Scientific Supercomputing at the NIH

Scientific Applications

The applications below are labelled according to the platform on which they are available. The platforms include:

Helix [Helix] is the front-end machine for the Helix Systems at NIH, and is to be used for interactive and general computational tasks.

The NIH Biowulf cluster [Biowulf] is a Linux parallel processing system that is for computationally challenging and batch jobs. Most applications that run on Helix can also run on the Biowulf cluster. Helix users are required to register for a Biowulf account in order to use the cluster.

Web-based applications [Web]: The Helix Systems supports and develops a variety of web-based tools which are available to the intramural NIH community. Some tools require NIH authentication.

Sciware [Sciware] is an application service, where scientific applications are made available for running on your own desktop machine. The use of Sciware requires a Helix account.

Helix is the recommended system for interactive use, short or small numbers of jobs. Users who need to run computationally intensive or memory intensive jobs should apply for a Biowulf account. If you are unsure about which system is best suited to your needs or applications, contact the Helix staff at

Sequence Analysis

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InterProScan [Biowulf]

IPRScan is a tool that combines different protein signature recognition methods against multiple databases into one resource. These databases include PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR superfamily, SUPERFAMILY, Gene3D and PANTHER.

EMBOSS [Helix] [Biowulf] [Web]

EMBOSS (The European Molecular Biology Open Software Suite) is a nucleotide/protein sequence analysis package specially developed for the needs of the molecular biology user community. See also Equivalent tools for GCG programs.

Seaview [Helix]

is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows one to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.

Blast [Helix] [Biowulf]

Blast is a sequence database searching program which compares a nucleotide or protein query sequence against all sequences in a database.

Wu-Blast [Helix] [Biowulf]

WU-BLAST, developed at Washington University, is fast, gapped Blast with statistics, intended to find similarity between a query protein or DNA sequence and a sequence database.

BLAT [Helix] [Biowulf]

BLAT is a DNA/Protein Sequence Analysis program that is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. Available on Biowulf.

Fasta [Helix] [Biowulf] [Web]

The fasta program package contains many programs for searching DNA and protein databases and one program (prss) for evaluating statistical significance from randomly shuffled sequences.

RepeatMasker [Helix] [Biowulf]

Screens DNA sequences of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions

ClustalW [Helix] [Web: Multiple Alignment Workshop] [Sciware]

ClustalW is a general-purpose multiple alignment program for DNA or protein sequences.

Meme & Mast [Helix] [Biowulf]

Discover motifs in groups of DNA/protein sequences or databases.

RandFold [Helix] [Biowulf]

RandFold computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

HMMER [Helix] [Biowulf]

HMMER uses profile Hidden Markov models to perform sensitive database searching using statistical descriptions of a sequence family's consensus.

Sequence Format Converters [Helix & Biowulf]

These programs convert sequence data from one format to another.

MUMmer [Helix]

A system for aligning entire genomes extremely rapidly.

MFOLD [Helix] [Web]

MFOLD predicts DNA and RNA secondary structure.

DNAWorks [Web]

DNAWorks is a computer program that automates the design of oligonucleotides for gene synthesis by PCR-based gene assembly. The program requires simple input information: an amino acid sequence of the target protein or a DNA sequence, and a desired annealing temperature.

Sequence Assembly

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STADEN [Helix]

Staden is a package of programs in sequence assembly, mutation detection, sequence analysis, sequence trace and reading file manipulation, and Scripting utilities.

CAP3 & PCAP [Helix] [Biowulf]

CAP3 is a sequence assembly program for small-scale assembly of EST sequences with or without quality values. PCAP is for large-scale assembly of genomic sequences with quality values and with or without forward-reverse read pairs.

SOAP [Helix]

SOAP is a program package which provides full solution to next generation sequencing data analysis. Currently, it consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp) good for SNP. The indel finder ( SOAPindel ), structural variation scanner ( SOAPsv ) and de novo short reads assembler ( SOAPdenovo ) are joinging soon. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation ILLUMINA-SOLEXA sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping.

AMOS [Helix]

AMOS is not an assembler, rather a software infrastructure for developing assembly tools. However, AMOS indeed provides two assemblers: AMOScmp - a comparative assembler; and Minimus - a basic assembler for small datasets. It is important to realize that, with a little bit of programming, users can use AMOS to put together their own shotgun assembler customized for the specific characteristics of their data.

