Modules sse3: Difference between revisions

| align="center" | phys

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. Homepage: http://www.simulia.com/products/abaqus_fea.html URL: http://www.simulia.com/products/abaqus_fea.html Keyword:phys<br /><br /></div>

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| align="center" | chem

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Homepage: http://www.abinit.org/ URL: http://www.abinit.org/ Keyword:chem<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe URL: https://software.intel.com/intel-advisor-xe Keyword:tools<br /><br /></div>

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| align="center" | phys

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| <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 /></div>

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| <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<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Homepage: https://ant.apache.org/ URL: https://ant.apache.org/ Keyword:tools<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: http://bazel.io/ Keyword:tools<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants - Homepage: http://www.htslib.org/ Keyword:bio<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: http://www.bioperl.org/ Extensions: DBD::mysql-4.050, DBD::Pg-3.8.1, Devel::CheckLib-1.13, Devel::Cycle-1.12, IO::CaptureOutput-1.1104, PadWalker-2.3, Spiffy-0.46, Test::Base-0.89, Test::Memory::Cycle-1.06, Test::RequiresInternet-0.05, Test::Weaken-3.022000, Test::YAML-1.07, XML::DOM::XPath-0.14, XML::Filter::BufferText-1.01, XML::Parser-2.44, XML::RegExp-0.04, XML::XPathEngine-0.14, YAML-1.29 Keyword:bio<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. Homepage: http://blast.ncbi.nlm.nih.gov/ URL: http://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. - Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Homepage: https://github.com/marbl/canu Keyword:bio<br /><br /></div>

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| align="center" | geo

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm1.2/ URL: http://www.cesm.ucar.edu/models/cesm1.2/ Keyword:geo<br /><br /></div>

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| align="center" | vis

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// URL: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// Keyword:vis<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. Homepage: https://www.cgal.org/ URL: https://www.cgal.org/ Keyword:math<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. Homepage: https://www.cmake.org URL: https://www.cmake.org Keyword:tools<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Run VS Code on any machine anywhere and access it in the browser. Homepage: https://github.com/cdr/code-server URL: https://github.com/cdr/code-server<br /><br /></div>

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| align="center" | phys

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| <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 /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/ URL: https://cromwell.readthedocs.io/ Keyword:tools<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit URL: https://developer.nvidia.com/cuda-toolkit Keyword:tools<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn URL: https://developer.nvidia.com/cudnn Keyword:math<br /><br /></div>

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| align="center" | tools

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| <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 /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com URL: http://www.allinea.com<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com URL: http://www.allinea.com<br /><br /></div>

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| align="center" | -

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. Homepage: https://github.com/dellytools/delly URL: https://github.com/dellytools/delly<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Homepage: https://github.com/nanoporetech/dorado URL: https://github.com/nanoporetech/dorado<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime. Homepage: https://www.microsoft.com/net/ URL: https://www.microsoft.com/net/<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org/index.php?title=Main_Page URL: https://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: https://elpa.rzg.mpg.de URL: https://elpa.rzg.mpg.de Keyword:math<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings. Homepage: https://energyplus.net/downloads URL: https://energyplus.net/downloads<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) Homepage: http://expat.sourceforge.net/ URL: http://expat.sourceforge.net/ Keyword:tools<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: http://www.fftw.org URL: http://www.fftw.org Keyword:math<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: http://www.fftw.org URL: http://www.fftw.org Keyword:math<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/<br /><br /></div>

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| align="center" | chem

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS is built with Intel compilers and IntelMPI. It includes experimental MU CoupledCluster theory code. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools<br /><br /></div>

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| align="center" | phys

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: http://geant4.cern.ch/ URL: http://geant4.cern.ch/ Keyword:phys<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools<br /><br /></div>

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| align="center" | vis

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm URL: https://github.com/g-truc/glm Keyword:vis<br /><br /></div>

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| align="center" | tools

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: https://www.golang.org URL: https://www.golang.org Keyword:tools<br /><br /></div>

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| align="center" | chem

| align="center" | [[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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. Homepage: https://www.gnu.org/software/gsl/ URL: https://www.gnu.org/software/gsl/ Keyword:math<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile Keyword:tools<br /><br /></div>

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| align="center" | math

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| align="center" | [http://www.hdfgroup.org/h4toh5/ h4toh5]

| align="center" | io

| align="center" |  

| <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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io<br /><br /></div>

