +10317,7 @@ }, "libStatGen": { "description": "Set of classes for creating statistical genetic programs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen", @@ -10710,9 +10357,7 @@ }, "LibTIFF": { "description": "tiff: Library and tools for reading and writing TIFF data files", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://libtiff.gitlab.io/libtiff/", @@ -10776,9 +10421,7 @@ }, "libvdwxc": { "description": "libvdwxc is a general library for evaluating energy and potential for\nexchange-correlation (XC) functionals from the vdW-DF family that can be used with various\nof density functional theory (DFT) codes.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://libvdwxc.org", @@ -10818,9 +10461,7 @@ }, "libxc": { "description": "Libxc is a library of exchange-correlation functionals for density-functional theory.\n The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://libxc.gitlab.io", @@ -10892,9 +10533,7 @@ }, "libxsmm": { "description": "LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications\ntargeting Intel Architecture (x86).", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/hfp/libxsmm", @@ -10937,9 +10576,7 @@ }, "Liftoff": { "description": "Tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "gffutils-0.11.1", "interlap-0.2.7", @@ -11006,9 +10643,7 @@ }, "LINKS": { "description": "Alignment-free scaffolding of genome assembly drafts with long reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.bcgsc.ca/bioinfo/software/links", @@ -11034,9 +10669,7 @@ }, "LISFLOOD-FP": { "description": "The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by\nthe University of Bristol. It has undergone extensive development since\nconception and includes a collection of numerical schemes implemented to solve\na variety of mathematical approximations of the 2D shallow water equations of\ndifferent complexity.\nThe local inertia solver, known as the ACC solver, is widely used to simulate\nfloods with gradually-varying, subcritical flow over sufficiently rough\nsurfaces with Manning\u2019s coefficient of at least 0.03. It has a version with\nCPU-specific optimisations and enhanced with a subgrid channel model.\nLISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and\nfirst-order finite volume (FV1) solvers of the full shallow water equations for\nmodelling a wide range of flows, including rapidly-propagating, supercritical\nflows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are\nparallelised for the multi-core CPU architecture, but do not integrate with the\nsubgrid channel model nor with the CPU-specific optimisations.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.seamlesswave.com/LISFLOOD8.0.html", @@ -11057,9 +10690,7 @@ }, "LittleCMS": { "description": "Color management engine.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.littlecms.com/", @@ -11129,9 +10760,7 @@ }, "LongStitch": { "description": "A genome assembly correction and scaffolding pipeline using long reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bcgsc/LongStitch", @@ -11151,9 +10780,7 @@ }, "lp_solve": { "description": "Mixed Integer Linear Programming (MILP) solver.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://lpsolve.sourceforge.net/5.5/", @@ -11177,9 +10804,7 @@ }, "LSD2": { "description": "Least-squares methods to estimate rates and dates from phylogenies", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/tothuhien/lsd2", @@ -11201,9 +10826,7 @@ }, "LTR_retriever": { "description": "Highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/oushujun/LTR_retriever", @@ -11223,9 +10846,7 @@ }, "LUMPY": { "description": "A probabilistic framework for structural variant discovery.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/arq5x/lumpy-sv", @@ -11328,11 +10949,29 @@ "force_hide": "False", "force_show": "False" }, + "maeparser": { + "description": "maeparser is a parser for Schrodinger Maestro files.", + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://github.com/schrodinger/maeparser", + "support": "", + "versions": [ + "1.3.3-gompi-2026" + ], + "admin_list": [], + "network_licences": [], + "default": "1.3.3-gompi-2026", + "default_type": "latest", + "last_updated": 1786048457, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/maeparser/1.3.3-gompi-2026.lua", + "force_hide": "False", + "force_show": "False" + }, "maf_stream": { "description": "Collection of utilities to manipulate multiple alignments in the Multiple Alignment Format", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/joelarmstrong/maf_stream", @@ -11352,9 +10991,7 @@ }, "MAFFT": { "description": "Multiple sequence alignment program offering a range of methods.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://mafft.cbrc.jp/alignment/software/", @@ -11377,32 +11014,28 @@ }, "magma": { "description": "The MAGMA project aims to develop a dense linear algebra library similar to\n LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.", - "domains": [ - "gpu", - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://icl.cs.utk.edu/magma/", "support": "", "versions": [ + "2.10.0-foss-2026-CUDA-13.2.1", "2.7.1-gimkl-2022a-CUDA-11.6.2" ], "admin_list": [], "network_licences": [], - "default": "2.7.1-gimkl-2022a-CUDA-11.6.2", + "default": "2.10.0-foss-2026-CUDA-13.2.1", "default_type": "latest", - "last_updated": 1740132638, + "last_updated": 1785799084, "modulefile_text": "", - "module_path": "/opt/nesi/CS400_centos7_bdw/modules/all/magma/2.7.1-gimkl-2022a-CUDA-11.6.2.lua", + "module_path": "/opt/nesi/zen3/modules/all/magma/2.10.0-foss-2026-CUDA-13.2.1.lua", "force_hide": "False", "force_show": "False" }, "MAKER": { "description": "Genome annotation pipeline", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.yandell-lab.org/software/maker.html", @@ -11451,9 +11084,7 @@ }, "manta": { "description": "Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Illumina/manta", @@ -11473,9 +11104,7 @@ }, "mapDamage": { "description": "tracks and quantifies DNA damage patterns among ancient \nDNA sequencing reads generated by Next-Generation Sequencing platforms.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ginolhac.github.io/mapDamage/", @@ -11531,9 +11160,7 @@ }, "Mash": { "description": "Fast genome and metagenome distance estimation using MinHash", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://mash.readthedocs.org", @@ -11557,9 +11184,7 @@ }, "MashMap": { "description": "Implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/marbl/merqury", @@ -11579,9 +11204,7 @@ }, "Mashtree": { "description": "Create a tree using Mash distances.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Bio::Sketch-0.3", "Bio::Sketch::Mash-0.9", @@ -11606,9 +11229,7 @@ }, "MaSuRCA": { "description": "MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph \n and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing \n only short reads from Illumina sequencing or a mixture of short reads and long reads \n (Sanger, 454, Pacbio and Nanopore).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.genome.umd.edu/masurca.html", @@ -11630,14 +11251,9 @@ }, "MATLAB": { "description": "A high-level language and interactive environment for numerical computing.", - "domains": [ - "engineering", - "gpu", - "mathematics", - "visualisation" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "http://www.mathworks.com/products/matlab", "support": "", "versions": [ @@ -11883,10 +11499,7 @@ }, "matlab-proxy": { "description": "Python package which enables you to launch MATLAB and access it from a web browser.", - "domains": [ - "engineering", - "mathematics" - ], + "domains": [], "extensions": [ "aiohappyeyeballs-2.4.3", "aiohttp-3.10.5", @@ -11940,9 +11553,7 @@ }, "MaxBin": { "description": "MaxBin is software for binning assembled metagenomic sequences based on\n an Expectation-Maximization algorithm.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "HTTP::Status-6.44", "LWP::Simple-6.67" @@ -11966,10 +11577,7 @@ }, "MCL": { "description": "The MCL algorithm is short for the Markov Cluster Algorithm, a fast\nand scalable unsupervised cluster algorithm for graphs (also known as networks) based\non simulation of (stochastic) flow in graphs.", - "domains": [ - "biology", - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://micans.org/mcl/", @@ -11991,10 +11599,7 @@ }, "MCR": { "description": "The Matlab Compiler Runtime is required for running compiled MATLAB executables without MATLAB itself.", - "domains": [ - "engineering", - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.mathworks.com/products/compiler/mcr.html", @@ -12034,9 +11639,7 @@ }, "mctc-lib": { "description": "Common tool chain for working with molecular structure data in various\napplications. This library provides a unified way to perform operations on\nmolecular structure data, like reading and writing to common geometry file\nformats.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://grimme-lab.github.io/mctc-lib", @@ -12076,10 +11679,7 @@ }, "medaka": { "description": "Medaka is a tool to create a consensus sequence from nanopore sequencing data.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/nanoporetech/medaka", @@ -12103,9 +11703,7 @@ }, "MEGAHIT": { "description": "An ultra-fast single-node solution for large and complex\n metagenomics assembly via succinct de Bruijn graph", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/voutcn/megahit", @@ -12125,10 +11723,7 @@ }, "megalodon": { "description": "Tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads \nby anchoring the information rich basecalling neural network output to a reference genome/transcriptome.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [ "coloredlogs-15.0.1", "flatbuffers-23.1.21", @@ -12174,9 +11769,7 @@ }, "Merqury": { "description": "Evaluate genome assemblies with k-mers and more", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/marbl/merqury", @@ -12196,9 +11789,7 @@ }, "Mesa": { "description": "Mesa is an open-source implementation of the OpenGL specification -\n a system for rendering interactive 3D graphics.\n\n Note that this build enables CPU-based rendering with OpenSWR and LLVM.\n The module is intended to be used with visualisation software, such as\n ParaView, on nodes where no GPU hardware is available.\n\n Both on-screen and off-screen rendering are supported.