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Scientific Applications

A++/P++ A++ and P++ are both C++ array class libraries, providing the user with array objects to simplify the development of serial and parallel numerical codes.
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.
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.
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.
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.
AUTO-07p AUTO is a software for continuation and bifurcation problems in ordinary differential equations
autostem calculate 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.
BEAGLE an application programming interface (API) and library for high-performance statistical phylogenetic inference - See more at: http://gpuscience.com/articles/beagle-an-application-programming-interface-and-hpc-library-for-statistical-phylogenetics/#sthash.VLcZRaIV.dpuf
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-format-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.
boost 1.53 Boost provides free peer-reviewed portable C++ source libraries.
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-release                 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to 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.
chimeraslayer-4.29.2010-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.
clearcut-1.0.9-release            Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ)
Clustal W 2.1 Clustal W is a general purpose multiple alignment program for DNA or proteins.
Cogent Cogent is a toolkit for statistical analysis of biological sequences.
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.
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
CULA R11, R14, sparse CULA™ is an implementation of the Linear Algebra PACK-age (LAPACK) interface for CUDA™-enabled NVIDIA® graphics processing units (GPUs).
cytoscape-2.7.0-release           Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
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.
drisee-1.2-release              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.
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.
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.
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).
gamess GAMESS is a program for ab initio molecular quantum chemistry. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.
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.
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,...).
gg_otus-4feb2011-release   GreenGenes OTU picker module for Qiime
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.
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.
GPUmat4 GPUmat allows standard MATLAB code to run on GPUs. The engine is written in C/C++ and based on NVIDIA CUDA.
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.
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.
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 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-release  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).
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.
Intel Memory Configuration Tool This application assists in finding optimal memory configurations for Intel ® Xeon ® Processor series platforms.
iPython Python is an easy to learn, powerful programming language. It has efficient high-level data structures and a simple but effective approach to object-oriented programming. Python’s elegant syntax and dynamic typing, together with its interpreted nature, make it an ideal language for scripting and rapid application development in many areas on most platforms.The Python interpreter and the extensive standard library are freely available in source or binary form for all major platforms from the Python Web site, http://www.python.org/, and may be freely distributed. The same site also contains distributions of and pointers to many free third party Python modules, programs and tools, and additional documentation.
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.
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.
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.
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.
magma 1.0.0 MAGMA provides implementations for CUDA, OpenCL, and Intel Xeon Phi.
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
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.
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.
mothur 1.29 This 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.
mpi4py Provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
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.
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.
mpqc 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.
mrbayes 3.1.2, 3.2 MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
MSAProbs MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities.
muscle-3.8.31-release      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.
mvapich2 MVAPICH2 (MPI-3 over InfiniBand) is an MPI-3 implementation based on MPICH ADI3 layer.
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
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.
NetLogo NetLogo is a programmable modeling environment for simulating natural and social phenomena.
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.
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.
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.
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.
openFOAM 2.1.1 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.
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.
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.
Pandaseq PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing.
paraview 3.12 ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.
parsinsert-1.0.4-release    ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.
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.
pplacer-1.1-release         Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
pprospector-1.0.1-release   Primer Prospector is a pipeline of programs to design and analyze PCR primers.
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.
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.
qchem 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.
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).
qrupdate Library for updating of QR and Cholesky decompositions
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.
QUAST 2.2 QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.
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. a
raxml-7.3.0-release         RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments.
rdpclassifier-2.2-release                       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
Roche 454 (2 versions) Analysis software for 454 Sequencing
ROMS 3.6 ROMS illustrates various computational pathways: standalone or coupled to atmospheric and/or wave models.
rtax-0.981-release RTAX is specifically designed for assigning taxonomy to paired-end reads, but additionally works on single-end reads
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.
sphinx-1.0.4-release Sphinx is a tool that makes it easy to create documentation for Python projects
SQLAlchemy-0.7.1-release 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.
suitesparse Mathematic packages for Matlab and Metis
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.
terachem TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.
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.
Tornado Tornado is a Python web framework and asynchronous networking library
trilinos 11.0 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.
turbomole TURBOMOLE has been designed for robust and fast quantum chemical applications.
uclust-1.2.22-release Extreme High-speed Sequence Clustering, Aligment and Database Search
vienna-1.8.4-release A package for RNA secondary structure prediction and comparison
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.
vmd 1.9 VMD incorporates many new improvements for high quality rendering and export of molecular scenes, new analysis features, support for new molecular data file formats, and many performance improvements. Many new and updated structure building and analysis tools have been added in this release, easing the process of preparing, running, and analyzing biomolecular simulations. This release also contains many performance and efficiency improvements that are particiularly beneficial for modeling, visualizing, and analyzing very large structures with up to 100 million atoms. VMD makes extensive use of multi-core processors and GPU acceleration to speed up computationally demanding analysis and visualization tasks including key structure and trajectory analysis features, interactive molecular dynamics, and high-quality ray tracing of molecular scenes. VMD now takes advantage of multiple GPUs for very fast display of molecular orbitals arising in quantum chemistry calculations.
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.
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.
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.