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| align="center" | io

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| <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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix - Homepage: http://www.htslib.org/ Keyword:bio<br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. Homepage: https://www.open-mpi.org/projects/hwloc/ URL: https://www.open-mpi.org/projects/hwloc/<br /><br /></div>

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| align="center" | bio

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html URL: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio<br /><br /></div>

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| align="center" | math

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ URL: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ URL: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br /><br /></div>

|-

| align="center" | mpi

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI. Note: like Open MPI, this module's mpicc calls the toolchain compiler. mpiicc calls icc, and mpigcc calls gcc, and similar for C++ and Fortran. Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <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 /></div>

|-

| align="center" | -

| align="center" |  

| <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 /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. Homepage: https://software.intel.com/en-us/articles/intel-ipp/ URL: https://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools<br /><br /></div>

|-

| align="center" | -

| align="center" |  

|-

| align="center" | [http://www.iqtree.org/ iq-tree]

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. Homepage: https://software.intel.com/en-us/intel-trace-analyzer/ URL: https://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <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: https://openjdk.java.net URL: https://openjdk.java.net Keyword:tools<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.genome.umd.edu/jellyfish.html URL: http://www.genome.umd.edu/jellyfish.html Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org URL: http://julialang.org Keyword:tools<br /><br /></div>

|-

| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-INTEL, -USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /></div>

|-

| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. It can be coupled to various programs. The following packages are not included within this version: -MSCG, -GPU, -KOKKOS, -KIM, -USER-QUIP, -USER-VTK, -QEQ, -USER-ATC, -MANYBODY Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /></div>

|-

| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc URL: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools<br /><br /></div>

|-

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. Homepage: http://lstc.com/products/ls-prepost URL: http://lstc.com/products/ls-prepost<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <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: https://www.mathworks.com/products/matlab URL: https://www.mathworks.com/products/matlab Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <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 /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html URL: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: http://www.mono-project.com/ URL: http://www.mono-project.com/ Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools<br /><br /></div>

|-

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Homepage: https://www.nektar.info/ Keyword:math<br /><br /></div>

|-

| align="center" | io

| align="center" |  

|-

| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /></div>

|-

| align="center" | io

| align="center" |  

|-

| align="center" | [http://www.lysator.liu.se/~nisse/nettle/ nettle]

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/<br /><br /></div>

|-

| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page URL: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page Keyword:chem<br /><br /></div>

|-

| align="center" | math

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: https://xianyi.github.com/OpenBLAS/ URL: https://xianyi.github.com/OpenBLAS/ Keyword:math<br /><br /></div>

|-

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: http://www.openexr.com/ Keyword:vis<br /><br /></div>

|-

| align="center" | phys

| align="center" |  

|-

| align="center" | [http://www.extend-project.de/ openfoam-extend]

| align="center" | vis

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: https://openimageio.org/ URL: https://openimageio.org/ Keyword:vis<br /><br /></div>

|-

| align="center" | mpi

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi<br /><br /></div>

|-

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/<br /><br /></div>

|-

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU's massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix<br /><br /></div>

|-

| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ URL: http://cec.mpg.de/forum/ Keyword:chem<br /><br /></div>

|-

| align="center" | vis

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.6, python/3.7, python/3.8 Keyword:vis<br /><br /></div>

