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RCMI Computational Systems Biology Core

Director: Wang, Zhiwei

Summary:

The objective of the Computational Systems Biology Core facility (CSBC) is to provide computational support for basic and translational health research at UTSA with the following specific aims:

- Build the computational infrastructure to support modeling and simulation of biological systems
- Live cell imaging
- Protein Biomarker research

Affiliations:

People:

Resources:

Instruments

Services

  • Assistance in developing statistical analytic plans ( Support service )

    "The Program is now providing statistical assistance to researchers in the design of genomic and proteomic experiments. Our input includes helping investigators choose the most appropriate experimental design to satisfy the needs of their project, ensuring that the study aims and endpoints are clearly defined, that sample size calculations are used to guide the utilization of precious laboratory resources, and appropriate analytic plans are included."

  • Biological computational software installation service ( Access service )

    "Open source software can be installed upon request.
    We also have the follow software that is available to install upon request: R, Splus, S+ArrayAnalyzer, SAS, mySQL, CPLEX, BLAST Suite, ClustalW/X, EMBOSS, InterPro, GenScan, SRS, phred/phrap/polyphred/consed, Seaview, LAGAN Toolkit, FastA, HMMER, SAM, MEME/MAST, PHYLIP, MEGA, PAUP, McClade, TreeView, DnaSP, MFOLD, PredictProtein, Rasmol, Bioperl, CLUSTER, DnaSP, Affymetrix Data Mining Tool, Bioconductor, SAM, dChip, Cluster, GeneX, ArrayDB, Neuron, IgorPro, OpenDX, Adobe Suite, Visual Molecular Dynamics, etc."

  • Computational systems biology data analysis assistance ( Data analysis service )

Software

  • COLUMBUS Quantum Chemistry Programs ( Software )

    "COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules. A variety of methods, including

    - MCSCF (multiconfiguration self-consistent field)

    - MR-CISD (multireference configuration interaction with all single and double excitations),

    - MR-ACPF (multireference averaged coupled-pair-functional) and

    - MR-AQCC (multi-reference average quadratic coupled-cluster)

    are available. An important feature of COLUMBUS is its flexibility. In addition to standard classes of reference wave functions, such as CAS or RAS, calculations can be performed with selected reference configurations. Though the multi-reference aspect of COLUMBUS is emphasized, single-reference calculations can also be carried out very efficiently."

  • General Atomic and Molecular Electronic Structure System ( Software )

    "GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code."

  • Genesis ( Software )

    "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."

  • GeneSpring GX ( Software )

    "GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data. Designed specifically for the needs of biologists, GeneSpring GX offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context."

  • Imaris/Autoquant ( Software )

    "Imaris is Bitplane’s core scientific software module that delivers all the necessary functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size. Conveniently load, process and visualize data and images acquired from almost any confocal and wide field microscope to gain new and groundbreaking insight from your image data."

  • Ingenuity Pathways Analysis ( Software )

    "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.

    IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity®Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."

  • Materials Studio ( Software )

    "Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and behavior. Using Materials Studio, researchers in many industries are engineering better performing materials of all types, including pharmaceuticals, catalysts, polymers and composites, metals and alloys, batteries and fuel cells, and more."

  • Mathematica ( Software )

    "At the core of Mathematica is its highly developed symbolic language, which unifies a broad range of programming paradigms, and uses its unique concept of symbolic programming to add a new level of flexibility to the very concept of programming."

  • MATLAB ( Software )

    "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."

  • MEME Systems ( Software )

    Motif-based sequence analysis tools.

  • NAG: Numerical Algorithms Group software suite ( Software )

    "NAG: Numerical Algorithms Group software suite is a mathematical and statistical software collection consisting of libraries and compilers for developing computational software."

  • NAMD - Scalable microdynamics ( Software )

    "The NAMD molecular dynamics program excels at simulating, in atomic detail, the complex molecular machinery of living cells. NAMD now enables hundred-million-atom simulations using the full capabilities of the nation's fastest supercomputers due to parallel programming innovations reported in a paper at the SC11 supercomputing conference. While parallel supercomputers have massive amounts of memory in aggregate, any part of the machine can directly access only a small fraction. To fit the molecular blueprint of cellular structures such as the chromatophore in the memory of such machines, a compressed data format was developed that exploits the repetitive nature of proteins, nucleic acids, lipid membranes, and solvent. This format requires only a small amount of data to be copied to all parts of the supercomputer, while the remainder is read from disks in parallel and distributed across the machine. Simulation output and the balancing of work loads are similarly distributed. The Charm++ parallel programming system, on which NAMD is built, was also extended to allow the molecular structure and other data to be shared among the increasing number of cores in modern processors. A hundred-million-atom simulation can now run on supercomputers with only 2 gigabytes of memory per node, such as the IBM BlueGene/P. The enhancements are available to computational biologists world-wide in special memory-optimized versions of NAMD 2.8."

  • Neuron ( Software )

    "NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties."

  • NWChem ( Software )

    "NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters."

  • R software ( Software )

    "R is a free software environment for statistical computing and graphics."

  • Solidworks Abaqus ( Software )

    "The Abaqus Unified FEA product suite offers powerful and complete solutions for both routine and sophisticated engineering problems covering a vast spectrum of industrial applications. In the automotive industry engineering work groups are able to consider full vehicle loads, dynamic vibration, multibody systems, impact/crash, nonlinear static, thermal coupling, and acoustic-structural coupling using a common model data structure and integrated solver technology. Best-in-class companies are taking advantage of Abaqus Unified FEA to consolidate their processes and tools, reduce costs and inefficiencies, and gain a competitive advantage."

  • VMD ( Software )

    "VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code."


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Last updated: 2014-07-07T08:47:45.889-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016