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 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div>
 |-
-| align="center" | [https://ambermd.org/amber.html amber]
+| align="center" | [http://ambermd.org/amber.html amber]
 | align="center" | chem
-| align="center" | 20.12-20.15, 20.9-20.15, 18.14-18.17, 22.5-23.5
+| align="center" | 18.14-18.17, 22.5-23.5, 20.9-20.15, 20.12-20.15
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://ambermd.org/AmberTools.php ambertools]
 | align="center" | chem
-| align="center" | 20, 21, 22, 23, 23.5
+| align="center" | 20, 21, 22, 23.5
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php Keyword:chem<br /><br /><br /></div>
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@@ Line 202: / Line 202: @@
 | align="center" | [https://arrow.apache.org arrow]
 | align="center" | tools
-| align="center" | 0.16.0, 0.17.1, 1.0.0, 2.0.0, 5.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0, 17.0.0
+| align="center" | 0.16.0, 0.17.1, 1.0.0, 2.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0, 17.0.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.12, python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div>
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@@ Line 772: / Line 772: @@
 | align="center" | [https://www.comsol.com comsol]
 | align="center" | phys
-| align="center" | 5.6, 6.0, 6.0.0.405, 6.1, 6.1.0.357, 6.2.0.415
+| align="center" | 5.6, 6.0, 6.0.0.405, 6.1.0.357, 6.2.0.415
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div>
 |-
@@ Line 1,538: / Line 1,538: @@
 | align="center" | -
 | align="center" | 3.3.2, 3.3.8
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Extensions: glfw-2.6.2<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org<br /><br /><br /></div>
 |-
 | align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm]
@@ Line 1,572: / Line 1,572: @@
 | align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap]
 | align="center" | bio
-| align="center" | 2020-11-14, 2019-09-12
+| align="center" | 2019-09-12, 2020-11-14
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program Homepage: http://research-pub.gene.com/gmap/ URL: http://research-pub.gene.com/gmap/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 1,647: / Line 1,647: @@
 | align="center" | [http://www.gromacs.org gromacs]
 | align="center" | chem
-| align="center" | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023.2, 2023.3, 2024.1
+| align="center" | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2024.1
 | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
 |-
@@ Line 1,653: / Line 1,653: @@
 | align="center" | chem
 | align="center" | 2020.6
-| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div>
+| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div>
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 | align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k]
@@ Line 1,672: / Line 1,672: @@
 | align="center" | [https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ gromacs-ramd]
 | align="center" | chem
-| align="center" | 2020.5-RAMD-2.0, 2024.1-RAMD-2.1
+| align="center" | 2024.1-RAMD-2.1, 2020.5-RAMD-2.0
-| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a CPU only build, containing both MPI and threadMPI builds. CC-Wiki: GROMACS Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a GPU enabled build, containing both MPI and threadMPI binaries. Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]
 | align="center" | chem
 | align="center" | 2021.7-0.5.1
-| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
+| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://www.gnu.org/software/gsl/ gsl]
@@ Line 1,743: / Line 1,743: @@
 | align="center" | io
 | align="center" | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, hdf5-blosc-1.0.1, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div>
 |-
 | align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]
@@ Line 1,917: / Line 1,917: @@
 | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]
 | align="center" | bio
-| align="center" | 5.64-96.0, 5.56-89.0, 5.50-84.0, 5.52-86.0, 5.55-88.0, 5.53-87.0, 5.63-95.0
+| align="center" | 5.64-96.0, 5.53-87.0, 5.55-88.0, 5.63-95.0, 5.50-84.0, 5.52-86.0, 5.56-89.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div>
 |-
 | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data]
 | align="center" | -
-| align="center" | 5.64-96.0, 5.63-95.0
+| align="center" | 5.63-95.0, 5.64-96.0
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/<br /><br /><br /></div>
 |-
@@ Line 2,007: / Line 2,007: @@
 | align="center" | [http://openjdk.java.net java]
 | align="center" | tools
-| align="center" | 1.8.0_192, 11.0.16_8, 1.8.0_292, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1
+| align="center" | 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1
 | Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools<br /><br /><br /></div>
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@@ Line 2,303: / Line 2,303: @@
 | align="center" | -
 | align="center" | 1.1.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>
 |-
 | align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9]
@@ Line 2,507: / Line 2,507: @@
 | align="center" | [http://www.mathworks.com/products/matlab matlab]
 | align="center" | tools
-| align="center" | 2020a, 2020b, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2
+| align="center" | 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2
 | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,527: / Line 2,527: @@
 | align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
 | align="center" | tools
-| align="center" | R2020b, R2024a, R2022b, R2021b
+| align="center" | R2020b, R2022b, R2024a, R2021b
 | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools<br /><br /><br /></div>
 |-
@@ Line 2,672: / Line 2,672: @@
 | align="center" | [https://mmseqs.com mmseqs2]
 | align="center" | -
-| align="center" | 15-6f452, 14-7e284, 13-45111
+| align="center" | 14-7e284, 15-6f452, 13-45111
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div>
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@@ Line 3,383: / Line 3,383: @@
 | align="center" | tools
 | align="center" | 5.30.2, 5.36.1
-| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.112, Algorithm::Diff-1.201, aliased-0.34, AnyEvent-7.17, App::Cmd-0.335, App::cpanminus-1.7046, AppConfig-1.71, Archive::Extract-0.88, Array::Transpose-0.06, Array::Utils-0.5, Authen::NTLM-1.09, Authen::SASL-2.16, AutoLoader-5.74, B::COW-0.007, B::Hooks::EndOfScope-0.26, B::Lint-1.20, boolean-0.46, Business::ISBN-3.008, Business::ISBN::Data-20230516.001, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, CGI-4.57, Class::Accessor-0.51, Class::Data::Inheritable-0.09, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Method::Modifiers-2.15, Class::Singleton-1.6, Class::Tiny-1.008, Class::Trigger-0.15, Class::XSAccessor-1.19, Clone-0.46, Clone::Choose-0.010, common::sense-3.75, Compress::Raw::Zlib-2.204, Config::General-2.65, Config::INI-0.029, Config::MVP-2.200013, Config::MVP::Reader::INI-2.101465, Config::Simple-4.58, Config::Tiny-2.29, Const::Exporter-1.2.2, Const::Fast-0.014, constant-1.33, CPAN::Meta::Check-0.017, CPAN::Uploader-0.103018, CPANPLUS-0.9914, Crypt::DES-2.07, Crypt::Rijndael-1.16, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.25, Data::Dumper-2.183, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.114, Data::Section-0.200008, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.226, Date::Handler-1.2, Date::Language-2.33, DateTime-1.59, DateTime::Locale-1.38, DateTime::TimeZone-2.60, DateTime::Tiny-1.07, DBD::CSV-0.60, DBD::SQLite-1.72, DBI-1.643, DBIx::Admin::CreateTable-2.11, DBIx::Admin::DSNManager-2.02, DBIx::Admin::TableInfo-3.04, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.16, Devel::Cycle-1.12, Devel::FindPerl-0.016, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.007, Devel::Size-0.83, Devel::StackTrace-2.04, Digest::HMAC-1.04, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.030, Email::Date::Format-1.008, Encode-3.19, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.45, Expect-1.35, Exporter-5.77, Exporter::Declare-0.114, Exporter::Tiny-1.006002, ExtUtils::CBuilder-0.280236, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.26, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.70, ExtUtils::ParseXS-3.44, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.16, File::Grep-0.02, File::HomeDir-1.006, File::Listing-6.15, File::Next-1.18, File::Path-2.18, File::pushd-1.016, File::Remove-1.61, File::ShareDir-1.118, File