Scientific Applications

Bioinformatics

A5pipeline – A5 is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running A5.

Afni – AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data

Ampliconnoise 1.25 – AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps: the removal of noise from the sequencing itself and the removal of PCR point errors.

ANTs – Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging.

bam2fastq – The BAM format is an efficient method for storing and sharing data from modern, highly parallel sequencers

BEAGLE – an application programming interface (API) and library for high-performance statistical phylogenetic inference.

BEAST 1.6.1 – BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.

Bioconductor – Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

BIOM 0.9.3 –  The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample.

Biopython – Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

BLAST 2.2.25, .26, .28 – Basic Local Alignment Search Tool is a sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query.

BLAT 3.5 – BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.

Bowtie 0.12.9, 2.0.6 – Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

BWA 0.7.0 – BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

cdbtools 10.11.2010 release – CDB (Constant DataBase) indexing and retrieval tools for multi-FASTA files

cdhit 3.1 – significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.

cghub – The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects.

checkm – Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Chimeraslayer 4.29.10 release – Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: (A) the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera; (B) candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence; the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences; and (D) an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences.

Circos – Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations.

clearcut 1.0.9 – Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ)

CLUSTALW 2.1 – CLUSTALW is a general purpose multiple alignment program for DNA or proteins.

Cogent 1.5.3 – Cogent is a toolkit for statistical analysis of biological sequences.

DRISEE 1.2 – DRISEE is a tool that utilizes artifactual duplicate reads (ADRs) to provide a platform independent assessment of sequencing error in metagenomic (or genomic) sequencing data. DRISEE is designed to consider shotgun data.

DSSP – DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)

Emirge – EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

exonerate 2.2 – exonerate is a generic tool for pairwise sequence comparison.It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

FastQC – FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines

FastTree – FastTree is open-source software that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

FreeSurfer – FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data

FSL – FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

GATK – The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data

gg_otus 4feb2011-release – GreenGenes OTU picker module for Qiime

GraPhlAn – GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees

HMMER – biosequence analysis using profile hidden Markov models

Homer – HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis

HT-Seq – HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

IDBA-UD – IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm.

IMa2 8.27.12 release – an implementation of the MCMC method for the analysis of genetic data under the Isolation with Migration model of population divergence. IMa2 applies this model to genetic data drawn from a pair of closely related populations or species. The results are estimates of the marginal posterior probability densities for each of the model parameters.

Infernal 1.0.2 – Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

LAMMPS – LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) 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.

LIBSVM 3.0 – LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.

MaSuRCA 2.0.0 – MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads

MeGAMerge – MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

Mothur 1.29 – his project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It has incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, they have added a number of other features including calculators and visualization tools.

mpiBLAST 1.6 – mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors.

MUMmer – MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

MUSCLE 3.8.31 – MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds.

MuTect – MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Pandaseq – PAired-eND Assembler for DNA sequences

ParsInsert 1.0.4 – ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

Paup – PAUP version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees

Picard – A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats

Plink – Whole genome association analysis toolset

Popoolation – PoPoolation is a pipeline for analysing pooled next generation sequencing data

pplacer 1.1 – Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

pprospector 1.1 – Primer Prospector is a pipeline of programs to design and analyze PCR primers.

Prodigal – Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

Prottest 3.2 – ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

Qiime – QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).

QUAST 2.2 – QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.

RAxML 7.3.0 – RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments.

rdpclassifier 2.2 – The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment

RTAX 0.981 – RTAX is specifically designed for assigning taxonomy to paired-end reads, but additionally works on single-end reads

Samtools – SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments

SnpEff – Genetic variant annotation and effect prediction toolbo

SOAPdenovo 2.04 – SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

SPAdes 2.5.0 – SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

SRA Toolkit – The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

STAR – RNAseq aligner

subread – The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program

TopHat – TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

trilinos 11 – The Trilinos Project is an effort to develop and implement robust algorithms and enabling technologies using modern object-oriented software design, while still leveraging the value of established libraries such as PETSc, Metis/ParMetis, SuperLU, Aztec, the BLAS and LAPACK. It emphasizes abstract interfaces for maximum flexibility of component interchanging, and provides a full-featured set of concrete classes that implement all abstract interfaces.

Trinity – Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, 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. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

uclust 1.2.22 – Extreme High-speed Sequence Clustering, Aligment and Database Search

VCFtools – VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project

vienna 1.8.4 – A package for RNA secondary structure prediction and comparison

wgs – Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.