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.mesa3d.org/", @@ -12239,9 +11830,7 @@ }, "MetaBAT": { "description": "An efficient tool for accurately reconstructing single genomes from complex microbial communities", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://bitbucket.org/berkeleylab/metabat", @@ -12263,9 +11852,7 @@ }, "METABOLIC": { "description": "Metabolic And Biogeochemistry anaLyses In microbes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/AnantharamanLab/METABOLIC/wiki", @@ -12285,9 +11872,7 @@ }, "MetaEuk": { "description": "MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic\n metagenomic contigs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://metaeuk.soedinglab.org", @@ -12309,9 +11894,7 @@ }, "MetaGeneAnnotator": { "description": "MetaGeneAnnotator is a gene-finding program for prokaryote and phage.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://metagene.nig.ac.jp/", @@ -12351,9 +11934,7 @@ }, "MetaPhlAn": { "description": "MetaPhlAn is a computational tool for profiling the composition of microbial\n communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing\n data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now\n possible to perform accurate strain-level microbial profiling.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "bcbio-gff-0.7.1", "CMSeq-1.0.4", @@ -12379,9 +11960,7 @@ }, "MetaPhlAn2": { "description": "MetaPhlAn is a computational tool for profiling the composition of microbial\n communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing\n data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now\n possible to perform accurate strain-level microbial profiling.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/", @@ -12401,9 +11980,7 @@ }, "MetaSV": { "description": "Structural-variant caller", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "MetaSV-0.5.4", "pybedtools-0.6.9", @@ -12431,9 +12008,7 @@ }, "metaWRAP": { "description": "Flexible pipeline for genome-resolved metagenomic data analysis.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://qiime2.org/", @@ -12453,9 +12028,7 @@ }, "Metaxa2": { "description": "Taxonomic classification of rRNA.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://microbiology.se/software/metaxa2/", @@ -12476,9 +12049,7 @@ }, "METIS": { "description": "METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes,\nand producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the\nmultilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview", @@ -12506,10 +12077,7 @@ }, "MiMiC": { "description": "MiMiC: A Framework for Multiscale Modeling in Computational Chemistry\n\nThis package includes mimicpy", - "domains": [ - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gitlab.com/MiMiC-projects", @@ -12529,9 +12097,7 @@ }, "MiMiC-CommLib": { "description": "The MiMiC communication library (MCL) enables communication between external programs \n coupled through the MiMiC framework.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://gitlab.com/MiMiC-projects", @@ -12551,9 +12117,7 @@ }, "miniasm": { "description": "Fast OLC-based de novo assembler for noisy long reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/minimap2", @@ -12573,9 +12137,7 @@ }, "miniBUSCO": { "description": "faster and more accurate reimplementation of BUSCO.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/huangnengCSU/minibusco", @@ -12595,9 +12157,7 @@ }, "Miniconda3": { "description": "A platform for Python-based data analytics", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.continuum.io/anaconda-overview", @@ -12656,9 +12216,7 @@ }, "minigraph": { "description": "Sequence-to-graph mapper and graph generator", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/minigraph", @@ -12678,9 +12236,7 @@ }, "Minimac3": { "description": "Low memory and more computationally efficient implementation of the genotype imputation algorithms.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://genome.sph.umich.edu/wiki/Minimac3", @@ -12700,9 +12256,7 @@ }, "Minimac4": { "description": "Low memory and more computationally efficient implementation of the genotype imputation algorithms.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://genome.sph.umich.edu/wiki/Minimac4", @@ -12722,9 +12276,7 @@ }, "minimap2": { "description": "Minimap2 is a fast sequence mapping and alignment\nprogram that can find overlaps between long noisy reads, or map long\nreads or their assemblies to a reference genome optionally with detailed\nalignment (i.e. CIGAR). At present, it works efficiently with query\nsequences from a few kilobases to ~100 megabases in length at an error\nrate ~15%. .", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/minimap2", @@ -12759,9 +12311,7 @@ }, "miniprot": { "description": "Aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift..", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/miniprot", @@ -12802,9 +12352,7 @@ }, "miRDeep2": { "description": "Completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rajewsky-lab/mirdeep2", @@ -12824,9 +12372,7 @@ }, "MitoZ": { "description": "Toolkit which aims to automatically filter pair-end raw data,\n assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome,\n and mitogenome visualization.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/linzhi2013/MitoZ", @@ -12868,9 +12414,7 @@ }, "MMseqs2": { "description": "MMseqs2: ultra fast and sensitive search and clustering suite", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://mmseqs.com", @@ -12894,9 +12438,7 @@ }, "modbam2bed": { "description": "A program to aggregate modified base counts stored in a modified-base BAM file to a bedMethyl file.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/epi2me-labs/modbam2bed", @@ -12916,9 +12458,7 @@ }, "ModDotPlot": { "description": "Novel dot plot visualization tool used to view tandem repeats", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "dash-2.11.0", "dash_daq-0.5.0", @@ -12948,9 +12488,7 @@ }, "ModelTest-NG": { "description": "Tool for selecting the best-fit model of evolution for DNA and protein alignments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ddarriba/modeltest", @@ -12970,9 +12508,7 @@ }, "modkit": { "description": "Tool for working with modified bases from Oxford Nanopore", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/nanoporetech/modkit", @@ -12994,9 +12530,7 @@ }, "Molpro": { "description": "Molpro is a complete system of ab initio programs for molecular electronic structure calculations.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://molpro.net", @@ -13036,9 +12570,7 @@ }, "Monocle3": { "description": "An analysis toolkit for single-cell RNA-seq.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "furrr-0.2.2", "future-1.21.0", @@ -13090,9 +12622,7 @@ }, "mosdepth": { "description": "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/brentp/mosdepth", @@ -13112,9 +12642,7 @@ }, "Mothur": { "description": "Mothur is a single piece of open-source, expandable software\n to fill the bioinformatics needs of the microbial ecology community.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.mothur.org/", @@ -13139,9 +12667,7 @@ }, "mpcci": { "description": "MpCCI is a vendor neutral and application independent interface for co-simulation. MpCCI offers advanced and proven features for multiphysics modelling.", - "domains": [ - "physics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.mpcci.de/", @@ -13162,9 +12688,7 @@ }, "MPFR": { "description": "The MPFR library is a C library for multiple-precision \n floating-point computations with correct rounding.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.mpfr.org", @@ -13189,10 +12713,7 @@ }, "MrBayes": { "description": "MrBayes is a program for the Bayesian estimation of phylogeny.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nbisweden.github.io/MrBayes/", @@ -13212,9 +12733,7 @@ }, "MultiQC": { "description": "Aggregate results from bioinformatics analyses across many samples into a single \n report.\n MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general\n use tool, perfect for summarising the output from numerous bioinformatics tools.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "annotated_types-0.7.0", "certifi-2022.9.24", @@ -13265,9 +12784,7 @@ }, "MUMmer": { "description": "MUMmer is a system for rapidly aligning entire genomes,\n whether in complete or draft form. AMOS makes use of it.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://mummer.sourceforge.net/", @@ -13291,9 +12808,7 @@ }, "MUMPS": { "description": "A parallel sparse direct solver", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://graal.ens-lyon.fr/MUMPS/", @@ -13320,9 +12835,7 @@ }, "muParser": { "description": "muParser is an extensible high performance math expression\nparser library written in C++. It works by transforming a mathematical\nexpression into bytecode and precalculating constant parts of the expression.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://beltoforion.de/article.php?a=muparser", @@ -13344,9 +12857,7 @@ }, "MUSCLE": { "description": "MUSCLE is a program for creating multiple alignments of amino acid or nucleotide\nsequences. A range of options is provided that give you the choice of optimizing accuracy, speed,\nor some compromise between the two.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://drive5.com/muscle/", @@ -13369,11 +12880,7 @@ }, "NAMD": { "description": "NAMD is a parallel molecular dynamics code designed for high-performance simulation of\n large biomolecular systems.", - "domains": [ - "biology", - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ks.uiuc.edu/Research/namd/", @@ -13414,9 +12921,7 @@ }, "NanoComp": { "description": "Comparing runs of Oxford Nanopore sequencing data and alignments", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "joypy-0.2.6", "NanoComp-1.20.0" @@ -13439,9 +12944,7 @@ }, "nanofilt": { "description": "Filtering and trimming of long read sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wdecoster/nanofilt", @@ -13461,9 +12964,7 @@ }, "nanoget": { "description": "Functions to extract information from Oxford Nanopore sequencing data and alignments", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wdecoster/nanoget", @@ -13484,9 +12985,7 @@ }, "NanoLyse": { "description": "Removing reads mapping to the lambda genome.