Software

BWA

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

Availability and Restrictions

The following versions of BWA are available on OSC clusters:

Bowtie1

Bowtie1 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).

Availability and Restrictions

The following versions of Bowtie1 are available on OSC clusters:

bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Availability and Restrictions

The following versions of bedtools are available on OSC clusters:

NWChem

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.

Availability and Restrictions

The following versions of NWChem are available on OSC clusters:

ABINIT

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

Allinea MAP

Allinea MAP is a full scale profiler for HPC programs. We recommend to use Allinea MAP after reviewing reports from Allinea Performance Reports. It supports pthreads, OpenMP, or MPI code on CPU, GPU, or MIC based architecture.

Schrodinger

The Schrodinger molecular modeling software suite includes a number of popular programs focused on drug design and materials science but of general applicability, for example Glide, Jaguar, and MacroModel.  Maestro is the graphical user interface for the suite.  It allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of mole

OpenMPI

MPI is a standard library for performing parallel processing using a distributed-memory model. The Oakley, Ruby, and Owens clusters at OSC can use the OpenMPI implementation of the Message Passing Interface (MPI), which is based on MPICH.

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