YASM – Yasm is a complete rewrite of the NASM assembler under the “new” BSD License

Chemistry/Materials Engineering

ADINA 8.7 – The ADINA System offers a one-system program for comprehensive finite element analyses of structures, fluids, heat transfer, electromagnetics and multiphysics.

Amber 11 – “Amber” refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

ATAT – ATAT is a generic name that refers to a collection of alloy theory tools

autostem – Calculates high resolution (atomic or near atomic) conventional and scanning transmission electron microscope (CTEM and STEM) images of thin specimens from first principles using the multislice method for electrons (with simplifying assumptions for the interactive versions) in the energy range of approximately 100 keV to 1OOO keV.

CALYPSO – (Crystal structure AnaLYsis by Particle Swarm Optimization) is an efficient structure prediction method and its same-name computer software

CFD-ACE – engineering design and analysis tool

delft3d 4.0, 5.0 – Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.

DiffPy – A free and open source software project to provide python software for diffraction analysis and the study of the atomic structure of materials.

gaussian 09 – Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments.

gromacs 4.6.1, 4.6.3, 5.0 – GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

LAMMPS – LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) 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.

molden – Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density.

mpcq 2.3.1 – MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from single many-core computers to massively parallel computers. Its design is object oriented, using the C++ programming language.

NAMD 2.83, 2.9 – a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR

NWchem 6.0 – NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

openMM 3.1.1 – OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. Itprovides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.

Pencil-Code – The Pencil Code is a high-order finite-difference code for compressible hydrodynamic flows with magnetic fields

Phono3py – This software calculates phonon-phonon interaction related properties

q-chem 4.0, 4.0.1 – Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra. The new release of Q-Chem 4 represents the state-of-the-art of methodology from the highest performance DFT/HF calculations to high level post-HF correlation methods

qhull – Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.

quantum espresso 4.3.2, 5.0.2 – An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

TeraChem – TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.

TURBOMOLE – TURBOMOLE has been designed for robust and fast quantum chemical applications.

Zephyr 2.0.3 – The current release of OpenMM Zephyr enables acceleration of molecular dynamics on specific NVIDIA and ATI GPU cards and operating systems.


Mathematics

ACML 4.4.0, 5.0.0 – ACML provides a free set of thoroughly optimized and threaded math routines for HPC, scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more.

Armadillo – Armadillo is a high quality C++ linear algebra library, aiming towards a good balance between speed and ease of use; the syntax (API) is deliberately similar to Matlab

AUTO 07p – AUTO is a software for continuation and bifurcation problems in ordinary differential equations

COMSOL 4.3 – COMSOL Multiphysics is a finite element analysis, solver and Simulation software / FEA Software package for various physics and engineering applications, especially coupled phenomena, or multiphysics. COMSOL Multiphysics also offers an extensive interface to MATLAB and its toolboxes for a large variety of programming, preprocessing and postprocessing possibilities.

CULA R11, R14, sparse – CULA™ is an implementation of the Linear Algebra PACK-age (LAPACK) interface for CUDA™-enabled NVIDIA® graphics processing units (GPUs).

fftw 2.1.5, 3.2.2, 3.3 – 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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

GPUmat4 – GPUmat allows standard MATLAB code to run on GPUs. The engine is written in C/C++ and based on NVIDIA CUDA.

Matlab R2008b, R2010b, R1011a, R2012a – MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications.

Metis 4.0 – METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.

Octave 3.2.4 – GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.

openFOAM – OpenFOAM is first and foremost a C++ library, used primarily to create executables, known as applications. The applications fall into two categories: solvers, that are each designed to solve a specific problem in continuum mechanics; and utilities, that are designed to perform tasks that involve data manipulation.

suitesparse – Mathematic packages for Matlab and Metis

wolfram mathematica 8 – Mathematica 8 introduces free-form linguistic input—a whole new way to compute. Enter plain English; get immediate results—no syntax required. It’s a new entry point into the complete Mathematica workflow, now upgraded with 500 additional functions and 7 application areas—including the world’s most advanced statistics capability and state-of-the-art image processing.

R 2.151, 3.0.1 – R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files.

qrupdate – Library for updating of QR and Cholesky decompositions


Development

A++/P++ -C++ array class libraries, providing the user with array objects to simplify the development of serial and parallel numerical codes.

boost 1.53 – Boost provides free peer-reviewed portable C++ source libraries.

CAFFEls  – Caffe is a deep learning framework

CUDA 4.2, 5 – CUDA (aka 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

GCC 4.5.3, 4.6.2, 4.7.0, 4.7.1 – The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,…).