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "mappy-2.22", "NanoLyse-1.2.0", @@ -13510,9 +13009,7 @@ }, "nanomath": { "description": "A few simple math function for other Oxford Nanopore processing scripts", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "nanomath-1.2.1", "Python-Deprecated-1.1.0" @@ -13541,9 +13038,7 @@ }, "NanoPlot": { "description": "Plotting suite for Oxford Nanopore sequencing data and alignments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "kaleido-0.2.1", "nanoget-1.19.3", @@ -13570,9 +13065,7 @@ }, "nanopolish": { "description": "Software package for signal-level analysis of Oxford Nanopore sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/jts/nanopolish", @@ -13593,9 +13086,7 @@ }, "nanoQC": { "description": "Create fastQC-like plots for Oxford Nanopore sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "nanoQC-0.9.4" ], @@ -13622,9 +13113,7 @@ }, "NanoStat": { "description": "Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/wdecoster/nanostat", @@ -13644,9 +13133,7 @@ }, "NASM": { "description": "NASM: General-purpose x86 assembler", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.nasm.us/", @@ -13669,9 +13156,7 @@ }, "ncbi-vdb": { "description": "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for\n using data in the INSDC Sequence Read Archives.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ncbi/ncbi-vdb", @@ -13694,9 +13179,7 @@ }, "NCCL": { "description": "The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective\ncommunication primitives that are performance optimized for NVIDIA GPUs.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.nvidia.com/nccl", @@ -13723,9 +13206,7 @@ }, "NCL": { "description": "NCL is an interpreted language designed specifically for scientific data analysis and visualization.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ncl.ucar.edu", @@ -13837,9 +13318,7 @@ }, "NECAT": { "description": "Rrror correction and de-novo assembly tool for Nanopore long noisy reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/xiaochuanle/NECAT", @@ -14001,9 +13480,7 @@ }, "NewHybrids": { "description": "This implements a Gibbs sampler to estimate the posterior probability that genetically sampled\nindividuals fall into each of a set of user-defined hybrid categories.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs", @@ -14023,9 +13500,7 @@ }, "Newton-X": { "description": "NX is a general-purpose program package for simulating the dynamics of electronically excited molecules and molecular assemblies.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://newtonx.org/", @@ -14046,9 +13521,7 @@ }, "Nextflow": { "description": "Nextflow is a reactive workflow framework and a programming DSL\n that eases writing computational pipelines with complex data", - "domains": [ - "workflow_management" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.nextflow.io/", @@ -14080,9 +13553,7 @@ }, "NextPolish2": { "description": "a fast and efficient genome polishing tool for long-read assembly", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Paralleltask-0.2.3" ], @@ -14225,9 +13696,7 @@ }, "NGS": { "description": "NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from\n Next Generation Sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ncbi/ngs", @@ -14250,9 +13719,7 @@ }, "Nim": { "description": "Nim is a systems and applications programming language.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nim-lang.org/", @@ -14317,9 +13784,7 @@ }, "nodejs": { "description": "Node.js is a platform built on Chrome's JavaScript runtime\n for easily building fast, scalable network applications. Node.js uses an\n event-driven, non-blocking I/O model that makes it lightweight and efficient,\n perfect for data-intensive real-time applications that run across distributed devices.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nodejs.org", @@ -14367,9 +13832,7 @@ }, "nseg": { "description": "Used to mask nucleic acid sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.google.com/?gws_rd=ssl#q=Wooton%2C+J.+C.+%26+Federhen%2C+S.+Comp.+Chem.+17%2C+149\u2212163+(1993)", @@ -14499,9 +13962,7 @@ }, "nullarbor": { "description": "Reads to report pipeline for bacterial isolate NGS data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/tseemann/nullarbor", @@ -14548,9 +14009,7 @@ }, "NVHPC": { "description": "C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.nvidia.com/hpc-sdk/", @@ -14576,9 +14035,7 @@ }, "NWChem": { "description": "NWChem aims to provide its users with computational chemistry tools that are scalable both in\n their ability to treat large scientific computational chemistry problems efficiently, and in their use of available\n parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.\n NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all\n combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties\n and relativity.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nwchemgit.github.io/", @@ -14642,10 +14099,7 @@ }, "ont-guppy-gpu": { "description": "Data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms,\nand several bioinformatic post-processing features", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://nanoporetech.com/products/minit", @@ -14688,10 +14142,7 @@ }, "OpenBabel": { "description": "Open Babel is a chemical toolbox designed to speak the many\n languages of chemical data. It's an open, collaborative project allowing anyone\n to search, convert, analyze, or store data from molecular modeling, chemistry,\n solid-state materials, biochemistry, or related areas.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://openbabel.org", @@ -14741,9 +14192,7 @@ }, "OpenCV": { "description": "OpenCV (Open Source Computer Vision Library) is an open source computer vision\n and machine learning software library. OpenCV was built to provide\n a common infrastructure for computer vision applications and to accelerate\n the use of machine perception in the commercial products.", - "domains": [ - "machine_learning" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://opencv.org/", @@ -14765,10 +14214,7 @@ }, "OpenFOAM": { "description": "OpenFOAM is a free, open source CFD software package.\n OpenFOAM has an extensive range of features to solve anything from complex fluid flows\n involving chemical reactions, turbulence and heat transfer,\n to solid dynamics and electromagnetics.", - "domains": [ - "chemistry", - "engineering" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.openfoam.com/", @@ -14804,6 +14250,47 @@ "force_hide": "False", "force_show": "False" }, + "OpenFold3": { + "description": "A fully open source biomolecular structure prediction model based on AlphaFold3", + "domains": [], + "extensions": [ + "absl-py-2.5.0", + "biotite-1.7.1", + "biotraj-1.2.2", + "deepspeed-0.19.3", + "einops-0.8.2", + "func-timeout-4.3.5", + "gemmi-0.7.5", + "hjson-3.1.0", + "ijson-3.5.1", + "kalign-python-3.6.0", + "lmdb-2.3.0", + "memory-profiler-0.61.0", + "ml-collections-1.1.0", + "nanobind-2.13.0", + "OpenFold3-0.4.4", + "patch-ng-1.19.1", + "pdbeccdutils-1.0.4", + "py-cpuinfo-9.0.0", + "sentry-sdk-2.66.1", + "wandb-0.28.1" + ], + "licence_type": "", + "homepage": "https://github.com/aqlaboratory/openfold-3", + "support": "", + "versions": [ + "0.4.4-foss-2026-CUDA-13.2.1" + ], + "admin_list": [], + "network_licences": [], + "default": "0.4.4-foss-2026-CUDA-13.2.1", + "default_type": "latest", + "last_updated": 1786054315, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/OpenFold3/0.4.4-foss-2026-CUDA-13.2.1.lua", + "force_hide": "False", + "force_show": "False" + }, "OpenJPEG": { "description": "An open-source JPEG 2000 codec written in C", "domains": [], @@ -14849,9 +14336,7 @@ }, "OpenMPI": { "description": "The Open MPI Project is an open source MPI-3 implementation.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.open-mpi.org/", @@ -14892,10 +14377,7 @@ }, "OpenSees": { "description": "OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes.", - "domains": [ - "earth_science", - "engineering" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://opensees.berkeley.edu", @@ -14918,10 +14400,7 @@ }, "OpenSeesPy": { "description": "Wraps OpenSees for Python. Load an OpenSees module as well.", - "domains": [ - "earth_science", - "engineering" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://openseespydoc.readthedocs.io/", @@ -14942,9 +14421,7 @@ }, "OpenSlide": { "description": "OpenSlide is a C library that provides a simple interface to\nread whole-slide images (also known as virtual slides).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://openslide.org/", @@ -14987,9 +14464,7 @@ }, "ORCA": { "description": "ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry\n with specific emphasis on spectroscopic properties of open-shell molecules.\n It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single-\n and multireference correlated ab initio methods.\n It can also treat environmental and relativistic effects.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://orcaforum.kofo.mpg.de", @@ -15012,9 +14487,7 @@ }, "OrthoFinder": { "description": "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "bottle-0.13.4", "brotli-1.2.0", @@ -15045,9 +14518,7 @@ }, "OSPRay": { "description": "OSPRay features interactive CPU rendering capabilities geared towards\nScientific Visualization applications. Advanced shading effects such\nas Ambient Occlusion, shadows, and transparency can be rendered\ninteractively, enabling new insights into data exploration.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ospray.org", @@ -15112,9 +14583,7 @@ }, "padloc": { "description": "Prokaryotic Antiviral Defence LOCator", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/padlocbio/padloc", @@ -15135,9 +14604,7 @@ }, "pairtools": { "description": "CLI tools to process mapped Hi-C data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "bioframe-0.4.1", "pairtools-1.0.2" @@ -15160,9 +14627,7 @@ }, "PALEOMIX": { "description": "pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://paleomix.readthedocs.io/en/latest/index.html", @@ -15182,9 +14647,7 @@ }, "PAML": { "description": "PAML is a package of programs for phylogenetic \n analyses of DNA or protein sequences using maximum likelihood.