The Core Facility is charged with providing support for the computational biology and bioinformatics software most used at both institutions. We have already established a substantial software library and are providing support for a number of laboratories. We have already provided assistance to several existing laboratories in setting up software and solving software- and hardware-related problems.
The Core Facility also coordinates and manages software site licenses to dramatically decrease the expense of outfitting individual machines with individual software licenses. We have set up floating licenses for a number of software packages now widely used within the two campuses including MATLAB, GeneSpring, and Igor. This has resulted in substantial cost savings to both institutions as well as made the software available to investigators who could not otherwise afford it. In addition to providing software, the facility will also manage training sessions and workshops on its use. Two such workshops are scheduled. Representatives from Genespring and Affiametrix will hold workshops in April 2006.
Currently the following software is available for use on our systems:
Windows Software
To start any Windows software, simply find the associated link in the Start Menu
Imaris/Autoquant
Imaris allows visualization of original and derived data objects in a real time interactive manner so you can quickly make visual assessments of your experiments in 3D and 4D to discover relationships that are otherwise hidden.
Autoquant offers the most powerful deconvolution tools available for life science research. Retrieve better data from your images using the most complete suite of 2D and 3D algorithms available. It offers an advanced Blind Deconvolution algorithm which is both iterative and constrained.
Is installed on workstations cbiws12, cbiws15, Kocher. Note:on workstation cbiws10 Autoquant is an older version that has a bug that requires admin permission to run. To use Autoquant on that workstation, please see CBI staff
Matlab
Matlab is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
Is installed on all of our workstations and servers. Available servers are: bishop.cbi.utsa.edu; cluster.cbi.utsa.edu;golgi.cbi.utsa.edu
Genespring
Genespring provides powerful, accessible statistical tools for fast visualization and analysis of expression data.
Is installed on workstations cbiws12, cbiws15, Kocher.
Mathematica
Mathematica provides you with the world's largest collection of algorithms in a single system--each able to operate across the widest applicable scope of numeric, symbolic, or graphical input.
Is installed on cluster.cbi.utsa.edu and bishop.cbi.utsa.edu To run, type mathematica for the graphical interface or math for the text interface.
Pathway Studio
Pathway Studio enables in-depth analysis of any list of interrelated biological data.
Linux/Unix
Most applications are in the path, so simply entering in the command for Matlab(ie matlab) will sufice. But if a program in not in the path, it must be executed explicitly with /path/to/executable
Genesis
Genesis is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.
Command: genesis
Location: /usr/local/share/genesis
Note:
Users must have a copy of the genesis config in their home directory first.
.simrc is for all genesis users, while
.nxsimrc is for genesis without xodus, and
.minsimrc is for minimal genesis without object libraries or xodus.
Neuron
Neuron is a simulation environment for modeling individual neurons and networks of neurons.
Command: nrngui
Location: /usr/local/nrn/
NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Command: namd2
Server: Cluster Only
Location: /usr/local/NAMD_2.6_Linux-amd64/
NAG
NAG: Numerical Algorithms Group is a mathematical and statistical software collection consisting of libraries and compilers for developing computational software.
Location: Cluster Only: Private Use Only: /opt/NAG
R
R is a free software environment for statistical computing and graphics.
Command: R
Abaqus
Abaqus is a Finite Element Analysis tool that runs simulations on models of real world components.
Command: abaqus
Location: On Bishop only: /opt/Abaqus/Commands
Materials Studio
Materials Studio is a modeling and simulation software for studying chemicals and materials.
Command: Private access only
Location: On Bishop only
NWChem
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters.
Command: nwchem
Location: On Bishop only: /usr/local/nwchem