Phred Phrap/cross_match/swat Consed/autofinish [Helix]

The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. phrap is a program for assembling shotgun DNA sequence data. cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties. Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap.

MIRA [Helix]

MIRA is a Whole Genome Shotgun and EST Sequence Assembler. It is able to perform true hybrid de-novo assemblies and mapping assemblies of data from the 454 and Illumina/Solexa sequencing machines, either on their own or together with Sanger type sequencing data (hybrid mapping assemblies).

Velvet [Helix]

A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed at the EBI.

Linkage Analysis

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Allegro [Helix]

Allegro, a new computer program for multipoint linkage analysis, was decribed as a faster version of genehunter.

CRI-MAP [Helix]

Designed to allow rapid, largely automated construction of multilocus linkage maps.

Eigensoft [Helix]

The EIGENSOFT package combines functionality from our population genetics methods and our EIGENSTRAT stratification correction method.

Fastlink [Helix] [Biowulf]

FASTLINK is a software package to do the computations for genetic linkage analysis.

Fastslink [Helix] [Biowulf]

FASTSLINK is a general simulation program for linkage analysis

Floss [Helix]

FLOSS software package uses input and output files from the MERLIN linkage analysis package to perform an ordered subset analysis

GeneHunter [Helix]

GeneHunter provides wide range of analyses for performing linkage and disequilibrium analyses.

Loki [Helix][Biowulf]

Loki is a linkage analysis package, primarily for large and complex pedigrees, which uses Markov chain Monte Carlo (MCMC) techniques to avoid many of the computational problems that prevent exact computational methods being used for large pedigrees.

MACH 1.0 [Helix]

MACH 1.0 is a Markov Chain based haplotyper. It can be resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Mega2 [Helix]

A data-handling program for facilitating genetic linkage and association analyses

Mendel [Helix]

A comprehensive package for exact statistical genetic analysis of qualitative and quantitative traits.

Merlin [Helix] [Biowulf]

MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).

Metal [Helix]

The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

MrBayes [Biowulf]

MrBayes performs Bayesian estimation of phylogeny.

Pbat [Helix][Biowulf]

PBAT: Tools for the statistical analysis of family-based association studies (FBAT).

Pdt [Helix]

The PDT analysis program allows the user to evaluate evidence of linkage disequilibrium (LD) in general pedigree data.

Pedcheck [Helix]

Program for detecting marker typing incompatibilities in pedigree data.

PLINK [Helix] [Biowulf]

PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

PREST [Helix]

PREST is a program that detects pedigree errors by use of genome-screen data. PREST incorporates the EIBD, AIBS, IBS, and MLLR test statistics.

Recode [Helix]

This program was written to recode alphabeticly coded systems into numbered alleles. It also will recode numerically coded systems into numbered alleles.

Relpair [Helix]

that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample.

SAGE [Helix]

A collection of compiled programs that perform a wide variety of genetic analyses.

Snplink [Helix]

Multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.

SimWalk2 [Helix] [Biowulf]

SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree.

Solar [Helix] [Biowulf]

SOLAR is a program for multipoint, oligogenic, variance component linkage analysis in pedigrees of arbitrary size and complexity (Almasy L; Blangero J, 1998).

UnPhased [Helix]

A suite of programs for association analysis of multilocus haplotypes from unphased genotype data.

Vitesse [Helix]

VITESSE is a software package that computes likelihoods with the functionality of the LINKMAP and MLINK programs from LINKAGE.

Phylogenetic Analysis

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BEAST [Biowulf]

BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences.

Phylip [Helix] [Sciware]

A package of programs for inferring phylogenies (evolutionary trees). Includes methods for parsimony, distance matrix and likelihood methods.

PAUP [Helix]

PAUP* (Phylogenetic Analysis Using Parsimony) is a software package for inference of evolutionary trees.

PAML [Helix]

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Tree-Puzzle [Biowulf]

TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch.

Microarray Analysis

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Affymetrix Power Tools (APT) [Helix]

APT are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChipR arrays. APT programs are intended for "power users" who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality.

Bioconductor and R [Biowulf] [Sciware]

An open source and open development software project for the analysis and comprehension of genomic data. It is an add-on to the R statistical analysis language and environment.