::ShareDir::Install-0.14, File::Slurp-9999.32, File::Slurp::Tiny-0.004, File::Slurper-0.014, File::Spec-3.75, File::Temp-0.2311, File::Which-1.27, Font::TTF-1.06, Getopt::Long-2.54, Getopt::Long::Descriptive-0.111, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9726, Graph::ReadWrite-2.10, Hash::Merge-0.302, Hash::Objectify-0.008, Heap-0.80, Hook::LexWrap-0.26, HTML::Entities::Interpolate-1.10, HTML::Form-6.11, HTML::Parser-3.81, HTML::Tagset-3.20, HTML::Template-2.97, HTML::Tree-5.07, HTTP::CookieJar-0.014, HTTP::Cookies-6.10, HTTP::Daemon-6.16, HTTP::Date-6.05, HTTP::Message-6.44, HTTP::Negotiate-6.01, HTTP::Tiny-0.082, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, Importer-0.026, Inline-0.86, IO::Compress::Zip-2.204, IO::File-1.51, IO::HTML-1.004, IO::Socket::SSL-2.083, IO::String-1.08, IO::Stringy-2.113, IO::TieCombine-1.005, IO::Tty-1.17, IO::Tty-1.17, IPC::Cmd-1.04, IPC::Run-20220807.0, IPC::Run3-0.048, IPC::System::Simple-1.30, JSON-4.10, JSON::MaybeXS-1.004005, JSON::XS-4.03, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.19, List::MoreUtils-0.430, List::MoreUtils::XS-0.430, List::SomeUtils-0.59, List::UtilsBy-0.12, local::lib-2.000029, Locale::Maketext::Simple-0.21, Log::Dispatch-2.71, Log::Dispatch::Array-1.005, Log::Dispatchouli-3.002, Log::Handler-0.90, Log::Log4perl-1.57, Log::Message-0.08, Log::Message::Simple-0.10, Log::Report-1.34, Log::Report::Optional-1.07, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.10, LWP::Simple-6.70, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::Utils-1.14, Math::VecStat-0.08, MCE::Mutex-1.884, Meta::Builder-0.004, MIME::Base64-3.16, MIME::Charset-v1.013.1, MIME::Lite-3.033, MIME::Types-2.24, Mixin::Linewise::Readers-0.111, Mock::Quick-1.111, Module::Build-0.4234, Module::Build::Tiny-0.045, Module::Build::XSUtil-0.19, Module::CoreList-5.20230423, Module::Implementation-0.09, Module::Install-1.21, Module::Load-0.36, Module::Load::Conditional-0.74, Module::Metadata-1.000038, Module::Path-0.19, Module::Path-0.19, Module::Pluggable-5.2, Module::Runtime-0.016, Module::Runtime::Conflicts-0.003, Moo-2.005005, Moose-2.2203, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.007, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.203, MooseX::Types-0.50, MooseX::Types::Perl-0.101344, Mouse-v2.5.10, Mozilla::CA-20221114, MRO::Compat-0.15, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.15, Net::HTTP-6.22, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.92, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.18, Package::Stash-0.40, Package::Stash::XS-0.30, PadWalker-2.5, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.102, Params::Validate-1.31, Params::ValidationCompiler-0.31, parent-0.241, Parse::RecDescent-1.967015, Parse::Yapp-1.21, Path::Tiny-0.144, PDF::API2-2.044, Perl::OSType-1.010, Perl::PrereqScanner-1.100, PerlIO::utf8_strict-0.010, Pod::Elemental-0.103006, Pod::Escapes-1.07, Pod::Eventual-0.094003, Pod::LaTeX-0.61, Pod::Man-5.01, Pod::Parser-1.66, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.45, Pod::Weaver-4.019, PPI-1.276, Readonly-2.05, Ref::Util-0.204, Regexp::Common-2017060201, Role::HasMessage-0.007, Role::Identifiable::HasIdent-0.009, Role::Tiny-2.002004, Scalar::Util-1.63, Scalar::Util::Numeric-0.40, Scope::Guard-0.21, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Object-1.42, Set::Scalar-1.29, Shell-0.73, Socket-2.036, Software::License-0.104003, Specio-0.48, Spiffy-0.46, SQL::Abstract-2.000001, SQL::Statement-1.414, Statistics::Basic-1.6611, Statistics::Descriptive-3.0800, Storable-3.25, strictures-2.000006, String::Errf-0.009, String::Flogger-1.101246, String::Formatter-1.235, String::Print-0.94, String::RewritePrefix-0.009, String::Truncate-1.100603, String::TtyLength-0.03, Sub::Exporter-0.989, Sub::Exporter::ForMethods-0.100055, Sub::Exporter::GlobExporter-0.006, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Info-0.002, Sub::Install-0.929, Sub::Name-0.27, Sub::Quote-2.006008, Sub::Uplevel-0.2800, SVG-2.87, Switch-2.17, Sys::Info-0.7811, Sys::Info::Base-0.7807, Sys::Info::Driver::Linux-0.7905, Sys::Info::Driver::Linux::Device::CPU-0.7905, Sys::Info::Driver::Unknown-0.79, Sys::Info::Driver::Unknown::Device::CPU-0.79, Template-3.101, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.45, Term::Table-0.