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Bowtie

"Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line." (http://bowtie-bio.sourceforge.net/manual.shtml)

Software Forms

Several of our software packages require that users complete a form that is then kept on record here before we can grant access to the software. Academic users should download, print, complete, and return the form to OSC. Non-academic users should contact OSC Help for assistance.

Python

Python is a high-level, multi-paradigm programming language that is both easy to learn and useful in a wide variety of applications.  Python has a large standard library as well as a large number of third-party extensions, most of which are completely free and open source. We highly recommend using the module to access Python, as we have added a lot of Python modules and tuned them to perform well on our systems.

Storage Environment at OSC

OSC has over two petabytes (PB) of disk storage capacity distributed over several file systems, plus almost 2PB of backup tape storage. (A petabyte is 1015, or a quadrillion, bytes.) This guide describes the various storage environments, their characteristics, and their uses.

VASP

The Vienna Ab initio Simulation Package, VASP, is a program package for ab-initio quantum-mechanical molecular dynamics (MD) simulations and electronic structure calculations, from first principles.

Stata

Stata is a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics. Release 13 32-processor SMP is currently available at OSC.

SPRNG

Computational stochastic approaches (Monte Carlo methods) based on random sampling are becoming extremely important research tools not only in their "traditional" fields such as physics, chemistry or applied mathematics but also in social sciences and, recently, in various branches of industry. An indication of importance is, for example, the fact that Monte Carlo calculations consume about one half of the supercomputer cycles. One of the indispensable and important ingredients for reliable and statistically sound calculations is the source of pseudo random numbers. SPRNG provides a scalable package for parallel pseudo random number generation which will be easy to use on a variety of architectures, especially in large-scale parallel Monte Carlo applications.

SPRNG 1.0 provides the user the various SPRNG random number generators each in its own library. For most users this is acceptable, as one rarely uses more than one type of generator in a single program. However, if the user desires this added flexibility, SPRNG 2.0 provides it. In all other respects, SPRNG 1.0 and SPRNG 2.0 are identical.

ScaLAPACK

ScaLAPACK is a library of high-performance linear algebra routines for clusters supporting MPI. It contains routines for solving systems of linear equations, least squares problems, and eigenvalue problems.

This page documents usage of the ScaLAPACK library installed by OSC from source. An optimized implementation of ScaLAPACK is included in MKL; see the software documentation page for Intel Math Kernel Library for usage information.

R

R is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques, and is highly extensible.

PGI Compilers

Fortran, C and C++ compilers from the Portland Group. PGI compilers are the default, recommended compilers on Glenn.

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