MAT [Helix]

MAT is an algorithm to reliably detect regions enriched by transcription factor Chromatin ImmunoPrecipitation (ChIP) on Affymetrix tiling arrays (chip).

Systems Biology

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ExPlain [Web]

Analysis System promotes biological interpretation of high throughput experiments like microarrays, proteomic data, and ChIP-chip experiments. The intuitive workflow allows systematic creation of experimentally testable hypothesis for both gene transcription regulation and signalling networks. (NIH-only: requires an NIH domain username & password)

Biobase Knowledge Library (TransFac, TransPath and Proteome) [Web]

BKL Mammalian Suite of databases offers researchers easily accessible, up-to-date gene, protein or disease information that has been expertly curated from the published literature. Using the BioKnowledge Retriever tool, researchers can easily access comprehensive data and retrieve sets of relevant proteins based on their characteristics. BKL Mammalian plus ExPlain offers disease-related information presented in three categories: Biomarker, Therapeutic Target, and Molecular Mechanism. BKL signal transduction information is both detailed and comprehensive, providing step by step interaction details, pathway building capabilities, and pre-drawn canonical maps.

TrxFacMiner [Web]

A web-based interface that uses the Transfac database to report all known genes in the human genome that are near or overlap a chosen transcription activation factor binding site. (NIH-only: requires an NIH domain username & password)

Computational Chemistry

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AMBER [Biowulf]

AMBER is a package of molecular simulation programs.

APBS [Biowulf]

APBS (Adaptive Poisson-Boltzmann Solver) is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.

CHARMm [Biowulf]

CHARMm is a general and flexible software application for modeling the structure and behavior of molecular systems.

GAMESS [Biowulf]

GAMESS is a general ab initio quantum chemistry package.

Gaussian [Biowulf]

Gaussian is a connected system of programs for performing semiempirical and ab initio molecular orbital (MO) calculations.

GROMACS [Biowulf]

GROMACS is a versatile package to perform molecular dynamics.

LAMMPS [Biowulf]

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a Molecular Dynamics Simulator which can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.

NAMD [Biowulf]

NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available on both Helix and Biowulf.

Q-Chem [Biowulf]

An ab initio electronic structure program capable of performing first principles calculations on both the ground and excited states of molecules.

Molecular Modeling

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Autodock [Biowulf]

Autodock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Biodesigner [Sciware]

Biodesigner is a molecular modeling and visualization program for personal computers. The program is freely available for downloading. Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models.

HADDOCK [Biowulf]

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an approach for predicting protein-protein complex structures that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data.

PROSPECT [Biowulf] [Web]

PROSPECT is a threading-based protein structure prediction system.

Rosetta++ [Biowulf]

The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more...

CSRosetta [Biowulf]

Chemical-Shift-ROSETTA is a robust protocol to use NMR chemical shifts for de novo protein structure generation by SPARTA-based selection of protein fragments from the PDB, in conjunction with a regular ROSETTA Monte Carlo assembly and relaxation method.

RNAstructure [Sciware]

The core of RNAstructure is an implementation of the Zuker Algorithm to predict RNA secondary structures from sequence based on the principle of minimizing free energy. The thermodynamic data used for these predictions are the latest available from the Turner laboratory. Several modules are provided to extend the capabilities of the Zuker Algorithm and to make this a user-friendly RNA folding program.

Schrödinger [Helix] [Biowulf]

A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI on Helix.

ZDOCK [Biowulf]

ZDOCK predicts protein-docking models, and uses a fast Fourier transform to search all possible binding modes for proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics.

Nest [Biowulf]

Command-line homology model builder (written by Jason (Zhexin) Xiang) on par with MODELER. To use, type nest at the prompt. Nest can be used in conjuction with PROSPECT using


A small collection of molecular modeling software is available on the helix systems through the auspices of the Molecular Modeling Interest Group. Type mmignet list to display the programs available. To run any of these programs, at the helix prompt you should type:

[user@helix ~]$ mmignet program_name

If multiple versions are available, they will be listed. Program parameters can be added at the end of the command line.

Structural Biology

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AMoRe [Biowulf]

AMoRe is an automated utility for performing molecular replacement using fast rotation and translation functions in a step-wise fashion.

