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://ambermd.org/AmberTools.php ambertools]

| align="center" | chem

| <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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| 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://github.com/infphilo/centrifuge centrifuge]

| align="center" | bio

| <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" | 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" | -

| align="center" | 3.0.4, 3.2.0, 3.3.1, 3.4.4

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| align="center" | [http://www.flintlib.org/ flint]

| 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" | -

| align="center" | 3.3.2, 3.3.8

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| align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm]

| 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" | chem

| align="center" | 2021.7-0.5.1

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| align="center" | [https://www.gnu.org/software/gsl/ gsl]

| 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" | [https://www.mathworks.com/products/compiler/mcr/ mcr]

| align="center" | tools

| 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" | 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" | [https://mmseqs.com mmseqs2]

| align="center" | -

| <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" | [https://www.openfoam.com/ openfoam]

| align="center" | phys

| Documentation: [[OpenFOAM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys<br /><br /><br /></div>

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| 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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| align="center" | [http://www.portaudio.com/ portaudio]

| align="center" | -

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

| <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" | -

| align="center" | 8.6.1.6

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