Bioinformatics
Compilers and Programming Tools
Computational Chemistry
File System
Finite Element Solvers
Graphics
Miscellaneous
Numerical Libraries
Optimization
Parallel Programming Languages and Tools
Queueing and Scheduling Systems
Solid Modeling
Statistics

BLAST

National Center for Biotechnology Information

BLAST is the Basic Local Alignment Search Tool. It is a set of search programs designed to explore all available sequence databases in either protein or DNA. This software has been designed to achieve great speeds while keeping a well-defined statistical interpretation.

BLAST is available on the following HPC machines:

LION-XL

2.2.8

http://gears.aset.psu.edu/hpc/software/bioinf/blast

07-Oct-2004

Versions listed in bold are the default version.

Cister

Martin Frith

Cister predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.

Cister is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/cister

07-Oct-2004

Versions listed in bold are the default version.

ClustalW

Institut de Genetique et de Biologie Moleculaire et Cellulaire

ClustalW is a general purpose multiple alignment program for DNA or proteins.

ClustalW is available on the following HPC machines:

LION-XL

1.82

http://gears.aset.psu.edu/hpc/software/bioinf/clustalw

07-Oct-2004

Versions listed in bold are the default version.

ClustalX

Institut de Genetique et de Biologie Moleculaire et Cellulaire

Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display.

ClustalX is available on the following HPC machines:

LION-XL

1.81

http://gears.aset.psu.edu/hpc/software/bioinf/clustalx

07-Oct-2004

Versions listed in bold are the default version.

Comet

Martin Frith

Comet finds statistically significant clusters of cis-element motifs in a DNA sequence.

Comet is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/comet

07-Oct-2004

Versions listed in bold are the default version.

Dotter

Karolinska Institutet Center for Genomics Research

Dotter is a graphical dotplot program for detailed comparison of two sequences.

Dotter is available on the following HPC machines:

LION-XL

3.0

http://gears.aset.psu.edu/hpc/software/bioinf/dotter

07-Oct-2004

Versions listed in bold are the default version.

FASTA

National Center for Biotechnology Information

No product description available.

FASTA is available on the following HPC machines:

LION-XL

3.4t10

http://gears.aset.psu.edu/hpc/software/bioinf/fasta

07-Oct-2004

Versions listed in bold are the default version.

fastDNAml

Ribosomal Database Project

fastDNAml is an attempt to solve the same problem as DNAML (part of the PHYLIP package), but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable.

fastDNAml is available on the following HPC machines:

LION-XL

3.3

http://gears.aset.psu.edu/hpc/software/bioinf/fastdnaml

07-Oct-2004

Versions listed in bold are the default version.

GeneMachine

National Human Genome Research Institute

GeneMachine is an integrated tool intended to perform both comparative and predictive gene identification techniques in a single run.

GeneM is available on the following HPC machines:

LION-XL

0.23

http://gears.aset.psu.edu/hpc/software/bioinf/genem

07-Oct-2004

Versions listed in bold are the default version.

GENSCAN

Christopher Burge

GENSCAN is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants.

GENSCAN is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/genscan

20-Feb-2007

Versions listed in bold are the default version.

HMMer

Washington University in St. Louis

Used to profile hidden Markov models.

HMMer is available on the following HPC machines:

LION-XL

2.2g

http://gears.aset.psu.edu/hpc/software/bioinf/hmmer

07-Oct-2004

Versions listed in bold are the default version.

HMMgene

Center for Biological Sequence Analysis

HMMgene is a program for prediction of genes in anonymous DNA.

HMMgene is available on the following HPC machines:

LION-XL

1.1e

http://gears.aset.psu.edu/hpc/software/bioinf/hmmgene

07-Oct-2004

Versions listed in bold are the default version.

MrBayes

John P. Huelsenbeck and Fredrik Ronquist

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.

MrBayes is available on the following HPC machines:

LION-XL

2.01

http://gears.aset.psu.edu/hpc/software/bioinf/mrbayes

07-Oct-2004

Versions listed in bold are the default version.

MZEF

Cold Spring Harbor Laboratory

MZEF predicts internal coding exons in genomic DNA sequences. It allows users to predict putative internal protein coding exons, adjust prior probability and to output alternative overlapping exons.

MZEF is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/mzef

07-Oct-2004

Versions listed in bold are the default version.