016, Term::UI-0.50, Test-1.26, Test2::Plugin::NoWarnings-0.09, Test2::Require::Module-0.000155, Test::Base-0.89, Test::CheckDeps-0.010, Test::ClassAPI-1.07, Test::CleanNamespaces-0.24, Test::Deep-1.204, Test::Differences-0.69, Test::Exception-0.43, Test::FailWarnings-0.008, Test::Fatal-0.017, Test::File-1.993, Test::File::ShareDir::Dist-1.001002, Test::Harness-3.44, Test::LeakTrace-0.17, Test::Memory::Cycle-1.06, Test::More::UTF8-0.05, Test::Most-0.38, Test::Needs-0.002010, Test::NoWarnings-1.06, Test::Object-0.08, Test::Output-1.033, Test::Pod-1.52, Test::Requires-0.11, Test::RequiresInternet-0.05, Test::Simple-1.302195, Test::SubCalls-1.10, Test::Sys::Info-0.23, Test::Version-2.09, Test::Warn-0.37, Test::Warnings-0.031, Test::Without::Module-0.21, Test::YAML-1.07, Text::Aligner-0.16, Text::Balanced-2.06, Text::CSV-2.02, Text::CSV_XS-1.50, Text::Diff-1.45, Text::Format-0.62, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.31, Text::Soundex-3.05, Text::Table-1.135, Text::Table::Manifold-1.03, Text::Template-1.61, Thread::Queue-3.13, threads-2.21, Throwable-1.001, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9764, Time::Local-1.35, Time::Piece-1.3401, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.32, Try::Tiny-0.31, Type::Tiny-2.004000, Types::Serialiser-1.01, Types::Serialiser-1.01, Unicode::EastAsianWidth-12.0, Unicode::LineBreak-2019.001, UNIVERSAL::moniker-0.08, Unix::Processors-2.046, Unix::Processors-2.046, URI-5.19, Variable::Magic-0.63, version-0.9929, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Expat-0.51, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::Writer-0.900, XML::XPath-1.48, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.74 Keyword:tools<br /><br /><br /></div>
+| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Carp-1.50, constant-1.33, Data::Dumper-2.183, Exporter-5.77, File::Path-2.18, File::Spec-3.75, Getopt::Long-2.54, IO::File-1.51, Text::ParseWords-3.31, Thread::Queue-3.13, threads-2.21 Keyword:tools<br /><br /><br /></div>
 |-
 | align="center" | [http://www.mcs.anl.gov/petsc petsc]
@@ Line 3,512: / Line 3,512: @@
 | align="center" | [https://www.cog-genomics.org/plink/2.0/ plink]
 | align="center" | bio
-| align="center" | 2.00a5.8, 1.9b_6.21-x86_64, 2.00a3.6, 2.00-20231024-avx2, 2.00-10252019-avx2
+| align="center" | 1.9b_6.21-x86_64, 2.00-10252019-avx2, 2.00a5.8, 2.00-20231024-avx2, 2.00a3.6
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio<br /><br /><br /></div>
 |-
@@ Line 3,557: / Line 3,557: @@
 | align="center" | [http://www.portaudio.com/ portaudio]
 | align="center" | -
-| align="center" | 190600_20161030, 190700_20210406
+| align="center" | 190700_20210406, 190600_20161030
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: PyAudio-0.2.13<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: PyAudio-0.2.11<br /><br /><br /></div>
 |-
 | align="center" | [https://www.postgresql.org/ postgresql]
@@ Line 3,900: / Line 3,900: @@
 | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. The method has the following properties It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios It can process multiple phenotypes at once For binary traits it supports Firth logistic regression and an SPA test It can perform gene/region-based burden tests It is fast and memory efficient It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats It is ideally suited for implementation in Apache Spark (see GLOW) Citation Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 10971103 (2021). https://doi.org/10.1038/s41588-021-00870-7 Homepage: https://rgcgithub.github.io/regenie/ URL: https://rgcgithub.github.io/regenie/<br /><br /><br /></div>
 |-
-| align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ relion]
+| align="center" | [https://bitbucket.org/scheres/relion-3.0_beta.git relion]
 | align="center" | chem
 | align="center" | 3.1.1, 4.0.0
-| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://www3.mrc-lmb.cam.ac.uk/relion/ URL: https://www3.mrc-lmb.cam.ac.uk/relion/ Keyword:chem<br /><br /><br /></div>
+| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://bitbucket.org/scheres/relion-3.0_beta.git URL: https://bitbucket.org/scheres/relion-3.0_beta.git Keyword:chem<br /><br /><br /></div>
 |-
 | align="center" | [https://repast.github.io/ repasthpc]