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://abacus.gene.ucl.ac.uk/software/paml.html", @@ -15205,9 +14668,7 @@ }, "panaroo": { "description": "A pangenome analysis pipeline.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "argcomplete-2.0.0", "argh-0.26.2", @@ -15342,9 +14803,7 @@ }, "parallel-fastq-dump": { "description": "parallel fastq-dump wrapper", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rvalieris/parallel-fastq-dump", @@ -15384,10 +14843,7 @@ }, "ParaView": { "description": "ParaView is a scientific parallel visualizer.", - "domains": [ - "engineering", - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.paraview.org", @@ -15412,9 +14868,7 @@ }, "ParMETIS": { "description": "ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs,\n meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes\n routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in\n ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning\n schemes.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview", @@ -15457,9 +14911,7 @@ }, "pauvre": { "description": "Tools for plotting Oxford Nanopore and other long-read data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "pauvre-0.2.3" ], @@ -15529,10 +14981,7 @@ }, "PDAL": { "description": "PDAL is Point Data Abstraction Library. It is a C/C++ open source library and applications for\n translating and processing point cloud data. It is not limited to LiDAR data, although the focus and impetus\n for many of the tools in the library have their origins in LiDAR.", - "domains": [ - "climate_science", - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://pdal.io/", @@ -15553,9 +15002,7 @@ }, "PEAR": { "description": "Memory-efficient,fully parallelized and highly accurate pair-end read merger.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://cme.h-its.org/exelixis/web/software/pear/", @@ -15575,9 +15022,7 @@ }, "Perl": { "description": "Larry Wall's Practical Extraction and Report Language", - "domains": [ - "language" - ], + "domains": [], "extensions": [ "Acme::Damn-0.09", "Algorithm::Dependency-1.112", @@ -16103,9 +15548,7 @@ }, "pggb": { "description": "PanGenome Graph Builder(pggb)", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.repeatmasker.org/", @@ -16125,9 +15568,7 @@ }, "pgge": { "description": "pangenome graph evaluator", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/pangenome/pgge", @@ -16147,9 +15588,7 @@ }, "phonopy": { "description": "Phonopy is an open source package of phonon calculations based on the supercell approach.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [ "hatchling-1.25.0", "nanobind-2.1.0", @@ -16178,9 +15617,7 @@ }, "PhyloPhlAn": { "description": "Integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://huttenhower.sph.harvard.edu/phylophlan/", @@ -16201,9 +15638,7 @@ }, "PhyML": { "description": "Phylogenetic estimation using Maximum Likelihood", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/stephaneguindon/phyml", @@ -16223,9 +15658,7 @@ }, "phyx": { "description": "phyx performs phylogenetics analyses on trees and sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/FePhyFoFum/phyx", @@ -16249,9 +15682,7 @@ }, "picard": { "description": "A set of tools (in Java) for working with next generation sequencing data in the BAM format.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sourceforge.net/projects/picard", @@ -16296,9 +15727,7 @@ }, "PILERCR": { "description": "PILER-CR is a program specifically designed for the identification and analysis of CRISPR repeats.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.drive5.com/pilercr/", @@ -16318,9 +15747,7 @@ }, "Pilon": { "description": "Pilon is an automated genome assembly improvement and variant detection tool", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/broadinstitute/pilon", @@ -16341,9 +15768,7 @@ }, "PISM": { "description": "The Parallel Ice Sheet Model (PISM) is a computer program used in climate \nscience to simulate the past and future of glaciers and ice sheets, including the Earth\u2019s \ntwo large ice sheets in Greenland and Antarctica.", - "domains": [ - "climate_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.pism.io/", @@ -16383,9 +15808,7 @@ }, "pixman": { "description": "Pixman is a low-level software library for pixel manipulation, providing features such as image\ncompositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.", - "domains": [ - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.pixman.org/", @@ -16428,9 +15851,7 @@ }, "PLINK": { "description": "PLINK is a free, open-source whole genome association analysis toolset, \n designed to perform a range of basic, large-scale analyses in a computationally efficient manner.\n The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for \n steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). \n Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, \n annotation and storage of results.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.cog-genomics.org/plink2", @@ -16453,9 +15874,7 @@ }, "PLUMED": { "description": "PLUMED is an open source library for free energy calculations in molecular systems which\n works together with some of the most popular molecular dynamics engines. Free energy calculations can be\n performed as a function of many order parameters with a particular focus on biological problems, using\n state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.\n The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.plumed-code.org", @@ -16561,9 +15980,7 @@ }, "pod5": { "description": "File format for storing nanopore dna data in an easily accessible way.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Deprecated-1.2.18", "iso8601-2.1.0", @@ -16597,9 +16014,7 @@ }, "Porechop": { "description": "Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.\n Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle,\n it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments\n to effectively find adapters, even at low sequence identity", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rrwick/Porechop", @@ -16621,9 +16036,7 @@ }, "Porechop_ABI": { "description": "Extension of Porechop whose purpose is to process adapter sequences in ONT reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://busco.ezlab.org/", @@ -16666,9 +16079,7 @@ }, "pplacer": { "description": "Places query sequences on a fixed reference phylogenetic tree \nto maximize phylogenetic likelihood or posterior probability according to a reference alignment", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://matsen.fhcrc.org/pplacer/", @@ -16688,9 +16099,7 @@ }, "PRANK": { "description": "Probabilistic multiple alignment program for DNA, codon and amino-acid sequences. .", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://wasabiapp.org/software/prank/", @@ -16711,9 +16120,7 @@ }, "preseq": { "description": "Software for predicting library complexity and genome coverage in high-throughput sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://smithlabresearch.org/software/preseq", @@ -16733,9 +16140,7 @@ }, "prodigal": { "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) \n is a microbial (bacterial and archaeal) gene finding program developed \n at Oak Ridge National Laboratory and the University of Tennessee.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://prodigal.ornl.gov/", @@ -16759,9 +16164,7 @@ }, "Prodigal": { "description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) \n is a microbial (bacterial and archaeal) gene finding program developed \n at Oak Ridge National Laboratory and the University of Tennessee.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://prodigal.ornl.gov/", @@ -16781,9 +16184,7 @@ }, "prodigal-gv": { "description": "A fork of Prodigal meant to improve gene calling \nfor giant viruses and viruses that use alternative genetic codes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/apcamargo/prodigal-gv", @@ -16804,9 +16205,7 @@ }, "PROJ": { "description": "Program proj is a standard Unix filter function which converts \ngeographic longitude and latitude coordinates into cartesian coordinates", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://trac.osgeo.org/proj/", @@ -16834,9 +16233,7 @@ }, "prokka": { "description": "Prokka is a software tool for the rapid annotation of prokaryotic genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.vicbioinformatics.com/software.prokka.shtml", @@ -16885,9 +16282,7 @@ }, "ProtHint": { "description": "Pipeline for predicting and scoring hints (in the form of introns, start and\n stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of\n reference protein sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "File::HomeDir-1.006", "Math::Utils-1.14", @@ -16942,9 +16337,7 @@ }, "psmc": { "description": "Infers population size history from a diploid sequence using the PSMC model.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/psmc", @@ -17010,9 +16403,7 @@ }, "pullseq": { "description": "Utility program for extracting sequences from a fasta/fastq file", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bcthomas/pullseq", @@ -17053,9 +16444,7 @@ }, "purge_dups": { "description": "purge haplotigs and overlaps in an assembly based on read depth", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "runner-20191220" ], @@ -17077,9 +16466,7 @@ }, "purge_haplotigs": { "description": "Pipeline to help with curating heterozygous diploid genome assemblies", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Time::Piece-1.3401" ], @@ -17121,9 +16508,7 @@ }, "pyani": { "description": "Whole-genome classification using Average Nucleotide Identity", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "namedlist-1.8", "pyani-0.2.12", @@ -17167,9 +16552,7 @@ }, "pycoQC": { "description": "Computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "pycoQC-2.5.2", "tqdm-4.61.1" @@ -17192,10 +16575,7 @@ }, "pymol-open-source": { "description": "PyMOL (open source version) molecular visualization system.", - "domains": [ - "chemistry", - "visualisation" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/schrodinger/pymol-open-source", @@ -17236,12 +16616,7 @@ }, "Python": { "description": "Python is a programming language that lets you work more quickly and integrate your systems more effectively.", - "domains": [ - "data_analytics", - "language", - "machine_learning", - "visualisation" - ], + "domains": [], "extensions": [ "altair-6.1.0", "ase-3.28.0", @@ -17387,9 +16762,7 @@ }, "Python-Geo": { "description": "Python packages for geospatial data I/O, mostly based on the OSGEO libraries GDAL and OGR", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [ "affine-2.4.0", "cligj-0.7.2", @@ -17457,33 +16830,56 @@ }, "PyTorch": { "description": "Tensors and Dynamic neural networks in Python with strong GPU acceleration.