|-

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.111, Algorithm::Diff-1.1903, aliased-0.34, AnyEvent-7.17, App::Cmd-0.331, App::cpanminus-1.7044, AppConfig-1.71, Archive::Extract-0.86, Array::Utils-0.5, Authen::SASL-2.16, AutoLoader-5.74, B::Hooks::EndOfScope-0.24, B::Lint-1.20, boolean-0.46, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, Class::Accessor-0.51, Class::Data::Inheritable-0.08, 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::Singleton-1.5, Class::Trigger-0.14, Clone-0.43, Clone::Choose-0.010, Config::General-2.63, Config::INI-0.025, Config::MVP-2.200011, Config::Tiny-2.24, constant-1.33, CPANPLUS-0.9906, Crypt::DES-2.07, Crypt::Rijndael-1.14, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.23, Data::Dumper-2.173, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.110, Data::Section-0.200007, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.224, Date::Handler-1.2, Date::Language-2.32, DateTime-1.52, DateTime::Locale-1.25, DateTime::TimeZone-2.38, DateTime::Tiny-1.07, DBD::SQLite-1.64, DBI-1.643, DBIx::Admin::TableInfo-3.03, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.14, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.005, Devel::StackTrace-2.04, Digest::HMAC-1.03, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.014, Email::Date::Format-1.005, Encode-3.04, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.44, Expect-1.35, Exporter-5.74, Exporter::Declare-0.114, Exporter::Tiny-1.002001, ExtUtils::CBuilder-0.280234, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.21, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.44, ExtUtils::ParseXS-3.35, 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-1.15, File::Grep-0.02, File::HomeDir-1.004, File::Listing-6.04, File::Next-1.18, File::Path-2.16, File::pushd-1.016, File::Remove-1.58, File::ShareDir-1.116, File::ShareDir::Install-0.13, File::Slurp-9999.30, File::Slurp::Tiny-0.004, File::Slurper-0.012, File::Spec-3.75, File::Temp-0.2309, File::Which-1.23, Font::TTF-1.06, Getopt::Long-2.51, Getopt::Long::Descriptive-0.105, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9704, Graph::ReadWrite-2.09, Hash::Merge-0.300, HTML::Entities::Interpolate-1.10, HTML::Form-6.07, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.07, HTTP::Cookies-6.08, HTTP::Daemon-6.06, HTTP::Date-6.05, HTTP::Negotiate-6.01, HTTP::Request-6.22, HTTP::Tiny-0.076, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, IO::File-1.42, IO::Handle-1.42, IO::HTML-1.001, IO::Seekable-1.42, IO::Select-1.42, IO::Socket-1.42, IO::Socket::SSL-2.067, IO::String-1.08, IO::Stringy-2.113, IO::Tty-1.14, IPC::Cmd-1.04, IPC::Run-20180523.0, IPC::Run3-0.048, JSON-4.02, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.16, List::MoreUtils-0.428, List::SomeUtils-0.58, List::Util-1.54, List::UtilsBy-0.11, Locale::Maketext::Simple-0.21, Log::Dispatch-2.69, Log::Dispatchouli-2.019, Log::Handler-0.88, Log::Log4perl-1.49, Log::Message-0.08, Log::Message::Simple-0.10, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.07, LWP::Simple-6.43, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::VecStat-0.08, MCE::Mutex-1.866, Meta::Builder-0.004, MIME::Base64-3.15, MIME::Lite-3.031, MIME::Types-2.17, Mixin::Linewise::Readers-0.108, Mock::Quick-1.111, Module::Build-0.4231, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.19, Module::CoreList-5.20200314, Module::Implementation-0.09, Module::Install-1.19, Module::Load-0.34, Module::Load::Conditional-0.70, Module::Metadata-1.000037, Module::Pluggable-5.2, Module::Runtime-0.016, Moo-2.003006, Moose-2.2012, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.005, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.200002, MooseX::Types-0.50, MooseX::Types::Perl-0.101343, Mouse-v2.5.9, Mozilla::CA-20180117, MRO::Compat-0.13, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.11, Net::HTTP-6.19, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.88, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.17, Package::Stash-0.38, Package::Stash::XS-0.29, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.07, Params::Validate-1.29, Params::ValidationCompiler-0.30, parent-0.238, Parse::RecDescent-1.967015, Path::Tiny-0.112, PDF::API2-2.037, Perl::OSType-1.010, PerlIO::utf8_strict-0.007, Pod::Elemental-0.103005, Pod::Escapes-1.07, Pod::Eventual-0.094001, Pod::LaTeX-0.61, Pod::Man-4.14, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.40, Pod::Weaver-4.015, Readonly-2.05, Regexp::Common-2017060201, Role::HasMessage-0.006, Role::Identifiable::HasIdent-0.007, Role::Tiny-2.001004, Scalar::List::Utils-1.54, Scalar::Util-1.54, Scalar::Util::Numeric-0.40, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, Socket-2.029, Software::License-0.103014, Specio-0.46, SQL::Abstract-1.86, SQL::Statement-1.412, Statistics::Basic-1.6611, Statistics::Descriptive-3.0702, Storable-3.15, strictures-2.000006, String::Flogger-1.101245, String::RewritePrefix-0.008, String::Truncate-1.100602, Sub::Exporter-0.987, Sub::Exporter::ForMethods-0.100052, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Install-0.928, Sub::Name-0.26, Sub::Quote-2.006006, Sub::Uplevel-0.2800, Sub::Uplevel-0.2800, SVG-2.84, Switch-2.17, Template-3.007, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.36, Term::UI-0.46, Test-1.26, Test::ClassAPI-1.07, Test::Deep-1.130, Test::Differences-0.67, Test::Exception-0.43, Test::Fatal-0.014, Test::Harness-3.42, Test::LeakTrace-0.16, Test::More-1.302172, Test::Most-0.35, Test::NoWarnings-1.04, Test::Output-1.031, Test::Pod-1.52, Test::Requires-0.10, Test::RequiresInternet-0.05, Test::Simple-1.302172, Test::Version-2.09, Test::Warn-0.36, Test::Warnings-0.029, Text::Aligner-0.13, Text::Balanced-2.03, Text::CSV-2.00, Text::Diff-1.45, Text::Format-0.61, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.30, Text::Soundex-3.05, Text::Table-1.133, Text::Template-1.58, Thread::Queue-3.13, Throwable-0.200013, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9760, Time::Local-1.30, Time::Piece-1.34, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.31, Try::Tiny-0.30, UNIVERSAL::moniker-0.08, URI-1.76, URI::Escape-3.31, version-0.9924, 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::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::XPath-1.44, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.73 Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/ URL: http://www.pgroup.com/<br /><br /></div>

