Bowtie 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).
The following versions of Bowtie1 are available on OSC clusters:
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.
The following versions of bedtools are available on OSC clusters:
Submitting a job without specifying the proper shell will return a warning like below:
sbatch: WARNING: Job script lacks first line beginning with #! shell. Injecting '#!/bin/bash' as first line of job script.
If an error is encountered, the job is rejected.
It is required to specify an account for a job to run. Please use the --account=<project-code> option to do this.
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 molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.
MPI is a standard library for performing parallel processing using a distributed memory model. The Pitzer, Ascend, and Cardinal clusters at OSC can use the OpenMPI implementation of the Message Passing Interface (MPI).
ANSYS Workbench platform is the backbone for delivering a comprehensive and integrated simulation system to users. See ANSYS Workbench platform for more information.
ANSYS Workbench is available on Cardinal Cluster. You can see the currently available versions in the table on the main Ansys page here.
ANSYS Mechanical is a finite element analysis (FEA) tool that enables you to analyze complex product architectures and solve difficult mechanical problems. You can use ANSYS Mechanical to simulate real world behavior of components and sub-systems, and customize it to test design variations quickly and accurately.
ANSYS Mechanical is available on the Cardinal Cluster. You can see the currently available versions in the table on the main Ansys page here.
OSC timely installs new software versions on OSC systems, and periodically do coordinated software refresh (update the default versions to be more up-to-date and remove some versions that are quite out of date) on OSC systems. While we encourage everyone to use up-to-date software, the old defaults will still be available till the next software refresh, in case some users prefer to use the old defaults. The software refresh is usually made during the scheduled downtime, while we will send out notifications to all users ahead of time for any questions/suggestions/concerns.
Fortran, C and C++ compilers produced by the GNU Project.
The GNU Compiler Collection (GCC) are available on all our clusters. These are the versions currently available:
Dedicated compute services at OSC (also refered to as Condo model) involves users purchasing one or more compute nodes for the shared cluster while OSC provides the infrastructure, as well as maintenance and services. CCAPP Condo on Cardinal cluster is owned by the Center for Cosmology and AstroParticle Physics, at OSU.
