diff --git a/includes/data/software.yml b/includes/data/software.yml
index 83867a857..9b6c335b9 100644
--- a/includes/data/software.yml
+++ b/includes/data/software.yml
@@ -4577,14 +4577,21 @@ software_modules:
   - name: biology
     packages:
     - categories: biology, genomics
-      defaultVersionName: 1.2.13_py27
-      description: OBITools is a set of programs designed for analyzing NGS data in
-        a DNA metabarcoding context.
-      package: py-obitools
-      url: https://pythonhosted.org/OBITools/index.html
+      defaultVersionName: 4.6.0.0
+      description: GATK (Genome Analysis Toolkit) offers a wide variety of tools with
+        a primary focus on variant discovery and genotyping.
+      package: gatk
+      url: https://software.broadinstitute.org/gatk/
       versions:
-      - {description: OBITools is a set of programs designed for analyzing NGS data
-          in a DNA metabarcoding context., markedDefault: false, versionName: 1.2.13_py27}
+      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
+          with a primary focus on variant discovery and genotyping., markedDefault: false,
+        versionName: 4.1.0.0}
+      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
+          with a primary focus on variant discovery and genotyping., markedDefault: false,
+        versionName: 4.1.4.1}
+      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
+          with a primary focus on variant discovery and genotyping., markedDefault: false,
+        versionName: 4.6.0.0}
     - categories: biology, molecular biology
       defaultVersionName: 4.0.3
       description: DSSP is an application to assign secondary structure to proteins.
@@ -4711,17 +4718,16 @@ software_modules:
       - {description: 'AFNI (Analysis of Functional NeuroImages) is a set of C programs
           for processing, analyzing, and displaying functional MRI (FMRI) data - a
           technique for mapping human brain activity.', markedDefault: false, versionName: 21.3.00}
-    - categories: biology, neurology
-      defaultVersionName: 1.3.1
-      description: Connectome Workbench is an open source, freely available visualization
-        and discovery tool used to map neuroimaging data, especially data generated
-        by the Human Connectome Project.
-      package: workbench
-      url: https://www.humanconnectome.org/software/connectome-workbench
+    - categories: biology, genomics
+      defaultVersionName: 1.1.3_py27
+      description: Fit-Hi-C is a tool for assigning statistical confidence estimates
+        to chromosomal contact maps produced by genome architecture assays.
+      package: py-fithic
+      url: https://github.com/ay-lab/fithic
       versions:
-      - {description: 'Connectome Workbench is an open source, freely available visualization
-          and discovery tool used to map neuroimaging data, especially data generated
-          by the Human Connectome Project.', markedDefault: false, versionName: 1.3.1}
+      - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates
+          to chromosomal contact maps produced by genome architecture assays., markedDefault: false,
+        versionName: 1.1.3_py27}
     - categories: biology, pathology
       defaultVersionName: 3.4.1
       description: OpenSlide is a C library that provides a simple interface to read
@@ -4732,21 +4738,16 @@ software_modules:
       - {description: OpenSlide is a C library that provides a simple interface to
           read whole-slide images (also known as virtual slides)., markedDefault: false,
         versionName: 3.4.1}
-    - categories: biology, neurology
-      defaultVersionName: 0.10.9_py36
-      description: The Maastricht Diffusion Toolbox, MDT, is a framework and library
-        for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging
-        (MRI) modeling.
-      package: py-mdt
-      url: https://github.com/cbclab/MDT
+    - categories: biology, genomics
+      defaultVersionName: 0.38.1
+      description: breseq is a computational pipeline for finding mutations relative
+        to a reference sequence in short-read DNA resequencing data.
+      package: breseq
+      url: http://barricklab.org/breseq
       versions:
-      - description: The Maastricht Diffusion Toolbox, MDT, is a framework and library
-          for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging
-          (MRI) modeling.
-        markedDefault: false
-        properties:
-          arch: {gpu: 1}
-        versionName: 0.10.9_py36
+      - {description: breseq is a computational pipeline for finding mutations relative
+          to a reference sequence in short-read DNA resequencing data., markedDefault: false,
+        versionName: 0.38.1}
     - categories: biology, genomics
       defaultVersionName: '20110325'
       description: The METAL software is designed to facilitate meta-analysis of large
@@ -4862,21 +4863,17 @@ software_modules:
           the DICOM format to the NIfTI format., markedDefault: false, versionName: 1.0.20171215}
       - {description: dcm2niix is a program esigned to convert neuroimaging data from
           the DICOM format to the NIfTI format., markedDefault: false, versionName: 1.0.20211006}
-    - categories: biology, computational biology
-      defaultVersionName: 1.84_py312
-      description: Biopython is a set of freely available tools for biological computation
-        written in Python.
-      package: py-biopython
-      url: http://biopython.org
+    - categories: biology, genomics
+      defaultVersionName: 0.98.5
+      description: GEMMA is a software toolkit for fast application of linear mixed
+        models (LMMs) and related models to genome-wide association studies (GWAS)
+        and other large-scale data sets.
