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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://dalexander.github.io/admixture/ admixture] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.3.0 | | align="center" | 1.3.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: https://dalexander.github.io/admixture/ URL: https://dalexander.github.io/admixture/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | | align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | ||
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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" | | | align="center" | 18.14-18.17, 22.5-23.5, 20.12-20.15, 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" | [http://www.ansys.com ansys] | | align="center" | [http://www.ansys.com ansys] | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | 2024R1.03, 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2 | | align="center" | 2024R1.03, 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2, 2024R1 | ||
| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys<br /><br /><br /></div> | | Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys<br /><br /><br /></div> | ||
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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, 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, 4.0.0, 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> | | <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://github.com/infphilo/centrifuge centrifuge] | | align="center" | [https://github.com/infphilo/centrifuge centrifuge] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.0.4-beta | | align="center" | 1.0.4-beta, 1.0.4 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<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, 6.0, 6.0.0.405, 6.1, 6.1.0.357 | | align="center" | 5.6, 6.0, 6.0.0.405, 6.1, 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" | 6.13 | | align="center" | 6.13 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools<br /><br /><br /></div> | ||
|- | |||
| align="center" | [https://www.daltonprogram.org/www/citation.html. dalton] | |||
| align="center" | chem | |||
| align="center" | 2020.0, 2020.1 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html. Homepage: https://daltonprogram.org/ URL: https://daltonprogram.org/ Keyword:chem<br /><br /><br /></div> | |||
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| align="center" | [https://github.com/cmks/DAS_Tool das_tool] | | align="center" | [https://github.com/cmks/DAS_Tool das_tool] | ||
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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" | [http://research-pub.gene.com/gmap/ gmap-gsnap] | | align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | | | align="center" | 2020-11-14, 2024-08-20, 2019-09-12 | ||
| <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> | | <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> | ||
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| align="center" | chem | | 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, 2023.2, 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 | | 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 GPU enabled build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [http://colvars.github.io/ gromacs-colvars] | | align="center" | [http://colvars.github.io/ gromacs-colvars] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 2024.1-RAMD-2.1, 2020.5-RAMD-2.0 | | align="center" | 2024.1-RAMD-2.1, 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 CPU only build, containing both MPI and threadMPI builds. 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] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 2021.7-0.5.1 | | 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 | | 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> | ||
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| align="center" | [https://www.gnu.org/software/gsl/ gsl] | | align="center" | [https://www.gnu.org/software/gsl/ gsl] | ||
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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" | 5.64-96.0, 5. | | align="center" | 5.64-96.0, 5.63-95.0, 5.50-84.0, 5.56-89.0, 5.52-86.0, 5.53-87.0, 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://openjdk.java.net java] | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 1.8.0_292, 1.8.0_192 | | align="center" | 1.8.0_292, 11.0.16_8, 1.8.0_192, 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" | [http://www.mathworks.com/products/matlab matlab] | | align="center" | [http://www.mathworks.com/products/matlab matlab] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2020a | | 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> | | 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> | ||
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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" | R2024a, R2020b, R2021b, R2022b | ||
| 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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| align="center" | [https://mmseqs.com mmseqs2] | | align="center" | [https://mmseqs.com mmseqs2] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 15-6f452 | | 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> | | <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/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 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" | 3.1.1 | | align="center" | 3.1.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://openbabel.org openbabel-omp] | | align="center" | [https://openbabel.org openbabel-omp] | ||
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| align="center" | [http://opencv.org/ opencv] | | align="center" | [http://opencv.org/ opencv] | ||
| align="center" | vis | | align="center" | vis | ||
| align="center" | 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 4.9 | | align="center" | 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 4.9.0, 4.10.0-2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:vis<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.10, python/3.11, python/3.12 Keyword:vis<br /><br /><br /></div> | ||
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| align="center" | [http://www.openmx-square.org/ openmx] | | align="center" | [http://www.openmx-square.org/ openmx] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 3.9.9 | | align="center" | 3.9, 3.9.9 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://sites.astro.caltech.edu/~tjp/pgplot/ pgplot] | | align="center" | [https://sites.astro.caltech.edu/~tjp/pgplot/ pgplot] | ||
| align="center" | vis | | align="center" | vis | ||
| align="center" | 5.2.2 | | align="center" | 5.2, 5.2.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: https://sites.astro.caltech.edu/~tjp/pgplot/ URL: https://sites.astro.caltech.edu/~tjp/pgplot/ Keyword:vis<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: https://sites.astro.caltech.edu/~tjp/pgplot/ URL: https://sites.astro.caltech.edu/~tjp/pgplot/ Keyword:vis<br /><br /><br /></div> | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platanus-allee is an assembler derived from Platanus assembler, however, it was developed with another concept. Platanus-allee tries to construct each haplotype sequence from the beginning and pair them as homologous chromosomes, while Platanus constructs consensus sequence of homologous chromosomes at first and tries to split into each haplotype sequence. Therefore, Platanus-allee marks better performance for highly heterozygous species genome or highly diverged genomic regions. Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platanus-allee is an assembler derived from Platanus assembler, however, it was developed with another concept. Platanus-allee tries to construct each haplotype sequence from the beginning and pair them as homologous chromosomes, while Platanus constructs consensus sequence of homologous chromosomes at first and tries to split into each haplotype sequence. Therefore, Platanus-allee marks better performance for highly heterozygous species genome or highly diverged genomic regions. Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div> | ||
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| align="center" | [https://www.cog-genomics.org/plink/ | | align="center" | [https://www.cog-genomics.org/plink/2.0/ plink] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2. | | align="center" | 2.00a3.6, 1.9b_6.21-x86_64, 2.00-20231024-avx2, 2.00a5.8, 2.00-10252019-avx2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description | | <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> | ||
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| align="center" | [http://plplot.sourceforge.net plplot] | | align="center" | [http://plplot.sourceforge.net plplot] | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0 | | align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11, python/3.12<br /><br /><br /></div> | ||
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| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm] | | align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm] | ||