Modules avx512: Difference between revisions

| align="center" | [http://ambermd.org/amber.html amber]

| align="center" | chem

| <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://arrow.apache.org arrow]

| align="center" | tools

| <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" | -

| <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" | phys

| <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" | -

| <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" | bio

| <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" | [https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ gromacs-ramd]

| align="center" | chem

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| align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]

| align="center" | [https://github.com/NanoComp/harminv harminv]

| align="center" | math

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. Homepage: https://github.com/NanoComp/harminv URL: https://github.com/NanoComp/harminv Keyword:math<br /><br /><br /></div>

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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]

| align="center" | bio

| <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" | tools

| 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" | 1.1.0

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| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9]

| align="center" | 5.5.2.5

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ URL: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>

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| align="center" | [http://www.lstc.com/products/ls-opt ls-opt]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>

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| align="center" | tools

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| align="center" | [https://grimme-lab.github.io/mctc-lib mctc-lib]

| align="center" | bio

| align="center" | 1.2.9

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| align="center" | [http://meme-suite.org meme]

| <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" | -

| align="center" | 1.0.2

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| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]

| align="center" | chem

| align="center" | 3.1.1

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| align="center" | [https://openbabel.org openbabel-omp]

| align="center" | chem

| align="center" | 3.1.1

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| align="center" | [http://www.openblas.net/ openblas]

| align="center" | [http://openmm.org openmm]

| align="center" | chem

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| align="center" | [http://openmm.org openmm-alphafold]

| align="center" | [http://www.openmx-square.org/ openmx]

| align="center" | chem

| <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://www.cog-genomics.org/plink/2.0/ plink]

| align="center" | bio

| <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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| <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>

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| align="center" | chem

| align="center" | 3.1.1, 4.0.0

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| align="center" | [https://repast.github.io/ repasthpc]

| align="center" | [https://www.htslib.org/ samtools]

| align="center" | bio

| <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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| align="center" | -

| align="center" | 8.6.1.6

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| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]