Glenn

Clustal W

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.

BLAT

BLAT is a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box. The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment. Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little more than 2 gigabytes.

Bioperl

Bioperl offers a set of perl modules which can be used for sequence manipulation. Knowledge of PERL programming is required.

Getting Connected

There are two ways to connect to our systems. The traditional way will require you to install some software locally on your machine, including an SSH client, SFTP client, and optionally an X Windows server. The alternative is to use our zero-client web portal, OnDemand.

ANSYS

ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. Supports are provided by ANSYS, Inc

CUDA

CUDA™ (Compute Unified Device Architecture) is a parallel computing platform and programming model developed by Nvidia that enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU).

FLUENT

ANSYS FLUENT (called FLUENT hereafter) is a state-of-the-art computer program for modeling fluid flow and heat transfer in complex geometries.

Availability and Restrictions

FLUENT is available on Oakley and Glenn Clusters. The versions currently available at OSC are:

Software List

Ohio Supercomputer Center (OSC) has a variety of software applications to support all aspects of scientific research. We are actively updating this documentation to ensure it matches the state of the supercomputers. This page is currently missing some content; use module avail on each system for a comprehensive list of available software.

Supercomputing Support

oschelp contact information and recommendations

Do not send your password to oschelp, or to anyone, by email

hours: 9 a.m.- 5 p.m., Monthday through Friday, except on OSU holidays

contact--email: oschelp@osc.edu

contact--toll free: (800) 686-6472

contact--local: (614)292-1800

address: 1224 Kinnear Road, Columbus OH 43212

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