+      package: gemma
+      url: https://github.com/genetics-statistics/GEMMA
       versions:
-      - {description: Biopython is a set of freely available tools for biological
-          computation written in Python., markedDefault: false, versionName: 1.70_py27}
-      - {description: Biopython is a set of freely available tools for biological
-          computation written in Python., markedDefault: false, versionName: 1.79_py36}
-      - {description: Biopython is a set of freely available tools for biological
-          computation written in Python., markedDefault: false, versionName: 1.79_py39}
-      - {description: Biopython is a set of freely available tools for biological
-          computation written in Python., markedDefault: false, versionName: 1.84_py312}
+      - {description: GEMMA is a software toolkit for fast application of linear mixed
+          models (LMMs) and related models to genome-wide association studies (GWAS)
+          and other large-scale data sets., markedDefault: false, versionName: 0.98.5}
     - categories: biology, genomics
       defaultVersionName: 1.3.3
       description: RSEM is a software package for estimating gene and isoform expression
@@ -4940,6 +4937,14 @@ software_modules:
       - {description: 'Cufflinks assembles transcripts, estimates their abundances,
           and tests for differential expression and regulation in RNA-Seq samples.',
         markedDefault: false, versionName: 2.2.1}
+    - categories: biology, genomics
+      defaultVersionName: 2.10.0
+      description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.'
+      package: hic-pro
+      url: https://github.com/nservant/HiC-Pro
+      versions:
+      - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.',
+        markedDefault: false, versionName: 2.10.0}
     - categories: biology, cryo-em
       defaultVersionName: 4.1.13
       description: ctffind is a program for finding CTFs of electron micrographs.
@@ -4993,24 +4998,21 @@ software_modules:
           parallel: {mpi: 1}
         versionName: 4.0.1
     - categories: biology, genomics
-      defaultVersionName: 2.10.0
-      description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.'
-      package: hic-pro
-      url: https://github.com/nservant/HiC-Pro
-      versions:
-      - {description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.',
-        markedDefault: false, versionName: 2.10.0}
-    - categories: biology, genomics
-      defaultVersionName: 0.98.5
-      description: GEMMA is a software toolkit for fast application of linear mixed
-        models (LMMs) and related models to genome-wide association studies (GWAS)
-        and other large-scale data sets.
-      package: gemma
-      url: https://github.com/genetics-statistics/GEMMA
+      defaultVersionName: 0.44.0
+      description: kallisto is a program for quantifying abundances of transcripts
+        from RNA-Seq data using high-throughput sequencing reads.
+      package: kallisto
+      url: https://pachterlab.github.io/kallisto/
       versions:
-      - {description: GEMMA is a software toolkit for fast application of linear mixed
-          models (LMMs) and related models to genome-wide association studies (GWAS)
-          and other large-scale data sets., markedDefault: false, versionName: 0.98.5}
+      - {description: kallisto is a program for quantifying abundances of transcripts
+          from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
+        versionName: 0.46.1}
+      - {description: kallisto is a program for quantifying abundances of transcripts
+          from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
+        versionName: 0.50.1}
+      - {description: kallisto is a program for quantifying abundances of transcripts
+          from RNA-Seq data using high-throughput sequencing reads., markedDefault: true,
+        versionName: 0.44.0}
     - categories: biology, cryo-em
       defaultVersionName: 4.11.5
       description: IMOD is a set of image processing, modeling and display programs
@@ -5034,105 +5036,116 @@ software_modules:
           arch: {gpu: 1}
         versionName: 4.11.5
     - categories: biology, genomics
-      defaultVersionName: 0.38.1
-      description: breseq is a computational pipeline for finding mutations relative
-        to a reference sequence in short-read DNA resequencing data.
-      package: breseq
-      url: http://barricklab.org/breseq
-      versions:
-      - {description: breseq is a computational pipeline for finding mutations relative
-          to a reference sequence in short-read DNA resequencing data., markedDefault: false,
-        versionName: 0.38.1}
-    - categories: biology, genomics
-      defaultVersionName: 1.1.3_py27
-      description: Fit-Hi-C is a tool for assigning statistical confidence estimates
-        to chromosomal contact maps produced by genome architecture assays.
-      package: py-fithic
-      url: https://github.com/ay-lab/fithic
-      versions:
-      - {description: Fit-Hi-C is a tool for assigning statistical confidence estimates
-          to chromosomal contact maps produced by genome architecture assays., markedDefault: false,
-        versionName: 1.1.3_py27}
-    - categories: biology, genomics
-      defaultVersionName: 0.44.0
-      description: kallisto is a program for quantifying abundances of transcripts
-        from RNA-Seq data using high-throughput sequencing reads.
-      package: kallisto
-      url: https://pachterlab.github.io/kallisto/
-      versions:
-      - {description: kallisto is a program for quantifying abundances of transcripts
-          from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
-        versionName: 0.46.1}
-      - {description: kallisto is a program for quantifying abundances of transcripts
-          from RNA-Seq data using high-throughput sequencing reads., markedDefault: false,
-        versionName: 0.50.1}
-      - {description: kallisto is a program for quantifying abundances of transcripts
-          from RNA-Seq data using high-throughput sequencing reads., markedDefault: true,
-        versionName: 0.44.0}
-    - categories: biology, genomics
-      defaultVersionName: 3.3.1_py36
-      description: Tools to process and analyze deep sequencing data.
-      package: py-deeptools
-      url: https://github.com/deeptools/deepTools/
+      defaultVersionName: 2.30.0
+      description: The bedtools utilities are a swiss-army knife of tools for a wide-range
+        of genomics analysis tasks.