\nPyTorch is a deep learning framework that puts Python first.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [ - "skorch-0.12.1" + "skorch-1.4.0", + "triton-3.7.1" ], "licence_type": "", "homepage": "https://pytorch.org/", "support": "", "versions": [ - "1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2" + "1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2", + "2.13.0-foss-2026-Python-3.14.4-CUDA-13.2.1" ], "admin_list": [], "network_licences": [], - "default": "1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2", + "default": "2.13.0-foss-2026-Python-3.14.4-CUDA-13.2.1", "default_type": "latest", - "last_updated": 1740132633, + "last_updated": 1785965820, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/PyTorch/2.13.0-foss-2026-Python-3.14.4-CUDA-13.2.1.lua", + "force_hide": "False", + "force_show": "False" + }, + "PyTorch-Lightning": { + "description": "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers.", + "domains": [], + "extensions": [ + "jsonargparse-4.50.0", + "lightning-utilities-0.15.3", + "pytorch-lightning-2.6.5", + "torchmetrics-1.9.0" + ], + "licence_type": "", + "homepage": "https://pytorchlightning.ai", + "support": "", + "versions": [ + "2.6.5-foss-2026-Python-3.14.4-CUDA-13.2.1" + ], + "admin_list": [], + "network_licences": [], + "default": "2.6.5-foss-2026-Python-3.14.4-CUDA-13.2.1", + "default_type": "latest", + "last_updated": 1786048305, "modulefile_text": "", - "module_path": "/opt/nesi/CS400_centos7_bdw/modules/all/PyTorch/1.12.1-gimkl-2022a-Python-3.10.5-CUDA-11.6.2.lua", + "module_path": "/opt/nesi/zen3/modules/all/PyTorch-Lightning/2.6.5-foss-2026-Python-3.14.4-CUDA-13.2.1.lua", "force_hide": "False", "force_show": "False" }, "qcat": { "description": "Command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "parasail-1.2.2" ], @@ -17505,11 +16901,9 @@ }, "QChem": { "description": "", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "", "support": "", "versions": [ @@ -17530,9 +16924,7 @@ }, "QIIME2": { "description": "An open-source bioinformatics pipeline for microbiome analysis\n from raw DNA sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://qiime2.org/", @@ -17579,9 +16971,7 @@ }, "QuantumESPRESSO": { "description": "Quantum ESPRESSO is an integrated suite of computer codes\nfor electronic-structure calculations and materials modeling at the nanoscale.\nIt is based on density-functional theory, plane waves, and pseudopotentials\n(both norm-conserving and ultrasoft).", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.quantum-espresso.org", @@ -17603,9 +16993,7 @@ }, "QUAST": { "description": "Evaluates genome assemblies", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "QUAST-5.2.0", "simplejson-3.17.2" @@ -17630,9 +17018,7 @@ }, "QuickTree": { "description": "Efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments .", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/khowe/quicktree", @@ -17658,12 +17044,7 @@ }, "R": { "description": "R is a free software environment for statistical computing and graphics.", - "domains": [ - "data_analytics", - "language", - "machine_learning", - "visualisation" - ], + "domains": [], "extensions": [ "abind-1.4-8", "acepack-1.6.3", @@ -18222,9 +17603,7 @@ }, "R-bundle-Bioconductor": { "description": "Bioconductor provides tools for the analysis and comprehension\n of high-throughput genomic data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "affxparser-1.84.0", "affy-1.90.0", @@ -18620,9 +17999,7 @@ }, "R-Geo": { "description": "R packages for Geometric and Geospatial data which depend \non GEOS and/or GDAL.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [ "CFtime-1.7.3", "DCluster-0.2-10", @@ -18722,10 +18099,7 @@ }, "Racon": { "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lbcb-sci/racon", @@ -18747,9 +18121,7 @@ }, "Ragout": { "description": "Tool for chromosome assembly using multiple references.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://fenderglass.github.io/Ragout/", @@ -18773,10 +18145,7 @@ }, "randfold": { "description": "Minimum free energy of folding randomization test software", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bioinformatics.psb.ugent.be/software/details/Randfold", @@ -18796,9 +18165,7 @@ }, "RapidNJ": { "description": "An algorithmic engineered implementation of canonical neighbour-joining.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://birc.au.dk/software/rapidnj", @@ -18818,9 +18185,7 @@ }, "rasusa": { "description": "Randomly subsample sequencing reads to a specified coverage.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/mbhall88/rasusa", @@ -18840,9 +18205,7 @@ }, "Ratatosk": { "description": "Phased hybrid error correction of long reads using colored de Bruijn graphs", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/DecodeGenetics/Ratatosk", @@ -18862,9 +18225,7 @@ }, "Raven": { "description": "De novo genome assembler for long uncorrected reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://mmseqs.com", @@ -18884,9 +18245,7 @@ }, "RAxML": { "description": "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/stamatak/standard-RAxML", @@ -18907,9 +18266,7 @@ }, "RAxML-NG": { "description": "RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML)\n optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree\n Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/amkozlov/raxml-ng", @@ -18952,9 +18309,7 @@ }, "Rcorrector": { "description": "kmer-based error correction method for RNA-seq data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/mourisl/Rcorrector", @@ -18972,11 +18327,29 @@ "force_hide": "False", "force_show": "False" }, + "RDKit": { + "description": "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.", + "domains": [], + "extensions": [], + "licence_type": "", + "homepage": "https://www.rdkit.org", + "support": "", + "versions": [ + "2025.09.6-foss-2026" + ], + "admin_list": [], + "network_licences": [], + "default": "2025.09.6-foss-2026", + "default_type": "latest", + "last_updated": 1786051845, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/RDKit/2025.09.6-foss-2026.lua", + "force_hide": "False", + "force_show": "False" + }, "RDP-Classifier": { "description": "The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic\n assignments from domain to genus, with confidence estimates for each assignment.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://sourceforge.net/projects/rdp-classifier", @@ -19037,9 +18410,7 @@ }, "RECON": { "description": "De novo identification and classification of repeat sequence families from genomic sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://eddylab.org/software/recon/", @@ -19059,10 +18430,7 @@ }, "Relion": { "description": "RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) \n is a stand-alone computer program that employs an empirical Bayesian \n approach to refinement of (multiple) 3D reconstructions or 2D class \n averages in electron cryo-microscopy (cryo-EM).", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page", @@ -19082,9 +18450,7 @@ }, "RepeatMasker": { "description": "RepeatMasker is a program that screens DNA sequences for interspersed repeats\n and low complexity DNA sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.repeatmasker.org/", @@ -19107,9 +18473,7 @@ }, "RepeatModeler": { "description": "De novo transposable element (TE) family identification and modeling package.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Devel::Size-0.83" ], @@ -19133,9 +18497,7 @@ }, "RepeatScout": { "description": "De novo identification of repeat families in large genomes", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bix.ucsd.edu/repeatscout/", @@ -19155,9 +18517,7 @@ }, "REViewer": { "description": "Tool for visualizing alignments of reads in regions containing tandem repeats", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Illumina/REViewer", @@ -19177,11 +18537,7 @@ }, "RFdiffusion": { "description": "Structure generation, with or without conditional information (a motif, target etc) It can perform a whole range of protein design challenges as we have outlined \nin the RFdiffusion paper.", - "domains": [ - "biology", - "chemistry", - "gpu" - ], + "domains": [], "extensions": [ "antlr4-python3-runtime-4.9.3", "colorama-0.4.6", @@ -19228,9 +18584,7 @@ }, "RFPlasmid": { "description": "Predicting plasmid contigs from assemblies", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "RFPlasmid-0.0.18" ], @@ -19252,9 +18606,7 @@ }, "Riskscape": { "description": "RiskScape is an open-source spatial data processing application used for multi-hazard risk analysis. RiskScape is highly customisable, letting modellers tailor the risk analysis to suit the problem domain and input data being modelled.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://riskscape.org.nz/", @@ -19294,9 +18646,7 @@ }, "RMBlast": { "description": "RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:\nSupport for custom matrices ( without KA-Statistics ).\nSupport for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.\nSupport for cross_match-like masklevel filtering..", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.repeatmasker.org/RMBlast.html", @@ -19318,9 +18668,7 @@ }, "RNAmmer": { "description": "consistent and rapid annotation of ribosomal RNA genes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.cbs.dtu.dk/services/RNAmmer", @@ -19341,9 +18689,7 @@ }, "rnaQUAST": { "description": "Tool for evaluating RNA-Seq assemblies using reference genome and gene database", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "argcomplete-1.12.2", "argh-0.26.2", @@ -19369,9 +18715,7 @@ }, "Roary": { "description": "Rapid large-scale prokaryote pan genome analysis", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Digest::MD5::File-0.08", " File::Grep-0.02", @@ -19427,10 +18771,7 @@ }, "Rosetta": { "description": "Rosetta is the premier software suite for modeling macromolecular structures. As a flexible,\nmulti-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and\nnucleic acids.