Molecules To Go [Web]

Allows a search of the PDB database and displays the result as text, image or interactive structure.

Qs [Biowulf]

Qs (Queen of Spades) is a "brute force" style molecular replacement program which uses a method based on a reverse Monte Carlo minimisation of the conventional crystallographic R-factor in the 6n-dimensional space defined by the rotational and translational parameters of the n molecules.

Phenix [Helix]

PHENIX is a new software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.

ProFit [Helix] [Biowulf]

ProFit is designed to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc.

StrucTools [Web]

Calculates surfaces, volumes, B-factor plots, hydrogen bonds, secondary structure and more from a PDB coordinate ID or uploaded PDB file.

XPLOR-NIH [Biowulf]

XPLOR-NIH is a structure determination program which builds on the X-PLOR v3.851 program, including additional tools developed at the NIH.

Mathematical Analysis

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Comsol [Helix] [Biowulf] [Sciware]

COMSOL Multiphysics (previously named FEMLAB) is a modeling package for the simulation of any physical process you can describe with partial differential equations (PDEs). It features state-of-the-art solvers that address complex problems quickly and accurately, while its intuitive structure is designed to provide ease of use and flexibility.

IDL [Helix] [Sciware]

IDL is software for data analysis, visualization, and cross-platform application development. IDL combines all of the tools you need for any type of project, from "quick-look," interactive analysis and display to large-scale commercial programming projects. IDL can be used to rapidly develop algorithms, interfaces, and powerful visualizations and quickly crunch through large numerical problems.

Mathematica [Helix] [Biowulf] [Sciware]

An interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. Graphics may be viewed on interactive terminals, X11 window servers and PostScript printers. See the file /usr/local/doc/Mathematica.txt for an introduction to the use of Mathematica on the NIH Helix Systems. The Mathematica man pages can be perused by typing man math, man mathremote, and man psfix.

Matlab [Helix] [Biowulf] [Sciware]

A high-performance interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically.

S-PLUS [Helix]

An object-oriented language for data analysis, with many functions for statistical, numerical and graphical techniques. Users can extend the language by designing new functions using the S language. Graphics may be displayed on interactive terminals or X-Window servers

R [Helix] [Biowulf] [Sciware]

R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).

Scilab [Biowulf] [Sciware]

Scilab is an open-source alternative to Matlab which includes hundreds of mathematical functions and the ability to interactively add C/Fortran programs. It includes a Matlab->Scilab converter.

GAUSS [Biowulf]

The GAUSS Mathematical and Statistical System is an easy-to-use data analysis environment based on the fast and powerful GAUSS Matrix Programming Language designed for computationally intensive tasks. GAUSS has over 400 functions built in, including LINPACK, EISPACK, and BLAS routines. In addition you can add your own functions to this library.

Octave [Biowulf]

GNU Octave is an open-source language for numerical calculations that has a command-line interface and can interpret many (but not all) Matlab scripts. It is not license-limited and so can be used for many simultaneous independent runs.

Physica [Biowulf]

PHYSICA is a high level, interactive programming environment with user friendly graphics and sophisticated mathematical analysis capabilities.

SAS [Helix] [Biowulf]

Base SAS provides a scalable, integrated software environment specially designed for data access, transformation and reporting.

ROOT [Helix]

The ROOT system provides a set of Object-Oriented frameworks with all the functionality needed to handle and analyse large amounts of data in a very efficient way. Having the data defined as a set of objects, specialised storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histograming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimisation, graphics and visualization classes to allow the easy setup of an analysis system that can query and process the data interactively or in batch mode.


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Mascot [Web]

The Mascot search engine uses mass spectrometry data to identify proteins from primary sequence databases. Mascot searches can be run directly from, or by using the Mascot daemon on your own desktop PC.

OMSSA [Biowulf]

An efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST.

X!Tandem [Biowulf]

Matches tandem mass spectra with peptide sequences for protein identification.

Image Analysis

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AFNI [Biowulf] [Sciware]

AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

Analyze [Helix] [Sciware]

Analyze is a comprehensive, robust and powerful software package for 3D biomedical image visualization and analysis. Requires an X-Windows capable desktop machine. To use it, type analyze at the prompt.

EMAN [Biowulf]

EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community, though it is beginning to be used in other fields as well.