+      package: bedtools
+      url: https://bedtools.readthedocs.io
       versions:
-      - {description: Tools to process and analyze deep sequencing data., markedDefault: false,
-        versionName: 3.3.1_py36}
-    - categories: biology, genomics
-      defaultVersionName: 0.11.8
-      description: FastQC aims to provide a simple way to do some quality control
-        checks on raw sequence data coming from high throughput sequencing pipelines.
-      package: fastqc
-      url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+      - {description: The bedtools utilities are a swiss-army knife of tools for a
+          wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1}
+      - {description: The bedtools utilities are a swiss-army knife of tools for a
+          wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0}
+    - categories: biology, population genetics
+      defaultVersionName: 0.6.1_py36
+      description: Admixfrog is a HMM to infer ancestry frogments (fragments) from
+        low-coverage, contaminated data.
+      package: py-admixfrog
+      url: https://github.com/BenjaminPeter/admixfrog
       versions:
-      - {description: FastQC aims to provide a simple way to do some quality control
-          checks on raw sequence data coming from high throughput sequencing pipelines.,
-        markedDefault: false, versionName: 0.11.8}
-    - categories: biology, genomics
-      defaultVersionName: 2.3.10_py39
-      description: A software package for animal pose estimation.
-      package: py-deeplabcut
-      url: http://deeplabcut.org
+      - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments)
+          from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36}
+    - categories: biology, neurology
+      defaultVersionName: 0.10.9_py36
+      description: The Maastricht Diffusion Toolbox, MDT, is a framework and library
+        for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging
+        (MRI) modeling.
+      package: py-mdt
+      url: https://github.com/cbclab/MDT
       versions:
-      - description: A software package for animal pose estimation.
-        markedDefault: false
-        properties:
-          arch: {gpu: 1}
-        versionName: 2.2.3_py39
-      - description: A software package for animal pose estimation.
+      - description: The Maastricht Diffusion Toolbox, MDT, is a framework and library
+          for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging
+          (MRI) modeling.
         markedDefault: false
         properties:
           arch: {gpu: 1}
-        versionName: 2.3.10_py39
-    - categories: biology, genomics
-      defaultVersionName: 3.0.7
-      description: NCBI VDB is the database engine used by NCBI SRA tools.
-      package: ncbi-vdb
-      url: https://github.com/ncbi/ncbi-vdb
-      versions:
-      - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false,
-        versionName: 3.0.7}
+        versionName: 0.10.9_py36
     - categories: biology, genomics
-      defaultVersionName: 2.4.40
-      description: BEDOPS is an open-source command-line toolkit that performs highly
-        efficient and scalable Boolean and other set operations, statistical calculations,
-        archiving, conversion and other management of genomic data of arbitrary scale.
-      package: bedops
-      url: https://bedops.readthedocs.io/
+      defaultVersionName: 2.5.1
+      description: BamTools is a project that provides both a C++ API and a command-line
+        toolkit for reading, writing, and manipulating BAM (genome alignment) files.
+      package: bamtools
+      url: https://github.com/pezmaster31/bamtools
       versions:
-      - {description: 'BEDOPS is an open-source command-line toolkit that performs
-          highly efficient and scalable Boolean and other set operations, statistical
-          calculations, archiving, conversion and other management of genomic data
-          of arbitrary scale.', markedDefault: false, versionName: 2.4.40}
+      - {description: 'BamTools is a project that provides both a C++ API and a command-line
+          toolkit for reading, writing, and manipulating BAM (genome alignment) files.',
+        markedDefault: false, versionName: 2.5.1}
     - categories: biology, genomics
-      defaultVersionName: 4.6.0
-      description: MiXCR is a universal framework that processes big immunome data
-        from raw sequences to quantitated clonotypes.
-      package: mixcr
-      url: https://github.com/milaboratory/mixcr
+      defaultVersionName: '1.16'
+      description: BCFtools is a program for variant calling and manipulating files
+        in the Variant Call Format (VCF) and its binary counterpart BCF.
+      package: bcftools
+      url: https://github.com/samtools/bcftools
       versions:
-      - {description: MiXCR is a universal framework that processes big immunome data
-          from raw sequences to quantitated clonotypes., markedDefault: false, versionName: 2.1.12}
-      - {description: MiXCR is a universal framework that processes big immunome data
+      - {description: BCFtools is a program for variant calling and manipulating files
+          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
+        versionName: '1.6'}
+      - {description: BCFtools is a program for variant calling and manipulating files
+          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
+        versionName: '1.8'}
+      - {description: BCFtools is a program for variant calling and manipulating files
+          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
+        versionName: '1.16'}
+    - categories: biology, neurology
+      defaultVersionName: '20160502'
+      description: MRIcron is a cross-platform NIfTI format image viewer.
+      package: mricron
+      url: https://www.nitrc.org/projects/mricron
+      versions:
+      - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false,
+        versionName: '20160502'}
+    - categories: biology, genomics
+      defaultVersionName: '2.20'
+      description: The bcl2fastq2 conversion software can be used to convert BCL files
+        from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.
+      package: bcl2fastq
+      url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
+      versions:
+      - {description: 'The bcl2fastq2 conversion software can be used to convert BCL
+          files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.',
+        markedDefault: false, versionName: '2.20'}
+    - categories: biology, clinical science
+      defaultVersionName: '20180704'
+      description: Simvascular is a blood flow simulation and analysis toolkit. This
+        module provides the svFSI (Fluid Solid Interaction) solver.