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.rosettacommons.org", @@ -19450,9 +18791,7 @@ }, "RSEM": { "description": "Estimates gene and isoform expression levels from RNA-Seq data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://deweylab.biostat.wisc.edu/rsem/", @@ -19472,9 +18811,7 @@ }, "RSGISLib": { "description": "The Remote Sensing and GIS software library (RSGISLib) is a\n collection of tools for processing remote sensing and GIS datasets. The tools\n are accessed using Python bindings or an XML interface.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.rsgislib.org", @@ -19517,9 +18854,7 @@ }, "Ruby": { "description": "Ruby is a dynamic, open source programming language with\n a focus on simplicity and productivity. It has an elegant syntax that is\n natural to read and easy to write.", - "domains": [ - "language" - ], + "domains": [], "extensions": [ "activesupport-5.2.6", "addressable-2.8.0", @@ -19586,9 +18921,7 @@ }, "Rust": { "description": "Systems programming language that runs blazingly fast, prevents segfaults,\n and guarantees thread safety.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.rust-lang.org", @@ -19653,9 +18986,7 @@ }, "SAGE": { "description": "Ppackage containing programs for use in the genetic analysis of\nfamily, pedigree and individual data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://darwin.cwru.edu/sage/", @@ -19675,9 +19006,7 @@ }, "Salmon": { "description": "Salmon is a wicked-fast program to produce a highly-accurate,\n transcript-level quantification estimates from RNA-seq data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/COMBINE-lab/salmon", @@ -19710,9 +19039,7 @@ }, "Sambamba": { "description": "Tools for working with SAM/BAM data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://lomereiter.github.io/sambamba/", @@ -19732,9 +19059,7 @@ }, "samblaster": { "description": "samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. \nIt can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped \nreads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://github.com/GregoryFaust/samblaster", @@ -19775,9 +19100,7 @@ }, "SAMtools": { "description": "Samtools is a suite of programs for interacting with high-throughput sequencing data.\n SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.htslib.org/", @@ -19837,9 +19160,7 @@ }, "sc-RNA": { "description": "Bioconductor bundle for single-cell RNA-Seq Data analysis", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "BiocParallel-1.34.2", "clustree-0.5.0", @@ -19951,9 +19272,7 @@ }, "SCOTCH": { "description": "Software package and libraries for sequential and parallel graph partitioning,\nstatic mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.labri.fr/perso/pelegrin/scotch/", @@ -19980,9 +19299,7 @@ }, "screen_assembly": { "description": "Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "screen_assembly-1.2.8" ], @@ -20024,10 +19341,7 @@ }, "SeisSol": { "description": "SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG).", - "domains": [ - "earth_science", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.seissol.org", @@ -20047,9 +19361,7 @@ }, "SEPP": { "description": "SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic\nplacement of short reads into reference alignments and trees.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/smirarab/sepp", @@ -20073,9 +19385,7 @@ }, "SeqAn": { "description": "SeqAn is an open source C++ library of efficient algorithms and data structures\n for the analysis of sequences with the focus on biological data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/seqan/seqan", @@ -20095,9 +19405,7 @@ }, "SeqAn3": { "description": "C++ library of efficient algorithms and data structures for the \n analysis of sequences with the focus on biological data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/seqan/seqan3", @@ -20122,9 +19430,7 @@ }, "SeqKit": { "description": "Ultrafast toolkit for FASTA/Q file manipulation", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://bioinf.shenwei.me/seqkit/", @@ -20148,9 +19454,7 @@ }, "seqmagick": { "description": "Seqmagick is a utility built in the spirit of imagemagick to expose the\n file format conversion in Biopython in a convenient way. Instead of having a\n big mess of scripts, there is one that takes arguments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://fhcrc.github.io/seqmagick/", @@ -20171,9 +19475,7 @@ }, "seqtk": { "description": "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. \n It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/seqtk/", @@ -20196,9 +19498,7 @@ }, "SHAPEIT4": { "description": "Estimation of haplotypes (aka phasing) \nfor SNP array and high coverage sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://odelaneau.github.io/shapeit4/", @@ -20238,9 +19538,7 @@ }, "SiBELia": { "description": "A comparative genomics tool for analysing genomic variations that correlate with pathogens, or \n microorganisms adapt in different environments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bioinf.spbau.ru/en/sibelia", @@ -20260,9 +19558,7 @@ }, "Siesta": { "description": "SIESTA is both a method and its computer program implementation, to perform efficient electronic\n structure calculations and ab initio molecular dynamics simulations of molecules and solids.", - "domains": [ - "physics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://departments.icmab.es/leem/siesta", @@ -20289,9 +19585,7 @@ }, "SignalP": { "description": "SignalP predicts the presence and location of signal peptide cleavage sites\nin amino acid sequences from different organisms", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "torch-1.12.1" ], @@ -20314,9 +19608,7 @@ }, "simuG": { "description": "A general-purpose genome simulator", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/yjx1217/simuG", @@ -20376,9 +19668,7 @@ }, "sismonr": { "description": "Simulation of In Silico Multi-Omic Networks R package.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "corrplot-0.90", "ggpubr-0.4.0", @@ -20418,9 +19708,7 @@ }, "SKA2": { "description": "Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely\n related sequences, typically small haploid genomes such as bacteria and viruses.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://docs.rs/ska/latest/ska/", @@ -20440,9 +19728,7 @@ }, "skani": { "description": "accurate, fast nucleotide identity calculation for MAGs, genomes, and databases", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bluenote-1577/skani", @@ -20462,9 +19748,7 @@ }, "SKESA": { "description": "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ncbi/SKESA", @@ -20504,10 +19788,7 @@ }, "slow5-dorado": { "description": "Fork of nanopore's Dorado which supports S/BLOW5.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/hiruna72/slow5-dorado", @@ -20548,9 +19829,7 @@ }, "smoove": { "description": "simplifies and speeds calling and genotyping SVs for short reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/bcgsc/LongStitch", @@ -20570,9 +19849,7 @@ }, "SMRT-Link": { "description": "PacBio\u2019s open-source software suite is designed for use with Single Molecule, \n Real-Time (SMRT) Sequencing data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.pacb.com/support/software-downloads/", @@ -20593,9 +19870,7 @@ }, "snakemake": { "description": "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.", - "domains": [ - "workflow_management" - ], + "domains": [], "extensions": [ "appdirs-1.4.3", "ConfigArgParse-0.13.0", @@ -20667,9 +19942,7 @@ }, "Sniffles": { "description": "A fast structural variant caller for long-read sequencing.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Sniffles-2.6.3" ], @@ -20713,9 +19986,7 @@ }, "snp-sites": { "description": "Finds SNP sites from a multi-FASTA alignment file.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://sanger-pathogens.github.io/snp-sites/", @@ -20736,9 +20007,7 @@ }, "snpEff": { "description": "SnpEff is a variant annotation and effect prediction tool. \n It annotates and predicts the effects of genetic variants (such as amino acid changes).", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://pcingola.github.io/SnpEff/", @@ -20760,9 +20029,7 @@ }, "SNVoter-NanoMethPhase": { "description": "SNVoter - A top up tool to enhance SNV calling from Nanopore sequencing data & \nNanoMethPhase - Phase long reads and CpG methylations from Oxford Nanopore Technologies.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/vahidAK/", @@ -20782,9 +20049,7 @@ }, "somalier": { "description": "extract informative sites, evaluate relatedness, and \nperform quality-control on BAM/CRAM/BCF/VCF/GVCF", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/brentp/somalier", @@ -20804,9 +20069,7 @@ }, "SortMeRNA": { "description": "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bioinfo.lifl.fr/RNA/sortmerna/", @@ -20827,9 +20090,7 @@ }, "SourceTracker": { "description": "SourceTracker is a Bayesian approach to estimating the proportion of a novel community that comes\n from a set of source environments.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://sourceforge.net/projects/sourcetracker", @@ -20849,9 +20110,7 @@ }, "SPAdes": { "description": "Genome assembler for single-cell and isolates data sets", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ablab.github.io/spades/", @@ -20877,9 +20136,7 @@ }, "spaln": { "description": "Spaln (space-efficient spliced alignment) is a stand-alone program that maps\n and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ogotoh/spaln", @@ -20962,9 +20219,7 @@ }, "spoa": { "description": "c++ implementation of the partial order alignment (POA) algorithm\n which is used to generate consensus sequences", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rvaser/spoa", @@ -21014,9 +20269,7 @@ }, "SqueezeMeta": { "description": "Fully automated metagenomics pipeline, from reads to bins.