Software

MATLAB

MATLAB is a technical computing environment for high-performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment where problems and solutions are expressed just as they are written mathematically--without traditional programming.

NetCDF

NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD generally scales well on OSC platforms and offers a variety of modelling techniques. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR.

MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

MVAPICH2

MPI is a standard library for performing parallel processing using a distributed-memory model. The Glenn and Oakley clusters at OSC use the MVAPICH implementation of the Message Passing Interface (MPI), which is based on MPICH and optimized for the high-speed Infiniband interconnects.

MVAPICH2, based on the MPI-2 standard, is installed on both Oakley and Glenn. The older MVAPICH, based on the MPI-1 standard, is installed on Glenn only.

LAMMPS

The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems.  LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.

Jmol

Jmol is a simple molecular visualization program. It can read many file formats and can write various formats. Animations of normal modes and simulations are implemented. Jmol is an OpenScience Java application.

Intel Compilers

The Intel compilers for both C/C++ and FORTRAN.

Availability and Restrictions

Intel Compiler is available on Glenn, Oakley and Ruby Clusters. The versions currently available at OSC are:

HMMER

Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

  • if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
  • the top hits in a BLAST search are hypothetical sequences from genome projects.
  • your protein consists of several domains which are of different types.

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.

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