Globus 5.2.3 – The open source Globus® Toolkit is a fundamental enabling technology for the “Grid,” letting people share computing power, databases, and other tools securely online across corporate, institutional, and geographic boundaries without sacrificing local autonomy.

glog – C++ implementation of the Google logging module

gflags – Google Commandline Flags

glpk 4.4.5 – The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

GMAC 1.1.1 – GMAC is a user-level library that implements an Asymmetric Distributed Shared Memory model to be used by CUDA programs. An ADSM model allows CPU code to access data hosted in accelerator (GPU) memory.

gmp 4.3.2 – GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface.

hdf5 1.8.4, 1.8.6 – 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.

Intel compiler 11.1-059, 11.1-072, 12.1.5, 13.0.1, 13.1.0 – The Intel® Composer XE suites are available in several configurations that combine industry leading C, C++ and Fortran compilers, programming models including Intel® Cilk™ Plus and OpenMP*, performance libraries including Intel® Math Kernel Library (Intel® MKL), Intel® Integrated Performance Primitives (Intel® IPP) and Intel® Threading Building Blocks (Intel® TBB) for leadership application performance on systems using Intel® Core™ and Xeon® processors, Intel® Xeon Phi™ coprocessors and compatible processors.

Java developer kit 1.6, 1.7 – For Java Developers. Includes a complete JRE plus tools for developing, debugging, and monitoring Java applications.

Jinja2 – Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.

libjacket 1.1 – a broad and fast C/C++ library for GPU computing. With over 500 C/C++ functions, LIBJACKET represents the largest GPU computing library in the world. This CUDA-based library integrates seamlessly in any application enabling optimized utilization of NVIDIA CUDA-capable GPUs, including powerful Tesla compute devices.

lmdb – An Erlang NIF for the “Lightening MDB” BTREE used in OpenLDAP

Magma 1.0.0 – MAGMA provides implementations for CUDA, OpenCL, and Intel Xeon Phi.

mpi4py – Provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

mpiCH2 – MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs, and massively parallel processors. It also provides a vehicle for MPI implementation research and for developing new and better parallel programming environments.

mvapich2 – MVAPICH2 (MPI-3 over InfiniBand) is an MPI-3 implementation based on MPICH ADI3 layer.

netcdf 3.6.3, 4.1.1 – NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Numpy – NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

open64 4.2.2.2 – Open64 has been well-recognized as an industrial-strength production compiler.  It is the final result of research contributions from a number of compiler groups around the world. Formerly known as Pro64, Open64 was initially created by SGI from SGI’s MIPSPro compiler,  and licensed under the  GNU Public License (GPL v2).

opencurrent 1.1 – OpenCurrent is an open source C++ library for solving Partial Differential Equations (PDEs) over regular grids using the CUDA platform from NVIDIA.

OpenCV – OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library

openmpi 1.6.1 – The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

PGI 12.9 – PGI® Workstation: PGI’s suite of compilers and toolsPGI Workstation™ is PGI’s single-user scientific and engineering compilers and tools product.

Pygments – Pygments is a generic syntax highlighter for general use in all kinds of software such as forum systems, wikis or other applications that need to prettify source code.

Pynast – PyNAST is a reimplementation of NAST, introducing new features that increase its portability and flexibility. Its availability as an open source application with three convenient interfaces will allow the application of the NAST algorithm on a wider basis, to larger datasets, and in novel domains.

Python 2.7.2, 2.7.3, 2.7.5, 3.2.1, 3.2.3 – Python is a remarkably powerful dynamic programming language that is used in a wide variety of application domains. Python is often compared to Tcl, Perl, Ruby, Scheme or Java.

Pytz – PyTZ is a Python library that allows cross-platform and accurate timezone calculations.

Pyzmq – Pyzmq provides python bindings for ØMQ and allows you to leverage ØMQ in python applications.

rebar – Erlang build tool that makes it easy to compile and test Erlang applications, port drivers and releases.

sphinx 1.0.4 – Sphinx is a tool that makes it easy to create documentation for Python projects

SQLAlchemy 0.7.1 – SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. It provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.

sunstudio 12.1 – Sun Studio software includes compilers, libraries, and tools for application development in C, C++, and Fortran, on Solaris, OpenSolaris, and Linux systems, on SPARC and x86 platforms.

tornado – Tornado is a Python web framework and asynchronous networking library

visit 2.4.0, 2.5.2, 2.6.1 – VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

zmq – ØMQ (also seen as ZeroMQ, 0MQ, zmq) looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It’s fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. ØMQ is from iMatix and is LGPLv3 open source.