PHRED/PHRAP/Consed

Phil Green

PHRED/PHRAP/Consed | This software reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

PhPhC is available on the following HPC machines:

LION-XL

0.000925.c

No on-line instructions available

07-Oct-2004

Versions listed in bold are the default version.

PHYLIP

University of Washington Dept. of Genome Sciences

PHYLIP is a package of programs for inferring phylogenies.

PHYLIP is available on the following HPC machines:

LION-XL

3.5c

http://gears.aset.psu.edu/hpc/software/bioinf/phylip

07-Oct-2004

Versions listed in bold are the default version.

ReadSeq

Indiana University Dept. of Biology

Converts input DNA/AA sequence to specified format.

ReadSeq is available on the following HPC machines:

LION-XL

2.1.7

http://gears.aset.psu.edu/hpc/software/bioinf/readseq

07-Oct-2004

Versions listed in bold are the default version.

RepeatMasker

Genetic Information Research Institute

Screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.

repeatmasker is available on the following HPC machines:

LION-XL

20020713

http://gears.aset.psu.edu/hpc/software/bioinf/repeatmasker

07-Oct-2004

Versions listed in bold are the default version.

SEG

National Center for Biotechnology Information

SEG divides sequences into contrasting segments of low-complexity and high-complexity.

SEG is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/seg

07-Oct-2004

Versions listed in bold are the default version.

sim4

Comp. Sci. and Engr. and Biochem. and Mol. Bio. at Penn State Univ.

sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.

sim4 is available on the following HPC machines:

LION-XL

20011012

http://gears.aset.psu.edu/hpc/software/bioinf/sim4

07-Oct-2004

Versions listed in bold are the default version.

Sputnik

University of Washington Dept. of Molecular Biotechnology

Sputnik is a C language program that searches DNA sequence files in Fasta format for microsatellite repeats. A sequence file is specified on the command line and the resulting hits are written to stdout along with their position in the sequence, length, and a score determined by the length of the repeat and the number of errors.

Sputnik is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/bioinf/sputnik

07-Oct-2004

Versions listed in bold are the default version.

Treetool

Ribosomal Database Project

Treetool is an interactive tool for displaying, editing, and printing phylogenetic trees.

Treetool is available on the following HPC machines:

LION-XL

2.0.2

http://gears.aset.psu.edu/hpc/software/bioinf/treetool

07-Oct-2004

Versions listed in bold are the default version.

Absoft ProFortran

Absoft Corporation

Absoft Pro Fortran provides optimizing FORTRAN 77 and Fortran 90/95 compilers, as well as source level debuggers and compatibility libraries.

ProFortran is available on the following HPC machines:

LION-XL

8.0

http://gears.aset.psu.edu/hpc/software/comp/profortran/

03-Nov-2004

Versions listed in bold are the default version.

GNU Pascal

Free Software Foundation

The GNU Pascal Compiler

GPC is available on the following HPC machines:

LION-XL

20010308

http://gears.aset.psu.edu/hpc/software/comp/gpc

09-Feb-2005

Versions listed in bold are the default version.

Intel C++ Compiler

Intel

The Intel C++ Compiler delivers optimal performance on all Intel 32-bit processors, including the Pentium 4 and Intel Xeon, the 64-bit Intel Itanium Processor, the 64-bit x86_64 processor, and the AMD Opteron

ICC is available on the following HPC machines:

LION-XL

9.0

http://gears.aset.psu.edu/hpc/software/comp/icc

27-Sep-2006

Versions listed in bold are the default version.

Intel Fortran Compiler

Intel

The Intel Fortran Compiler delivers optimal performance on all Intel 32-bit processors,including the Pentium 4 and Intel Xeon processors, and the 64-bit Intel Itanium processor.

IFC is available on the following HPC machines:

LION-XL

9.0

http://gears.aset.psu.edu/hpc/software/comp/ifc

27-Sep-2006

Versions listed in bold are the default version.

Portland PGI Compilers and Tools

The Portland Group

The PGI Compilers and Tools suite offers parallel Fortran, C, and C++ Compilers and tools for Pentium Processor-based workstations.

PGI is available on the following HPC machines:

LION-XL

6.1-1

http://gears.aset.psu.edu/hpc/software/comp/pgi

27-Sep-2006

Versions listed in bold are the default version.

