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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> | | <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> | ||
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| align="center" | [ | | align="center" | [http://ambermd.org/amber.html amber] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20. | | align="center" | 20.12-20.15, 18.14-18.17, 22.5-23.5, 20.9-20.15 | ||
| <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: | | <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> | ||
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| align="center" | [https://ambermd.org/AmberTools.php ambertools] | | align="center" | [https://ambermd.org/AmberTools.php ambertools] | ||
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| align="center" | [https://arrow.apache.org arrow] | | align="center" | [https://arrow.apache.org arrow] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 0.16.0, 0.17.1 | | align="center" | 0.16.0, 0.17.1, 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 | ||
| <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> | | <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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| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle] | | align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 5.4-240301 | | align="center" | 5.4, 5.4-240301 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div> | ||
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| align="center" | [https://www.comsol.com comsol] | | align="center" | [https://www.comsol.com comsol] | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | 5.6 | | align="center" | 5.6, 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> | | <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> | ||
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| align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy] | | align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 2.1 | | align="center" | 2.1, 2.3.1, 2.4.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div> | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 3.3.2, 3.3.8 | | 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 | | <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> | ||
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| align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | | align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 2020.5-RAMD-2.0 | | align="center" | 2020.5-RAMD-2.0 | ||
| <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 | | <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> | ||
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| align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs] | | align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs] | ||
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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan] | | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 5. | | align="center" | 5.52-86.0, 5.50-84.0, 5.53-87.0, 5.63-95.0, 5.64-96.0, 5.56-89.0, 5.55-88.0 | ||
| <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> | | <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> | ||
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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data] | | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 5. | | 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> | | <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> | ||
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| align="center" | [http://openjdk.java.net java] | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.2, 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> | | 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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| align="center" | - | | align="center" | - | ||
| align="center" | 1.1.0 | | 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 | | <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> | ||
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| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | | align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | ||
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| align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr] | | align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | R2020b | | align="center" | R2022b, R2020b, R2021b, R2024a | ||
| 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> | | 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> | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: https://dtcenter.org/ URL: https://dtcenter.org/ Keyword:phys<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: https://dtcenter.org/ URL: https://dtcenter.org/ Keyword:phys<br /><br /><br /></div> | ||
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| align="center" | [https://docs. | | align="center" | [https://docs.alliancecan.ca/wiki/META-Farm meta-farm] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 1.0.2 | | align="center" | 1.0.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.alliancecan.ca/wiki/META-Farm URL: https://docs.alliancecan.ca/wiki/META-Farm<br /><br /><br /></div> | ||
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| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat] | | align="center" | [https://bitbucket.org/berkeleylab/metabat metabat] | ||
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| align="center" | [https://mmseqs.com mmseqs2] | | align="center" | [https://mmseqs.com mmseqs2] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 14-7e284 | | align="center" | 15-6f452, 14-7e284, 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> | | <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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| align="center" | math | | align="center" | math | ||
| align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1 | | align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:math<br /><br /><br /></div> | ||
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| align="center" | [https://nodejs.org nodejs] | | align="center" | [https://nodejs.org nodejs] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 7.5.0, 7.6.0, 7.7.0, 8.0.0 | | align="center" | 7.5.0, 7.6.0, 7.7.0, 8.0.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.10, python/3.11 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [http://openmm.org openmm-alphafold] | | align="center" | [http://openmm.org openmm-alphafold] | ||
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| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink] | | align="center" | [https://www.cog-genomics.org/plink/1.9/ plink] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | | | align="center" | 2.00-10252019-avx2, 2.00-20231024-avx2, 2.00a5.8, 2.00a3.6, 1.9b_6.21-x86_64 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ URL: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ URL: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://www.htslib.org/ samtools] | | align="center" | [https://www.htslib.org/ samtools] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.1.20, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18 | | align="center" | 0.1.20, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18, 1.20 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | ||
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