+      package: simvascular
+      url: https://simvascular.github.io
+      versions:
+      - {description: Simvascular is a blood flow simulation and analysis toolkit.
+          This module provides the svFSI (Fluid Solid Interaction) solver., markedDefault: false,
+        versionName: '20180704'}
+    - categories: biology, genomics
+      defaultVersionName: 2.4.40
+      description: BEDOPS is an open-source command-line toolkit that performs highly
+        efficient and scalable Boolean and other set operations, statistical calculations,
+        archiving, conversion and other management of genomic data of arbitrary scale.
+      package: bedops
+      url: https://bedops.readthedocs.io/
+      versions:
+      - {description: 'BEDOPS is an open-source command-line toolkit that performs
+          highly efficient and scalable Boolean and other set operations, statistical
+          calculations, archiving, conversion and other management of genomic data
+          of arbitrary scale.', markedDefault: false, versionName: 2.4.40}
+    - categories: biology, genomics
+      defaultVersionName: 4.6.0
+      description: MiXCR is a universal framework that processes big immunome data
+        from raw sequences to quantitated clonotypes.
+      package: mixcr
+      url: https://github.com/milaboratory/mixcr
+      versions:
+      - {description: MiXCR is a universal framework that processes big immunome data
+          from raw sequences to quantitated clonotypes., markedDefault: false, versionName: 2.1.12}
+      - {description: MiXCR is a universal framework that processes big immunome data
           from raw sequences to quantitated clonotypes., markedDefault: false, versionName: 4.6.0}
     - categories: biology, genomics
       defaultVersionName: '0.931'
@@ -5179,21 +5192,15 @@ software_modules:
           diffusion MRI analyses, from various forms of tractography through to next-generation
           group-level analyses.', markedDefault: false, versionName: 3.0.3}
     - categories: biology, genomics
-      defaultVersionName: '1.16'
-      description: C library for high-throughput sequencing data formats.
-      package: htslib
-      url: https://github.com/samtools/htslib
+      defaultVersionName: 0.11.8
+      description: FastQC aims to provide a simple way to do some quality control
+        checks on raw sequence data coming from high throughput sequencing pipelines.
+      package: fastqc
+      url: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       versions:
-      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
-        versionName: '1.6'}
-      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
-        versionName: '1.8'}
-      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
-        versionName: 1.10.2}
-      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
-        versionName: '1.14'}
-      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
-        versionName: '1.16'}
+      - {description: FastQC aims to provide a simple way to do some quality control
+          checks on raw sequence data coming from high throughput sequencing pipelines.,
+        markedDefault: false, versionName: 0.11.8}
     - categories: biology, neurology
       defaultVersionName: 7.4.1
       description: An open source software suite for processing and analyzing (human)
@@ -5212,24 +5219,25 @@ software_modules:
       - {description: An open source software suite for processing and analyzing (human)
           brain MRI images., markedDefault: false, versionName: 7.4.1}
     - categories: biology, genomics
-      defaultVersionName: 2.5.1
-      description: BamTools is a project that provides both a C++ API and a command-line
-        toolkit for reading, writing, and manipulating BAM (genome alignment) files.
-      package: bamtools
-      url: https://github.com/pezmaster31/bamtools
+      defaultVersionName: 2.2.9.1_py39
+      description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
+        analysis method.
+      package: py-macs2
+      url: https://github.com/taoliu/MACS
       versions:
-      - {description: 'BamTools is a project that provides both a C++ API and a command-line
-          toolkit for reading, writing, and manipulating BAM (genome alignment) files.',
-        markedDefault: false, versionName: 2.5.1}
-    - categories: biology, population genetics
-      defaultVersionName: 0.6.1_py36
-      description: Admixfrog is a HMM to infer ancestry frogments (fragments) from
-        low-coverage, contaminated data.
-      package: py-admixfrog
-      url: https://github.com/BenjaminPeter/admixfrog
+      - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
+          analysis method., markedDefault: false, versionName: 2.1.1_py27}
+      - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
+          analysis method., markedDefault: false, versionName: 2.2.9.1_py39}
+    - categories: biology, genomics
+      defaultVersionName: 0.4.17_py36
+      description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed
+        with MAGeCK.
+      package: py-vispr
+      url: https://bitbucket.org/liulab/vispr
       versions:
-      - {description: 'Admixfrog is a HMM to infer ancestry frogments (fragments)
-          from low-coverage, contaminated data.', markedDefault: false, versionName: 0.6.1_py36}
+      - {description: 'A visualization framework for CRISPR/Cas9 knockout screens,
+          analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36}
     - categories: biology, neurology
       defaultVersionName: 5.0.10
       description: FSL is a comprehensive library of analysis tools for FMRI, MRI
@@ -5249,17 +5257,17 @@ software_modules:
         properties:
           arch: {gpu: 1}
         versionName: 5.0.10
-    - categories: biology, genomics
-      defaultVersionName: 2.30.0
-      description: The bedtools utilities are a swiss-army knife of tools for a wide-range
-        of genomics analysis tasks.
-      package: bedtools
-      url: https://bedtools.readthedocs.io
+    - categories: biology, neurology
+      defaultVersionName: 0.7.00
+      description: BART is a toolbox for Computational Magnetic Resonance Imaging.