FreeSurfer [Biowulf] [Sciware]

FreeSurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FSL [Biowulf]

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

Geomview [Helix]

Interactive program for viewing and manipulating geometric objects

Huygens [Helix]

Image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes.

IDL/ENVI [Helix]

IDL is a complete computing environment for the interactive analysis and visualization of data. IDL integrates an array-oriented language with mathematical analysis and graphical display techniques. ENVI is designed for extracting information from geospatial and medical imagery.

ImageJ [Sciware]

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine.

Imaris [Sciware]

Imaris provides scientists with solutions for processing, visualizing and analyzing multi-dimensional microscopic images. It reads images in many of the most commonly used proprietary formats.

Matlab [Helix] [Biowulf] [Sciware]

Image processing toolbox.

MEDx [Sciware]

MEDx is a UNIX based software package used to visualize and analyze 2D and 3D medical image data.

MIPAV [Sciware]

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities (i.e. PET, MRI, CT, microscopy...). Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.

MRIcro [Sciware]

MRIcro allows Windows and Linux computers to view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms.

OpenDX [Sciware]

OpenDX is a uniquely powerful, full-featured software package for the visualization of scientific, engineering and analytical data: Its open system design is built on a standard interface environments.

OsiriX [Sciware]

OsiriX is an image processing software dedicated to DICOM images (".dcm" / ".DCM" extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format).

ParaView [Sciware]

ParaView uses the Visualization Toolkit (VTK), a software system for 3D computer graphics, image processing, and visualization, as its data processing and rendering engine. It is designed to visualize data sets of size varying from small to very large.

SUMA [Sciware]

SUMA is a program that adds cortical surface based functional imaging analysis to the AFNI suite of programs. It allows viewing 3D cortical surface models, and mapping volumetric data onto them. With SUMA, AFNI can simultaneously and in real-time render Functional Imaging data in 4 modes: Slice, Graph (time series), Volume and Surface with direct links between them.

Molecular Graphics

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GaussView [Helix]

GaussView is an X-Windows GUI for Gaussian. Please see here for documentation.

iMol [Sciware]

iMol allows loading molecules using several file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB, XYZ or BIO files. The BIO file stores all view and rendering settings (e.g. colors, lighting, orientation of molecules). iMol can easily handle both small and large molecules, it can load multiple molecules, move and rotate them independently.

Molscript [Helix]

MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. To use it, type 'molscript' at the prompt.

Molauto [Helix] [Biowulf]

MolAuto is a program for producing good first-approximation MolScript input files (scripts) from a coordinate file. To use it, type molauto at the helix prompt.

Physica [Biowulf]

Physica is a high level, interactive programming environment with user friendly graphics and sophisticated mathematical analysis capabilities.

POVRay [Helix] [Biowulf] [Sciware]

POVRAY (Persistence of Vision RAYtracer) is a high-quality tool for creating three-dimensional graphics. Raytraced images are publication-quality and 'photo-realistic', but are computationally expensive so that large images can take many hours to create. PovRay images can also require more memory than many desktop machines can handle. To address these concerns, a parallelized version of PovRay has been installed on the Biowulf system.

Rasmol [Helix] [Biowulf]

Rasmol is a program for molecular graphics visualization. To use, type rasmol at the Helix or Biowulf prompt.

Raster3D [Helix]

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.

Ribbons [Helix]

Ribbons interactively displays molecular models, analyzes crystallographic results, and creates publication quality images. The Ribbons GUI needs X-Windows for display. To run Ribbons, type mmignet ribbons 3.1 at the prompt.

VMD [Helix] [Biowulf]

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. To use, type vmd at the prompt.

Program Development

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Compilers [Helix] [Biowulf]

IMSL [Helix]

A widely used library of mathematical and statistical routines in Fortran. To use the IMSL libraries, type
source /local/bin/fnlsetup.csh

SCSL (Scientific Computing Software Library) [Helix] [Biowulf]

A collection of high-performance routines that provide support for mathematical and numerical techniques used in scientific and technical computing. Included in SCSL are:

Message-Passing Interface (MPI) [Biowulf]

MPI is a library specification for message-passing, designed for high performance on both massively parallel machines and on workstation clusters.


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Editors are used to create and modify text files.

Batch Systems

Batch systems are used to run programs at a later time or date, or to set up a large number of program runs.

