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Center for Computational and Integrative Biomedical Research

Houston, Texas

Computational and Integrative Biomedical Research Center
CIBR Center for Computational and Integrative Biomedical Research
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Software and Data

Software

The CIBR Center has purchased two computational software site licenses.

The following is a continually updated table of software and data collections that are produced and distributed by CIBR Center faculty members of BCM.

Software Source Description
Genboree Dr. Aleksandar Milosalvjevic Internet-based turnkey software system for genomic research
PASH
Fast and accurate sequence comparison and pattern discovery in genomic sequences by parallelization
Spikoscope Dr. Fabrizio Gabbiani Browsing and analysis of electrophysiology recordings.
OPUS suite Dr. Jianpeng Ma Molecular structure modeling.
Evolutionary Trace Server
Dr. Olivier Lichtarge Ranks amino acid residues in a protein sequence by their relative evolutionary importance. Pre-computed ET analyses for select PDB IDs.
Report Maker Ranks amino acid residues in a protein sequence with a UniProt accession number.
ET Viewer Performs ET analyses starting from PDB file names or PDB formatted files.
PyETV An Application for Mapping Evolutionary Traces onto Protein Structures in PyMOL
Evolutionary Trace Code Ranks amino acid residues in a protein sequence by their relative evolutionary importance.
Evolutionary Trace Annotation The server suggests molecular functions for proteins structures based on local structural similarities to proteins of known function identified using 3D templates.
Contact Metric Server Detection of similarity in protein structure and function through contact metric distances.
ClassA GPCRs Difference Evolutionary Trace Server for G Protein-Coupled Class A Receptors
SimPed Dr. Suzanne Leal Generates haplotype and/or genotype data for large numbers of marker loci.
BSMAP Dr. Wei Li General-purpose bisulfite mapping software for epigenomics.
CEAS
An integrated webserver for analyzing ChIP-chip data.
DANPOS
Comparison of nucleosome maps, histone modification maps, or protein binding maps generated based on high-throughput sequencing.
MACS
A model-based algorithm for finding enriched regions in ChIP-Seq experiments.
MAT
A model-based algorithm for finding enriched regions in ChIP-Chip experiments.
xMAN
Rapid mapping of millions of query oligonucleotide fragments to the genome of any given length.
BIMBAM Dr. Yongtao Guan Genotype imputation and statistical tests for disease association
piMASS
Multi-SNP association with disease phenotypes.
EMAN2 Dr. Steve Ludtke Scientific image processing suite, aimed at improving the resolution and quality of single particle reconstructions.
EMEN2 An extesible, object-oriented electronic lab notebook
Gorgon
Interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes.

Data

NCMI Public Data Server - NCMI

The database contains a variety of publicly accessible cryoEM single particle analysis data sets collected at NCMI.

HapMap3 - Dr. Fuli Yu

    The latest map of human genetic variation – dubbed HapMap3 – includes 11 populations from across the globe, identifying not only the single nucleotide polymorphisms (SNPs) or single letter changes in the 3 billion letter alphabet of the human genome but also variations that represent differences in the numbers of copies of genes or gene segments.

Human Microbiome Project

    BCM joins other institutions in characterizing the thousands of microbial species that co-exist in various parts of the human body, and shape human physiology.

Ataxia-causing Protein Interaction Network - Dr. Chad Shaw

    A protein interaction network comprised of direct and indirect interactions of human ataxia disease-causing proteins.

Signatures of Proliferation and Quiescence - Dr. Chad Shaw

    Affymetrix MGU74Av2 microarray data used in identifying signatures of proliferation and quiescence in hematopoetic stem cells.

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