SUN Java2

Sun Microsystems

Java 2 Platform, Standard Edition (J2SE) software is a premier solution for rapidly developing and deploying mission-critical, enterprise applications.

SunJava2 is available on the following HPC machines:

LION-XL

1.4.2_05

http://gears.aset.psu.edu/hpc/software/comp/sunjava2

07-Oct-2004

Versions listed in bold are the default version.

CPMD

CPMD Consortium

The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

CPMD is available on the following HPC machines:

LION-XL

3.9-1

No on-line instructions available

03-Nov-2004

Versions listed in bold are the default version.

Gaussian 03

Gaussian, Inc.

Gaussian 03 is designed to model a broad range of molecular systems under a variety of conditions performing its computations starting from the basic laws of quantum mechanics.

G03 is available on the following HPC machines:

LION-XL

C.02

http://gears.aset.psu.edu/hpc/software/compchem/g03

03-Jan-2008

Versions listed in bold are the default version.

Gaussian 98

Gaussian, Inc.

Gaussian 98 is designed to model a broad range of molecular systems under a variety of conditions performing its computations starting from the basic laws of quantum mechanics.

G98 is available on the following HPC machines:

LION-XL

A.11

http://gears.aset.psu.edu/hpc/software/compchem/g98

03-Nov-2004

Versions listed in bold are the default version.

GaussView

Gaussian, Inc.

GaussView makes using Gaussian 03 simple and straightforward: * Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. * Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run. * Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on. We’ll look at many of them in the following pages.

gv is available on the following HPC machines:

LION-XL

4.1

http://gears.aset.psu.edu/hpc/software/compchem/gv

20-Mar-2008

Versions listed in bold are the default version.

Jaguar

Schrödinger, Inc.

Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory.

Jaguar is available on the following HPC machines:

LION-XL

55.011

No on-line instructions available

03-Nov-2004

Versions listed in bold are the default version.

ABAQUS

Hibbitt, Karlsson & Sorensen, Inc. (HKS)

ABAQUS is a finite element solver used for stress, heat transfer, and other types of analysis in mechanical, structural, civil, biomedical, and related engineering applications.

Abaqus is available on the following HPC machines:

LION-XL

6.6-1

http://gears.aset.psu.edu/hpc/software/fem/abaqus

02-Apr-2007

Versions listed in bold are the default version.

ANSYS

Ansys, Inc.

ANSYS/Multiphysics is a finite element design and analysis software that allows a user to model problems in structures, thermal/fluid flow and electromagnetics.

Ansys is available on the following HPC machines:

LION-XL

11.0

http://gears.aset.psu.edu/hpc/software/fem/ansys

31-Mar-2008

Versions listed in bold are the default version.

GrADS

Institute of Global Environment and Society

The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data.

GrADS is available on the following HPC machines:

LION-XL

1.8SL7

http://gears.aset.psu.edu/hpc/software/graphics/grads

07-Oct-2004

Versions listed in bold are the default version.

ATLAS

netlib.org

The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.

ATLAS is available on the following HPC machines:

LION-XL

3.4.1

http://gears.aset.psu.edu/hpc/software/numlib/atlas

07-Oct-2004

Versions listed in bold are the default version.

BLAS

netlib.org

The BLAS (Basic Linear Algebra Subprograms) are high quality "building block" routines for performing basic vector and matrix operations. Level 1 BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations, and Level 3 BLAS do matrix-matrix operations.

BLAS is available on the following HPC machines:

LION-XL

N/A

http://gears.aset.psu.edu/hpc/software/numlib/blas

07-Oct-2004

Versions listed in bold are the default version.

IMSL

Visual Numerics

IMSL is a collection of mathematical and statistical functions that programmers can embed into their applications. The objective of IMSL is to provide high-performance computing and expertise needed to develop and execute sophisticated numerical applications.

IMSL is available on the following HPC machines:

LION-XL

CTT6

http://gears.aset.psu.edu/hpc/software/numlib/imsl

20-Feb-2007

Versions listed in bold are the default version.