+      package: bart
+      url: https://mrirecon.github.io/bart/
       versions:
-      - {description: The bedtools utilities are a swiss-army knife of tools for a
-          wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.27.1}
-      - {description: The bedtools utilities are a swiss-army knife of tools for a
-          wide-range of genomics analysis tasks., markedDefault: false, versionName: 2.30.0}
+      - description: BART is a toolbox for Computational Magnetic Resonance Imaging.
+        markedDefault: false
+        properties:
+          arch: {gpu: 1}
+        versionName: 0.7.00
     - categories: biology, genomics
       defaultVersionName: 0.0.14
       description: The FASTX-Toolkit is a collection of command line tools for Short-Reads
@@ -5335,14 +5343,15 @@ software_modules:
       - {description: FreeBayes is a Bayesian genetic variant detector designed to
           find small polymorphisms., markedDefault: false, versionName: 1.2.0}
     - categories: biology, genomics
-      defaultVersionName: 0.4.17_py36
-      description: A visualization framework for CRISPR/Cas9 knockout screens, analyzed
-        with MAGeCK.
-      package: py-vispr
-      url: https://bitbucket.org/liulab/vispr
+      defaultVersionName: 2.13.1
+      description: Trinity RNA-Seq de novo transcriptome assembly.
+      package: trinity
+      url: https://github.com/trinityrnaseq/trinityrnaseq
       versions:
-      - {description: 'A visualization framework for CRISPR/Cas9 knockout screens,
-          analyzed with MAGeCK.', markedDefault: false, versionName: 0.4.17_py36}
+      - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false,
+        versionName: 2.8.4}
+      - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false,
+        versionName: 2.13.1}
     - categories: biology, genomics
       defaultVersionName: 1.0.0_py39
       description: SCENIC+ is a python package to build enhancer driven gene regulatory
@@ -5384,21 +5393,16 @@ software_modules:
       - {description: 'OrthoFinder is a fast, accurate and comprehensive platform
           for comparative genomics.', markedDefault: false, versionName: 2.5.4_py39}
     - categories: biology, genomics
-      defaultVersionName: 4.6.0.0
-      description: GATK (Genome Analysis Toolkit) offers a wide variety of tools with
-        a primary focus on variant discovery and genotyping.
-      package: gatk
-      url: https://software.broadinstitute.org/gatk/
+      defaultVersionName: 0.8.13_py39
+      description: Tools for manipulating biological data, particularly multiple sequence
+        alignments.
+      package: py-bx-python
+      url: https://github.com/bxlab/bx-python
       versions:
-      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
-          with a primary focus on variant discovery and genotyping., markedDefault: false,
-        versionName: 4.1.0.0}
-      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
-          with a primary focus on variant discovery and genotyping., markedDefault: false,
-        versionName: 4.1.4.1}
-      - {description: GATK (Genome Analysis Toolkit) offers a wide variety of tools
-          with a primary focus on variant discovery and genotyping., markedDefault: false,
-        versionName: 4.6.0.0}
+      - {description: 'Tools for manipulating biological data, particularly multiple
+          sequence alignments.', markedDefault: false, versionName: 0.8.1_py27}
+      - {description: 'Tools for manipulating biological data, particularly multiple
+          sequence alignments.', markedDefault: false, versionName: 0.8.13_py39}
     - categories: biology, genomics
       defaultVersionName: 2.1.0
       description: HISAT2 is a fast and sensitive alignment program for mapping next-generation
@@ -5411,6 +5415,15 @@ software_modules:
           next-generation sequencing reads (both DNA and RNA) to a population of human
           genomes (as well as to a single reference genome)., markedDefault: false,
         versionName: 2.1.0}
+    - categories: biology, genomics
+      defaultVersionName: 2.1.0
+      description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium
+        Single Cell ATAC data.
+      package: cellranger-atac
+      url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
+      versions:
+      - {description: Cell Ranger ATAC is a set of analysis pipelines that process
+          Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0}
     - categories: biology, genomics
       defaultVersionName: 0.9.0_py39
       description: Pybedtools wraps and extends BEDTools and offers feature-level
@@ -5424,26 +5437,6 @@ software_modules:
           manipulations from within Python., markedDefault: false, versionName: 0.8.2_py36}
       - {description: Pybedtools wraps and extends BEDTools and offers feature-level
           manipulations from within Python., markedDefault: false, versionName: 0.9.0_py39}
-    - categories: biology, genomics
-      defaultVersionName: 2.1.0
-      description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium
-        Single Cell ATAC data.
-      package: cellranger-atac
-      url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
-      versions:
-      - {description: Cell Ranger ATAC is a set of analysis pipelines that process
-          Chromium Single Cell ATAC data., markedDefault: false, versionName: 2.1.0}
-    - categories: biology, genomics
-      defaultVersionName: 0.8.13_py39
-      description: Tools for manipulating biological data, particularly multiple sequence
-        alignments.
-      package: py-bx-python
-      url: https://github.com/bxlab/bx-python
-      versions:
-      - {description: 'Tools for manipulating biological data, particularly multiple
-          sequence alignments.', markedDefault: false, versionName: 0.8.1_py27}
-      - {description: 'Tools for manipulating biological data, particularly multiple
-          sequence alignments.', markedDefault: false, versionName: 0.8.13_py39}
     - categories: biology, workflow management
       defaultVersionName: 23.04.3
       description: Nextflow is a bioinformatics workflow manager that enables the
@@ -5462,6 +5455,14 @@ software_modules:
       versions:
       - {description: Library to work with mmCIF and PDB files., markedDefault: false,
         versionName: 3.0.0}
+    - categories: biology, genomics
+      defaultVersionName: 3.0.7
+      description: NCBI VDB is the database engine used by NCBI SRA tools.