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/jtamames/SqueezeMeta", @@ -21038,9 +20291,7 @@ }, "sratoolkit": { "description": "The SRA Toolkit, and the source-code SRA System Development\n Kit (SDK), will allow you to programmatically access data housed within SRA\n and convert it from the SRA format", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software", @@ -21060,9 +20311,7 @@ }, "SSAHA2": { "description": "Pairwise sequence alignment program designed for the efficient mapping of sequencing \n reads onto genomic reference sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.sanger.ac.uk/resources/software/ssaha2/", @@ -21082,9 +20331,7 @@ }, "Stacks": { "description": "Stacks is a software pipeline for building loci from short-read sequences, such as those generated on\n the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose\n of building genetic maps and conducting population genomics and phylogeography.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://creskolab.uoregon.edu/stacks/", @@ -21118,9 +20365,7 @@ }, "STAR": { "description": "Fast universal RNA-seq aligner", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/alexdobin/STAR", @@ -21148,9 +20393,7 @@ }, "StringTie": { "description": "StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://ccb.jhu.edu/software/stringtie/", @@ -21175,9 +20418,7 @@ }, "Structure": { "description": "The program structure is a free software package for using multi-locus genotype data to investigate\n population structure.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://web.stanford.edu/group/pritchardlab/structure.html", @@ -21198,9 +20439,7 @@ }, "Subread": { "description": "High performance read alignment, quantification and mutation discovery", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://subread.sourceforge.net/", @@ -21277,9 +20516,7 @@ }, "SUNDIALS": { "description": "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers", - "domains": [ - "mathematics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://computation.llnl.gov/projects/sundials", @@ -21319,9 +20556,7 @@ }, "Supernova": { "description": "Supernova is a software package for de novo assembly from Chromium Linked-Reads\n that are made from a single whole-genome library from an individual DNA source", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome", @@ -21341,9 +20576,7 @@ }, "SURVIVOR": { "description": "Tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples,\n and includes various methods to reformat or summarize SVs.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/fritzsedlazeck/SURVIVOR/wiki", @@ -21364,9 +20597,7 @@ }, "swarm": { "description": "A robust and fast clustering method for amplicon-based studies.\nThe purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons. Results of traditional clustering algorithms are strongly input-order dependent, and rely on an arbitrary global clustering threshold. swarm results are resilient to input-order changes and rely on a small local linking threshold d, representing the maximum number of differences between two amplicons.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/torognes/swarm", @@ -21432,9 +20663,7 @@ }, "tabix": { "description": "Generic indexer for TAB-delimited genome position files", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://samtools.sourceforge.net", @@ -21455,9 +20684,7 @@ }, "tabixpp": { "description": "C++ wrapper to tabix indexer", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/vcflib/tabixpp", @@ -21504,9 +20731,7 @@ }, "tbl2asn": { "description": "Command-line program that automates the creation of\n sequence records for submission to GenBank", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/", @@ -21526,9 +20751,7 @@ }, "Tcl": { "description": "Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language,\n suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.", - "domains": [ - "language" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.tcl.tk/", @@ -21569,12 +20792,31 @@ "force_hide": "False", "force_show": "False" }, + "tensorboardX": { + "description": "Tensorboard for PyTorch.", + "domains": [], + "extensions": [ + "tensorboardx-2.6.5" + ], + "licence_type": "", + "homepage": "https://github.com/lanpa/tensorboardX", + "support": "", + "versions": [ + "2.6.5-foss-2026" + ], + "admin_list": [], + "network_licences": [], + "default": "2.6.5-foss-2026", + "default_type": "latest", + "last_updated": 1786047890, + "modulefile_text": "", + "module_path": "/opt/nesi/zen3/modules/all/tensorboardX/2.6.5-foss-2026.lua", + "force_hide": "False", + "force_show": "False" + }, "TensorFlow": { "description": "An open-source software library for Machine Intelligence", - "domains": [ - "gpu", - "machine_learning" - ], + "domains": [], "extensions": [ "absl-py-1.4.0", "flatbuffers-23.5.26", @@ -21635,9 +20877,7 @@ }, "TensorRT": { "description": "NVIDIA TensorRT is a platform for high-performance deep learning inference", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://developer.nvidia.com/tensorrt", @@ -21662,9 +20902,7 @@ }, "TEtranscripts": { "description": "Takes RNA-seq (and similar data) and annotates reads\nto both genes & transposable elements.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "TEtranscripts-2.2.3" ], @@ -21709,10 +20947,7 @@ }, "TMHMM": { "description": "Prediction of transmembrane helices in proteins", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://services.healthtech.dtu.dk/software.php", @@ -21752,9 +20987,7 @@ }, "TOGA": { "description": "Implements a novel machine learning based paradigm to infer orthologous \ngenes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "joblib-1.2.0", "twobitreader-3.1.7", @@ -21778,9 +21011,7 @@ }, "tomo": { "description": "This code computes 2D Travel Time Tomography using the Reversible Jump\nalgorithm with a Voronoi cell parameterisation.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://iearth.edu.au/codes/rj-TOMO/", @@ -21800,9 +21031,7 @@ }, "TransDecoder": { "description": "TransDecoder identifies candidate coding regions within transcript sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/TransDecoder/TransDecoder/wiki", @@ -21823,9 +21052,7 @@ }, "TreeMix": { "description": "TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a\n set of populations.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bitbucket.org/nygcresearch/treemix", @@ -21845,9 +21072,7 @@ }, "trf": { "description": "Locates tandem repeats in DNA sequences.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://tandem.bu.edu/trf/trf.html", @@ -21868,9 +21093,7 @@ }, "trimAl": { "description": "Tool for automated alignment trimming in large-scale phylogenetic analyses", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/scapella/trimal", @@ -21891,9 +21114,7 @@ }, "TrimGalore": { "description": "A wrapper of FastQC and cutadapt to automate quality and adapter trimming \nas well as quality control, with some added functionality to remove biased methylation \npositions for RRBS sequence files", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/", @@ -21915,9 +21136,7 @@ }, "Trimmomatic": { "description": "Trimmomatic performs a variety of useful trimming tasks for illumina \n paired-end and single ended data.The selection of trimming steps and their associated \n parameters are supplied on the command line.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.usadellab.org/cms/?page=trimmomatic", @@ -21938,9 +21157,7 @@ }, "Trinity": { "description": "Trinity represents a novel method for the efficient and robust de novo reconstruction\n of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm,\n Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://trinityrnaseq.github.io", @@ -21972,9 +21189,7 @@ }, "Trinotate": { "description": "C++ library of efficient algorithms and data structures for the\n analysis of sequences with the focus on biological data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "HTML::Template-2.97" ], @@ -21998,9 +21213,7 @@ }, "tRNAscan-SE": { "description": "Transfer RNA detection", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/UCSC-LoweLab/tRNAscan-SE", @@ -22021,9 +21234,7 @@ }, "Trycycler": { "description": "Tool for generating consensus long-read assemblies for bacterial genomes.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "edlib-1.3.9" ], @@ -22047,9 +21258,7 @@ }, "TSEBRA": { "description": "Transcript Selector for BRAKER", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/Gaius-Augustus/TSEBRA", @@ -22074,7 +21283,7 @@ "description": "Hydraulic modelling software for flood, urban drainage, estuarine and coastal assessments.", "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "https://www.tuflow.com/", "support": "", "versions": [ @@ -22092,9 +21301,7 @@ }, "TuiView": { "description": "TuiView is a lightweight raster GIS with powerful raster attribute table manipulation\n abilities.", - "domains": [ - "earth_science" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://tuiview.org/", @@ -22116,9 +21323,7 @@ }, "TURBOMOLE": { "description": "Program Package For Electronic Structure Calculations.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.turbomole.org/", @@ -22158,9 +21363,7 @@ }, "TWL-NINJA": { "description": "Nearly Infinite Neighbor Joining Application.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/TravisWheelerLab/NINJA", @@ -22203,9 +21406,7 @@ }, "UCC-CUDA": { "description": "UCC (Unified Collective Communication) is a collective\ncommunication operations API and library that is flexible, complete, and\nfeature-rich for current and emerging programming models and runtimes.\n\nThis module adds the UCC CUDA support.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.openucx.org/", @@ -22226,9 +21427,7 @@ }, "UCX": { "description": "Unified Communication X\nAn open-source production grade communication framework for data centric\nand high-performance applications", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.openucx.org/", @@ -22256,9 +21455,7 @@ }, "UCX-CUDA": { "description": "Unified Communication X\nAn open-source production grade communication framework for data centric\nand high-performance applications\n\nThis module adds the UCX CUDA support.", - "domains": [ - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.openucx.org/", @@ -22279,9 +21476,7 @@ }, "UDUNITS": { "description": "UDUNITS supports conversion of unit specifications between formatted and binary forms,\n arithmetic manipulation of units, and conversion of values between compatible scales of measurement.", - "domains": [ - "physics" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://www.unidata.ucar.edu/software/udunits/", @@ -22305,10 +21500,7 @@ }, "Unicycler": { "description": "Assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets\n where it functions as a SPAdes-optimiser.", - "domains": [ - "biology", - "gpu" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/rrwick/Unicycler", @@ -22333,9 +21525,7 @@ }, "unimap": { "description": "Fork of minimap2 optimized for assembly-to-reference\nalignment.