docs: updated software list

includes/data/software.yml

@@ -3938,6 +3938,12 @@ software_modules:
           arch: {gpu: 1}
           parallel: {mpi: 1}
         versionName: 2.2.1_py312
+      - description: PyTorch is a deep learning framework that puts Python first.
+        markedDefault: false
+        properties:
+          arch: {gpu: 1}
+          parallel: {mpi: 1}
+        versionName: 2.4.1_py312
       - description: PyTorch is a deep learning framework that puts Python first.
         markedDefault: true
         properties:
@@ -5501,7 +5507,7 @@ 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, computational biology
-      defaultVersionName: 1.79_py39
+      defaultVersionName: 1.84_py312
       description: Biopython is a set of freely available tools for biological computation
         written in Python.
       package: py-biopython
@@ -5513,6 +5519,8 @@ software_modules:
           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: '1.8'
       description: A single molecule sequence assembler for genomes large and small.

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 version: biology/py-biopython version 1.84_py312</title>
+        <description>Biopython is a set of freely available tools for biological computation written in Python.</description>
+        <link>http://biopython.org</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.84_py312#py-biopython</guid>
+        <category>biology, computational biology</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Mon, 23 Sep 2024 13:50:04 -0700</pubDate>
+    </item>
     <item>
         <title>New version: chemistry/vasp version 6.4.3</title>
         <description>The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.</description>