+      package: ncbi-vdb
+      url: https://github.com/ncbi/ncbi-vdb
+      versions:
+      - {description: NCBI VDB is the database engine used by NCBI SRA tools., markedDefault: false,
+        versionName: 3.0.7}
     - categories: biology, genomics
       defaultVersionName: 2.5.1
       description: A C code library and several stand-alone programs for the prediction
@@ -5471,16 +5472,6 @@ software_modules:
       versions:
       - {description: A C code library and several stand-alone programs for the prediction
           and comparison of RNA secondary structures., markedDefault: false, versionName: 2.5.1}
-    - categories: biology, genomics
-      defaultVersionName: 2.13.1
-      description: Trinity RNA-Seq de novo transcriptome assembly.
-      package: trinity
-      url: https://github.com/trinityrnaseq/trinityrnaseq
-      versions:
-      - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false,
-        versionName: 2.8.4}
-      - {description: Trinity RNA-Seq de novo transcriptome assembly., markedDefault: false,
-        versionName: 2.13.1}
     - categories: biology, cryo-em
       defaultVersionName: 0.2.5_py39
       description: A pipeline for particle detection in cryo-electron microscopy images
@@ -5502,6 +5493,15 @@ software_modules:
         properties:
           arch: {gpu: 1}
         versionName: 0.2.5_py39
+    - categories: biology, genomics
+      defaultVersionName: 1.2.13_py27
+      description: OBITools is a set of programs designed for analyzing NGS data in
+        a DNA metabarcoding context.
+      package: py-obitools
+      url: https://pythonhosted.org/OBITools/index.html
+      versions:
+      - {description: OBITools is a set of programs designed for analyzing NGS data
+          in a DNA metabarcoding context., markedDefault: false, versionName: 1.2.13_py27}
     - categories: biology, radiology
       defaultVersionName: '4.2'
       description: The NBIA Data Retriever is an application to download radiology
@@ -5512,15 +5512,14 @@ software_modules:
       - {description: The NBIA Data Retriever is an application to download radiology
           images from the TCIA Radiology Portal., markedDefault: false, versionName: '4.2'}
     - categories: biology, genomics
-      defaultVersionName: '2.20'
-      description: The bcl2fastq2 conversion software can be used to convert BCL files
-        from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.
-      package: bcl2fastq
-      url: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
+      defaultVersionName: 2.3.4.1
+      description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+        sequencing reads to long reference sequences.
+      package: bowtie2
+      url: http://bowtie-bio.sourceforge.net/bowtie2
       versions:
-      - {description: 'The bcl2fastq2 conversion software can be used to convert BCL
-          files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.',
-        markedDefault: false, versionName: '2.20'}
+      - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+          sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1}
     - categories: biology, genomics
       defaultVersionName: 0.5.0
       description: Trim Galore! is a wrapper script to automate quality and adapter
@@ -5568,24 +5567,6 @@ software_modules:
         properties:
           arch: {gpu: 1}
         versionName: 1.3.1
-    - categories: biology, genomics
-      defaultVersionName: 2.3.4.1
-      description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning
-        sequencing reads to long reference sequences.
-      package: bowtie2
-      url: http://bowtie-bio.sourceforge.net/bowtie2
-      versions:
-      - {description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning
-          sequencing reads to long reference sequences., markedDefault: false, versionName: 2.3.4.1}
-    - categories: biology, genomics
-      defaultVersionName: 3.0.2_py27
-      description: Assessing genome assembly and annotation completeness with Benchmarking
-        Universal Single-Copy Orthologs (BUSCO).
-      package: py-busco
-      url: https://busco.ezlab.org/
-      versions:
-      - {description: Assessing genome assembly and annotation completeness with Benchmarking
-          Universal Single-Copy Orthologs (BUSCO)., markedDefault: false, versionName: 3.0.2_py27}
     - categories: biology, neurology
       defaultVersionName: 2.4.0
       description: ANTs computes high-dimensional mappings to capture the statistics
@@ -5599,6 +5580,23 @@ software_modules:
           of brain structure and function., markedDefault: false, versionName: 2.3.1}
       - {description: ANTs computes high-dimensional mappings to capture the statistics
           of brain structure and function., markedDefault: false, versionName: 2.4.0}
+    - categories: biology, genomics
+      defaultVersionName: 3.0.2_py27
+      description: Assessing genome assembly and annotation completeness with Benchmarking
+        Universal Single-Copy Orthologs (BUSCO).
+      package: py-busco
+      url: https://busco.ezlab.org/
+      versions:
+      - {description: Assessing genome assembly and annotation completeness with Benchmarking
+          Universal Single-Copy Orthologs (BUSCO)., markedDefault: false, versionName: 3.0.2_py27}
+    - categories: biology, genomics
+      defaultVersionName: 3.3.1_py36
+      description: Tools to process and analyze deep sequencing data.