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| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

|-

| align="center" | [http://www.well.ox.ac.uk/platypus platypus]

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio<br /><br /></div>

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| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: http://www.plumed-code.org Keyword:chem<br /><br /></div>

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| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Keyword:tools<br /><br /></div>

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| align="center" | geo

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: http://trac.osgeo.org/proj/ URL: http://trac.osgeo.org/proj/ Keyword:geo<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0 Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html URL: https://pypy.org/index.html Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/ URL: http://python.org/ Extensions: gnureadline-8.0.0, pip-19.3.1, setuptools-41.6.0, virtualenv-16.7.7, wheel-0.33.6 Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Keyword:tools<br /><br /></div>

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| align="center" | chem

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: https://www.quantum-espresso.org URL: https://www.quantum-espresso.org Keyword:chem<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ URL: http://www.r-project.org/ Keyword:tools<br /><br /></div>

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| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ReFrame is a framework for writing regression tests for HPC systems. Homepage: https://github.com/eth-cscs/reframe URL: https://github.com/eth-cscs/reframe Compatible modules: python/3.8.10, python/3.9.6, python/3.10.2 Extensions: attrs-21.4.0, certifi-2021.10.8, chardet-4.0.0, idna-3.3, importlib_resources-5.7.1, jsonschema-4.4.0, pyrsistent-0.18.1, reframe-3.12.0, requests-2.27.1, semver-2.13.0, urllib3-1.26.9, zipp-3.8.0<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: http://root.cern.ch/drupal/ URL: http://root.cern.ch/drupal/ Keyword:tools<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Homepage: https://lomereiter.github.io/sambamba/ URL: https://lomereiter.github.io/sambamba/ Keyword:bio<br /><br /></div>

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| align="center" | bio

| align="center" |  

| <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: http://www.htslib.org/ URL: http://www.htslib.org/ Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ URL: http://www.scala-sbt.org/ Keyword:tools<br /><br /></div>

|-

| align="center" | math

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Keyword:math<br /><br /></div>

|-

| align="center" | math

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: https://gforge.inria.fr/projects/scotch/ URL: https://gforge.inria.fr/projects/scotch/ Keyword:math<br /><br /></div>

|-

| align="center" | -

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ URL: https://www.seqan.de/<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: https://pcingola.github.io/SnpEff/ URL: https://pcingola.github.io/SnpEff/ Keyword:bio<br /><br /></div>

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| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ URL: http://cab.spbu.ru/software/spades/ Keyword:bio<br /><br /></div>

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| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools<br /><br /></div>

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| align="center" |  

| align="center" | 0.9.0

|-

| align="center" | [https://github.com/hall-lab/speedseq speedseq]

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std Keyword:bio<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://catchenlab.life.illinois.edu/stacks/ Keyword:bio<br /><br /></div>

|-

| align="center" | phys

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This verison uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /></div>

|-

| align="center" | phys

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /></div>

|-

| align="center" | math

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu URL: http://su2.stanford.edu Keyword:math<br /><br /></div>

|-

| align="center" | math

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. - Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools<br /><br /></div>

|-

| align="center" | ai

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. - Homepage: http://trinityrnaseq.github.io/ Keyword:bio<br /><br /></div>

|-

| align="center" | bio

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/ Keyword:bio<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune Profiler is a performance analysis tool for C, C++, C#, Fortran, Java, Python, Go, DPC++, and OpenCL. Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html Keyword:tools<br /><br /></div>

|-

| align="center" | tools

| align="center" |  

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. Homepage: http://xerces.apache.org/xerces-c/ URL: http://xerces.apache.org/xerces-c/ Keyword:tools<br /><br /></div>

|-