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/unimap", @@ -22379,9 +21569,7 @@ }, "USEARCH": { "description": "", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "", @@ -22473,9 +21661,7 @@ }, "VarScan": { "description": "Variant calling and somatic mutation/CNV detection for next-generation sequencing data", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/dkoboldt/varscan", @@ -22495,12 +21681,9 @@ }, "VASP": { "description": "The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale\nmaterials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,\nfrom first principles.", - "domains": [ - "chemistry", - "gpu" - ], + "domains": [], "extensions": [], - "licence_type": "proprietary", + "licence_type": "", "homepage": "http://www.vasp.at", "support": "", "versions": [ @@ -22536,9 +21719,7 @@ }, "VBZ-Compression": { "description": "VBZ compression HDF5 plugin for nanopolish", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/nanoporetech/vbz_compression", @@ -22558,9 +21739,7 @@ }, "VCF-kit": { "description": "VCF-kit is a command-line based collection of utilities for performing analysis on\n Variant Call Format (VCF) files.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "awesome-slugify-1.6.5", "clint-0.5.1", @@ -22590,9 +21769,7 @@ }, "vcflib": { "description": "vcflib provides methods to manipulate and interpret sequence variation as it can be\n described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended\n to concisely describe reference-indexed genetic variations between individuals.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/vcflib/vcflib", @@ -22613,9 +21790,7 @@ }, "VCFtools": { "description": "The aim of VCFtools is to provide \n methods for working with VCF files: validating, \n merging, comparing and calculate some basic population\n genetic statistics.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://vcftools.sourceforge.net/", @@ -22637,9 +21812,7 @@ }, "Velvet": { "description": "Sequence assembler for very short reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ebi.ac.uk/~zerbino/velvet/", @@ -22659,9 +21832,7 @@ }, "VelvetOptimiser": { "description": "Perl script for optimising the three primary parameter options of the Velvet de novo sequence assembler.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://bioinformatics.net.au/software.velvetoptimiser.shtml", @@ -22681,9 +21852,7 @@ }, "VEP": { "description": "Variant Effect Predictor (VEP) determines the effect of your\n variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,\n transcripts, and protein sequence, as well as regulatory regions.\n Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently\n used routines in VEP.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "Bio::EnsEMBL::XS-2.3.2" ], @@ -22697,23 +21866,22 @@ "113.3-GCC-11.3.0-Perl-5.34.1", "115.2-GCC-12.3.0-Perl-5.40.3", "115.2-GCC-15.2.0-Perl-5.42.1", - "116.0-GCC-15.2.0-Perl-5.42.1" + "116.0-GCC-15.2.0-Perl-5.42.1", + "116.1-GCC-15.2.0-Perl-5.42.1" ], "admin_list": [], "network_licences": [], - "default": "116.0-GCC-15.2.0-Perl-5.42.1", + "default": "116.1-GCC-15.2.0-Perl-5.42.1", "default_type": "latest", - "last_updated": 1781633481, + "last_updated": 1785895197, "modulefile_text": "", - "module_path": "/opt/nesi/zen3/modules/all/VEP/116.0-GCC-15.2.0-Perl-5.42.1.lua", + "module_path": "/opt/nesi/zen3/modules/all/VEP/116.1-GCC-15.2.0-Perl-5.42.1.lua", "force_hide": "False", "force_show": "False" }, "verkko": { "description": "Hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/marbl/verkko", @@ -22735,31 +21903,28 @@ }, "vg": { "description": "variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/vgteam/vg", "support": "", "versions": [ - "1.46.0" + "1.46.0", + "1.76.1" ], "admin_list": [], "network_licences": [], - "default": "1.46.0", + "default": "1.76.1", "default_type": "latest", - "last_updated": 1740132640, + "last_updated": 1785711610, "modulefile_text": "", - "module_path": "/opt/nesi/CS400_centos7_bdw/modules/all/vg/1.46.0.lua", + "module_path": "/opt/nesi/zen3/modules/all/vg/1.76.1.lua", "force_hide": "False", "force_show": "False" }, "VIBRANT": { "description": "Virus Identification By iteRative ANnoTation", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "scikit-learn-0.21.3" ], @@ -22781,9 +21946,7 @@ }, "ViennaRNA": { "description": "The Vienna RNA Package consists of a C code library and several\nstand-alone programs for the prediction and comparison of RNA secondary structures.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.tbi.univie.ac.at/RNA/", @@ -22823,9 +21986,7 @@ }, "VirHostMatcher": { "description": "Tools for computing various oligonucleotide frequency (ONF) based distance/dissimialrity measures.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/simroux/VirSorter", @@ -22845,9 +22006,7 @@ }, "VirSorter": { "description": "VirSorter: mining viral signal from microbial genomic data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "bz2file-0.98", "imbalanced-learn-0.7.0", @@ -22878,10 +22037,7 @@ }, "VMD": { "description": "VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular\n systems using 3-D graphics and built-in scripting.", - "domains": [ - "biology", - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ks.uiuc.edu/Research/vmd", @@ -22921,9 +22077,7 @@ }, "VSEARCH": { "description": "An open source alternative to the metagenomics tool USEARCH.\n\nPerforms chimera detection, clustering, full-length and prefix dereplication, rereplication, masking, \nall-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling \nand sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/torognes/vsearch", @@ -22945,9 +22099,7 @@ }, "vt": { "description": "A tool set for short variant discovery in genetic sequence data.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://genome.sph.umich.edu/wiki/Vt", @@ -23009,9 +22161,7 @@ }, "WAAFLE": { "description": "Workflow to Annotate Assemblies and Find LGT Events.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://huttenhower.sph.harvard.edu/waafle", @@ -23031,9 +22181,7 @@ }, "wannier90": { "description": "Wannier90 is an open-source code for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://wannier.org/", @@ -23073,9 +22221,7 @@ }, "wgsim": { "description": "Wgsim is a small tool for simulating sequence reads from a reference genome.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/wgsim/", @@ -23096,9 +22242,7 @@ }, "WhatsHap": { "description": "Tool for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [ "isal-1.1.0", "pyfaidx-0.7.1", @@ -23143,9 +22287,7 @@ }, "Winnowmap": { "description": "Winnowmap is a long-read mapping algorithm, and a result of our exploration\n into superior minimizer sampling techniques.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/marbl/Winnowmap", @@ -23165,9 +22307,7 @@ }, "Wise2": { "description": "Aligning proteins or protein HMMs to DNA", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "http://www.ebi.ac.uk/~birney/wise2/", @@ -23187,9 +22327,7 @@ }, "wtdbg": { "description": "de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies.", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/ruanjue/wtdbg2", @@ -23314,9 +22452,7 @@ }, "xPore": { "description": "A Python package for identification and quantification of differential RNA modifications from direct RNA sequencing", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/GoekeLab/xpore", @@ -23336,9 +22472,7 @@ }, "xtb": { "description": "xtb - An extended tight-binding semi-empirical program package.", - "domains": [ - "chemistry" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://xtb-docs.readthedocs.io", @@ -23383,9 +22517,7 @@ }, "yacrd": { "description": "Chimeric Read Detector for long reads", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/natir/yacrd", @@ -23429,9 +22561,7 @@ }, "yak": { "description": "Yet another k-mer analyzer", - "domains": [ - "biology" - ], + "domains": [], "extensions": [], "licence_type": "", "homepage": "https://github.com/lh3/minimap2", @@ -23620,4 +22750,4 @@ "force_hide": "False", "force_show": "False" } -} \ No newline at end of file +} From 4e26c4cdab5b4ef4a4b11eb83b7ddfee8a15109e Mon Sep 17 00:00:00 2001 From: geoffreyweal Date: Wed, 12 Aug 2026 08:46:53 +1200 Subject: [PATCH 3/3] Update path descriptions for OpenFold3 --- docs/Software/Available_Applications/OpenFold3.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/Software/Available_Applications/OpenFold3.md b/docs/Software/Available_Applications/OpenFold3.md index 7408b139d..a7145fcdc 100644 --- a/docs/Software/Available_Applications/OpenFold3.md +++ b/docs/Software/Available_Applications/OpenFold3.md @@ -78,10 +78,12 @@ If you are using OpenFold3 for the first time on Mahuika, you will need to downl If you get an error message relating to Biotite CCD, get in touch with support. -3. Add the following line to your `.bashrc` and source it: +3. Add the following line to your `.bashrc` and source it. **Make sure you change `OPENFOLD_CACHE` to what you gave in step 2**: ```bash - printf '\n# Path to your OpenFold3 Cache\nexport OPENFOLD_CACHE=/nesi/project///openfold3\n' >> ~/.bashrc + # Change the OPENFOLD_CACHE to what you used in step 2. + OPENFOLD_CACHE=/nesi/project///openfold3 + printf '\n# Path to your OpenFold3 Cache\nexport OPENFOLD_CACHE='${OPENFOLD_CACHE}'\n' >> ~/.bashrc source ~/.bashrc ``` @@ -91,7 +93,7 @@ If you are using OpenFold3 for the first time on Mahuika, you will need to downl echo $OPENFOLD_CACHE ``` - If this doesn't look right, you will need to change your `~/.bashrc` file by using `nano` or `vim` + If this doesn't look right, you will need to change your `~/.bashrc` file by using `nano` or `vim`. 4. Test that your setup was successful. In the terminal, copy the following json file from [openfold3](from https://github.com/aqlaboratory/openfold-3/blob/main/examples/example_inference_inputs/query_ubiquitin.json):