+      package: py-deeptools
+      url: https://github.com/deeptools/deepTools/
+      versions:
+      - {description: Tools to process and analyze deep sequencing data., markedDefault: false,
+        versionName: 3.3.1_py36}
     - categories: biology, genomics
       defaultVersionName: 1.16.1
       description: Tools (written in C using htslib) for manipulating next-generation
@@ -5612,22 +5610,30 @@ software_modules:
           sequencing data., markedDefault: false, versionName: '1.8'}
       - {description: Tools (written in C using htslib) for manipulating next-generation
           sequencing data., markedDefault: false, versionName: 1.16.1}
-    - categories: biology, genomics
-      defaultVersionName: '1.16'
-      description: BCFtools is a program for variant calling and manipulating files
-        in the Variant Call Format (VCF) and its binary counterpart BCF.
-      package: bcftools
-      url: https://github.com/samtools/bcftools
+    - categories: biology, computational biology
+      defaultVersionName: '3.14'
+      description: Rosetta is the premier software suite for modeling macromolecular
+        structures. As a flexible, multi-purpose application, it includes tools for
+        structure prediction, design, and remodeling of proteins and nucleic acids.
+      package: rosetta
+      url: https://www.rosettacommons.org
       versions:
-      - {description: BCFtools is a program for variant calling and manipulating files
-          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
-        versionName: '1.6'}
-      - {description: BCFtools is a program for variant calling and manipulating files
-          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
-        versionName: '1.8'}
-      - {description: BCFtools is a program for variant calling and manipulating files
-          in the Variant Call Format (VCF) and its binary counterpart BCF., markedDefault: false,
-        versionName: '1.16'}
+      - description: Rosetta is the premier software suite for modeling macromolecular
+          structures. As a flexible, multi-purpose application, it includes tools
+          for structure prediction, design, and remodeling of proteins and nucleic
+          acids.
+        markedDefault: false
+        properties:
+          parallel: {mpi: 1}
+        versionName: '3.8'
+      - description: Rosetta is the premier software suite for modeling macromolecular
+          structures. As a flexible, multi-purpose application, it includes tools
+          for structure prediction, design, and remodeling of proteins and nucleic
+          acids.
+        markedDefault: false
+        properties:
+          parallel: {mpi: 1}
+        versionName: '3.14'
     - categories: biology, genomics
       defaultVersionName: '202112.01'
       description: Sentieon Genomics software is a set of software tools that perform
@@ -5647,48 +5653,51 @@ software_modules:
         properties:
           license: {restricted: 1}
         versionName: '202112.01'
-    - categories: biology, neurology
-      defaultVersionName: '20160502'
-      description: MRIcron is a cross-platform NIfTI format image viewer.
-      package: mricron
-      url: https://www.nitrc.org/projects/mricron
-      versions:
-      - {description: MRIcron is a cross-platform NIfTI format image viewer., markedDefault: false,
-        versionName: '20160502'}
-    - categories: biology, computational biology
-      defaultVersionName: '3.14'
-      description: Rosetta is the premier software suite for modeling macromolecular
-        structures. As a flexible, multi-purpose application, it includes tools for
-        structure prediction, design, and remodeling of proteins and nucleic acids.
-      package: rosetta
-      url: https://www.rosettacommons.org
+    - categories: biology, genomics
+      defaultVersionName: 2.3.10_py39
+      description: A software package for animal pose estimation.
+      package: py-deeplabcut
+      url: http://deeplabcut.org
       versions:
-      - description: Rosetta is the premier software suite for modeling macromolecular
-          structures. As a flexible, multi-purpose application, it includes tools
-          for structure prediction, design, and remodeling of proteins and nucleic
-          acids.
+      - description: A software package for animal pose estimation.
         markedDefault: false
         properties:
-          parallel: {mpi: 1}
-        versionName: '3.8'
-      - description: Rosetta is the premier software suite for modeling macromolecular
-          structures. As a flexible, multi-purpose application, it includes tools
-          for structure prediction, design, and remodeling of proteins and nucleic
-          acids.
+          arch: {gpu: 1}
+        versionName: 2.2.3_py39
+      - description: A software package for animal pose estimation.
         markedDefault: false
         properties:
-          parallel: {mpi: 1}
-        versionName: '3.14'
-    - categories: biology, clinical science
-      defaultVersionName: '20180704'
-      description: Simvascular is a blood flow simulation and analysis toolkit. This
-        module provides the svFSI (Fluid Solid Interaction) solver.
-      package: simvascular
-      url: https://simvascular.github.io
+          arch: {gpu: 1}
+        versionName: 2.3.10_py39
+    - categories: biology, genomics
+      defaultVersionName: 0.7.3
+      description: Dorado is a high-performance, easy-to-use, open source basecaller
+        for Oxford Nanopore reads.
+      package: dorado
+      url: https://github.com/nanoporetech/dorado
       versions:
-      - {description: Simvascular is a blood flow simulation and analysis toolkit.
-          This module provides the svFSI (Fluid Solid Interaction) solver., markedDefault: false,
-        versionName: '20180704'}
+      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
+          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4}
+      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
+          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3}
+      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
+          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3}
+    - categories: biology, genomics
+      defaultVersionName: '1.16'
+      description: C library for high-throughput sequencing data formats.