Internet Tools

Web browsers and ftp are examples of tools that are used to communicate between computers.

Acroread [Helix] [Biowulf]

Acroread is the standard tool for reading Adobe PDF files. Type acroread at the prompt.

Eye of GNOME (eog) [Helix]

Eye of GNOME is the official image viewer for the GNOME Desktop environment. It displays images, no frills, no surprises. Type eog at the prompt.

Ghostscript [Helix] [Biowulf]

Ghostscript is an X-Windows viewer for Postscript files. To use, type ghostscript [postscript filename] at the prompt.

Gimp [Helix] [Biowulf] [Sciware]

Gimp is the the GNU Image Manipulation Program. It is a freely distributed piece of software suitable for such tasks as photo retouching, image composition and image authoring. It will display on a desktop machine running X-windows. To use, type gimp at the prompt.

ImageMagick [Helix] [Biowulf]

ImageMagick is a collection of tools and libraries to read, write and manipulate images in over 89 formats. To use, type the command line tool name (e.g., display, or convert) at the prompt.

Xnview [Helix] [Biowulf]

Xnview is a multipurpose image translater/viewer. HOWEVER, it will on occasion screw up CMYK color display... To use, type xnview [filename] at the prompt.

GnuPlot [Helix] [Biowulf] [Sciware]

Gnuplot is a command-driven interactive function plotting program. It can be used to plot 2D and 3D plots in many differen formats. To use, type gnuplot at the prompt.

Random Jungle [Helix] [Biowulf]

Random Jungle is a fast implementation of RandomForest(TM) for high dimensional data.

Grace [Helix] [Biowulf]

Grace is a WYSIWYG 2D plotting tool for the X-Window system. It is a successor to Xmgr. To use, type xmgrace at the prompt.

Scientific Databases

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BIOBASE Databases [Web]

A comprehensive portfolio of standard and customized databases, as well as analytical tools. NIH-only: requires an NIH domain username & password. These databases and tools include:

ExPlain Analysis System - promotes biological interpretation of high throughput experiments like microarrays, proteomic data, and ChIP-chip experiments. The intuitive workflow allows systematic creation of experimentally testable hypotheses for both gene transcription regulation and signalling networks.

TRANSPATH - provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signalling components.

TRANSPRO - a collection of annotated transcription start sites for human, mouse, and rat promoter sequences.

TRANSCOMPEL - a database of composite gene regulatory elements found in many promoters and enhancers.

TRANSFAC Professional - a web interface to the TRANSFAC database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.

Nucleotide & Protein Sequence Databases [Helix/Biowulf]

A large collection of major nucleotide and protein databases are maintained in several formats on the Helix Systems. A comprehensive list of all databases on our systems is available, displaying the database name, format(s), and update status.

Genome Browser Mirror Fragments [Web]

A partial mirror containing the reference sequences for the human, mouse, rat, and other vertebrate (and one insect) genomes, as well as tools for display and analysis.

EyeBrowse [Web]

This site displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome.

Protein Data Bank [Helix/Biowulf] [NFS-mountable]

The Helix Systems maintains a mirror of the Protein Data Bank entries, which can be accessed in the /pdb area on Helix, the Biowulf head node, or the Biowulf computational nodes.

The PDB mirror can also be NFS-mounted by any Unix system at NIH. To access this mirror via NFS, system administrators should add the following entry to /etc/fstab on your Unix desktop system:

    /pdb    nfs   ro

Type mkdir /pdb, and then mount -a to complete the mount. Contact with any questions.

Cambridge Structural Database System (CSDS) [Helix]

The Cambridge Structural Database System (CSDS) consists of two major components:

The Cambridge Structural Database (CSD)

Bibliographic, 2D chemical and 3D structural results from crystallographic analyses of organics, organometallics and metal complexes. Both X-ray and neutron diffraction studies are included for compounds containing up to ca. 500 atoms (including hydrogens).

Software for Search, Retrieval, Analysis and Display of CSD contents

Comprised of the programs QUEST/QUEST3D (for text, numeric, 2D substructure and 3D geometric searching), VISTA (for 3D analysis of QUEST3D searches), GSTAT (for 3D search and data analysis) and PLUTO (graphical display of 3D structures).

Other databases

The helix systems group also maintains a list of databases available elsewhere on the web.