Intel Math Kernel Library

Intel

The Intel Math Kernel Library provides developers of scientific and engineering software with a set of linear algebra, fast Fourier transforms and vector math functions optimized for the latest Intel Pentium 4 and Itanium processors, as well as the x86_64 processors from both Intel and AMD. MKL contains LAPACK, the basic linear algebra subprograms (BLAS), and the extended BLAS (sparse). In addition, there is a set of fast Fourier transforms in single- and double-precision, real and complex data types with both Fortran and C interfaces. MKL also includes a set of vectorized transcendental functions in the Vector Math Library (VML), offering both high performance and excellent accuracy compared to the libm functions for most of the processors.

MKL is available on the following HPC machines:

LION-XL

8.01

http://gears.aset.psu.edu/hpc/software/numlib/mkl

20-Feb-2007

Versions listed in bold are the default version.

Linear Algebra PACKage Libraries (LAPACK)

netlib.org

LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. Associated matrix factorizations are provided. Dense and banded matrices are handled, but not general sparse matrices.

lapack is available on the following HPC machines:

LION-XL

3.0

http://gears.aset.psu.edu/hpc/software/numlib/lapack

07-Oct-2004

Versions listed in bold are the default version.

PETSc

Argonne National Laboratory Mathematics and Computer Science Divison

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.

PETSc is available on the following HPC machines:

LION-XL

2.1.5

No on-line instructions available

07-Oct-2004

Versions listed in bold are the default version.

ILOG AMPL

ILOG

AMPL is a comprehensive, powerful and flexible algebraic modeling language for the linear, nonlinear and integer programming problems often encountered in optimization.

ampl is available on the following HPC machines:

LION-XL

9.0

No on-line instructions available

31-Jan-2006

LION-XL

9.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG CPLEX

ILOG

ILOG CPLEX delivers high-performance, robust, flexible optimizers for solving linear, mixed-integer and quadratic programming problems in mission-critical resource allocation applications.

cplex is available on the following HPC machines:

LION-XL

9.0

No on-line instructions available

31-Jan-2006

LION-XL

9.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG OPL Development Studio

ILOG

ILOG OPL Development Studio's modeling language helps you develop optimization applications quickly, avoiding low-level programming tasks like memory management. You slash the time necessary to deliver high-performance optimization applications.

opl is available on the following HPC machines:

LION-XL

4.0

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG Scheduler

ILOG

ILOG Scheduler is a software component that supplements ILOG Solver by providing specialized modeling and algorithmic enhancements for solving problems that involve scheduling resources and tasks over a given period of time.

scheduler is available on the following HPC machines:

LION-XL

6.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

ILOG SOLVER

ILOG

ILOG Solver is ILOG's constraint-based optimization engine, providing cutting-edge optimization technology that uses logical contraints to power scheduling, sequencing, timetabling, configuration, dispatching and resource-allocation applications.

solver is available on the following HPC machines:

LION-XL

6.1

No on-line instructions available

31-Jan-2006

Versions listed in bold are the default version.

MPICH

Argonne National Laboratory Mathematics and Computer Science Divison

MPICH is a freely avaliable, portable implementation of MPI, the standard for message-passing libraries. MPICH runs over fast-ethernet on the machines that it is installed on. It is recommended that if you have code that is communication-intensive that you use one of the MPIs that use a high-speed network.

MPICH is available on the following HPC machines:

LION-XL

1.2.5.2

http://gears.aset.psu.edu/hpc/software/parlib/mpich

07-Oct-2004

Versions listed in bold are the default version.

Maui Scheduler

Center for HPC Cluster Resource Management

Maui is an advanced batch scheduler with a large feature set well suited for High Performance Computing (HPC) platforms including large Alpha and PC clusters, SP, and O2K systems. It uses aggressive scheduling policies to optimize resource utilization and minimize job response time. Maui runs on top of queueing systems such as PBS and LoadLeveler and dictates the scheduling policies that they use.

Maui is available on the following HPC machines:

LION-XL

3.2.6p2

No on-line instructions available

03-Nov-2004

Versions listed in bold are the default version.

Portable Batch System (PBS)

Veridian Systems

The Portable Batch System (PBS) is a flexible batch queueing and workload management system.

PBS is available on the following HPC machines:

LION-XL

5.2.2

No on-line instructions available

03-Nov-2004

Versions listed in bold are the default version.

R

Free Software Foundation

R is a language and environment for statistical computing and graphics. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R is available on the following HPC machines:

LION-XL

2.2.1

http://gears.aset.psu.edu/hpc/software/statistics/r/

09-Nov-2006

Versions listed in bold are the default version.