+      package: htslib
+      url: https://github.com/samtools/htslib
+      versions:
+      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
+        versionName: '1.6'}
+      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
+        versionName: '1.8'}
+      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
+        versionName: 1.10.2}
+      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
+        versionName: '1.14'}
+      - {description: C library for high-throughput sequencing data formats., markedDefault: false,
+        versionName: '1.16'}
     - categories: biology, genomics
       defaultVersionName: 0.1.15
       description: VCFtools is a program package designed for working with VCF files,
@@ -5708,18 +5717,18 @@ software_modules:
       - {description: A Python framework for the analysis and visualization of trees.,
         markedDefault: false, versionName: 3.0.0_py27}
     - categories: biology, genomics
-      defaultVersionName: 0.7.3
-      description: Dorado is a high-performance, easy-to-use, open source basecaller
-        for Oxford Nanopore reads.
-      package: dorado
-      url: https://github.com/nanoporetech/dorado
+      defaultVersionName: 1.2.1_py312
+      description: scvi-tools (single-cell variational inference tools) is a package
+        for probabilistic modeling of single-cell omics data.
+      package: py-scvi-tools
+      url: https://scvi-tools.org/
       versions:
-      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
-          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.3.4}
-      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
-          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.5.3}
-      - {description: 'Dorado is a high-performance, easy-to-use, open source basecaller
-          for Oxford Nanopore reads.', markedDefault: false, versionName: 0.7.3}
+      - description: scvi-tools (single-cell variational inference tools) is a package
+          for probabilistic modeling of single-cell omics data.
+        markedDefault: false
+        properties:
+          arch: {gpu: 1}
+        versionName: 1.2.1_py312
     - categories: biology, genomics
       defaultVersionName: 1.0.0
       description: Longshot is a variant calling tool for diploid genomes using long
@@ -5730,16 +5739,16 @@ software_modules:
       - {description: Longshot is a variant calling tool for diploid genomes using
           long error prone reads., markedDefault: false, versionName: 1.0.0}
     - categories: biology, neurology
-      defaultVersionName: 0.7.00
-      description: BART is a toolbox for Computational Magnetic Resonance Imaging.
-      package: bart
-      url: https://mrirecon.github.io/bart/
+      defaultVersionName: 1.3.1
+      description: Connectome Workbench is an open source, freely available visualization
+        and discovery tool used to map neuroimaging data, especially data generated
+        by the Human Connectome Project.
+      package: workbench
+      url: https://www.humanconnectome.org/software/connectome-workbench
       versions:
-      - description: BART is a toolbox for Computational Magnetic Resonance Imaging.
-        markedDefault: false
-        properties:
-          arch: {gpu: 1}
-        versionName: 0.7.00
+      - {description: 'Connectome Workbench is an open source, freely available visualization
+          and discovery tool used to map neuroimaging data, especially data generated
+          by the Human Connectome Project.', markedDefault: false, versionName: 1.3.1}
     - categories: biology, genomics
       defaultVersionName: '1.8'
       description: A single molecule sequence assembler for genomes large and small.
@@ -5748,17 +5757,21 @@ software_modules:
       versions:
       - {description: A single molecule sequence assembler for genomes large and small.,
         markedDefault: false, versionName: '1.8'}
-    - categories: biology, genomics
-      defaultVersionName: 2.2.9.1_py39
-      description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
-        analysis method.
-      package: py-macs2
-      url: https://github.com/taoliu/MACS
+    - categories: biology, computational biology
+      defaultVersionName: 1.84_py312
+      description: Biopython is a set of freely available tools for biological computation
+        written in Python.
+      package: py-biopython
+      url: http://biopython.org
       versions:
-      - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
-          analysis method., markedDefault: false, versionName: 2.1.1_py27}
-      - {description: MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq
-          analysis method., markedDefault: false, versionName: 2.2.9.1_py39}
+      - {description: Biopython is a set of freely available tools for biological
+          computation written in Python., markedDefault: false, versionName: 1.70_py27}
+      - {description: Biopython is a set of freely available tools for biological
+          computation written in Python., markedDefault: false, versionName: 1.79_py36}
+      - {description: Biopython is a set of freely available tools for biological
+          computation written in Python., markedDefault: false, versionName: 1.79_py39}
+      - {description: Biopython is a set of freely available tools for biological
+          computation written in Python., markedDefault: false, versionName: 1.84_py312}
     - categories: biology, genomics
       defaultVersionName: 2.2.1_py36
       description: mapDamage2 is a computational framework which tracks and quantifies
diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml
index 7c2863cc6..7f88e3028 100644
--- a/src/docs/software/updates.xml
+++ b/src/docs/software/updates.xml
@@ -5,6 +5,15 @@
 <description>Sherlock software update feed</description>
 <link>https://www.sherlock.stanford.edu/docs/software/list</link>
 <atom:link href="https://www.sherlock.stanford.edu/docs/software/updates.xml" rel="self" type="application/rss+xml"/>
+    <item>
+        <title>New module: biology/py-scvi-tools version 1.2.1_py312</title>
+        <description>scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling of single-cell omics data.</description>
+        <link>https://scvi-tools.org/</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.2.1_py312#py-scvi-tools</guid>
+        <category>biology, genomics</category>
+        <author>kilian@stanford.edu (Kilian Cavalotti)</author>
+        <pubDate>Fri, 6 Dec 2024 16:51:04 -0800</pubDate>
+    </item>
     <item>
         <title>New version: math/py-jax version 0.4.36_py312</title>
         <description>JAX is Autograd and XLA, brought together for high-performance numerical computing.</description>