A key benefit of using CCV's computing resources is that we install and maintain a large collection of computational research software. We can install most software packages upon request.
List of software packages
Full list of software packages at CCV
Visit the CIS Software Catalog for additional software.
Here are some popular packages are already available, followed by a comprehensive list:
Developed by MathWorks, MATLAB is a numerical computing environment. It is useful for performing numerical computations with matrices and vectors, data visualization (e.g. plotting of functions and data), and implementation of models and algorithms. MATLAB can also interface with programs written in other languages, including C, C++, Java, and Fortran.
Python is a general-purpose programming language with a design philosophy that emphasizes code readability. Its efficient high-level data structures and approach to object-oriented programming makes it an easy to learn, powerful programming language. Altogether, Python is an ideal language for scripting and rapid application development.
R (Statistical Language)
R is a programming language and environment for statistical computing and graphics. The R language is widely used among statisticians and data miners to analyze data and develop applications.
MPI (Message Passing Interface)
Standard C and Fortran do not have constructs that support parallelism.
The Message Passing Interface (MPI) was developed as a standard using commonly-available operating system services to create parallel processes and exchange information among these processes.
SeqDB, a file format, compressor and storage tool for the raw data produced by Next-Generation Sequencing platforms like the like the Illumina HiSeq 2000 and MiSeq and the Life Technologies Ion Torrent PGM.
BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
Agalma, an automated pipeline for assembling and analyzing transcriptone data.
PyModules, an alternative implementation of the Environment Modules system for managing software environments on research computing clusters.
HPCmatlab, a framework for fast prototyping of parallel applications in Matlab. It uses the Message Passing Interface (MPI) for sending and receiving messages among different Matlab processes.