Software Tools


Software tools developed by CCS include:


h-GCAT logoh-GCAT is an online tool designed for the analysis of whole exome/genome sequencing data obtained from families affected by genetic disorder(s). Integrated with several important clinical and biological databases, h-GCAT provides the user with a relatively simple and intuitive interface to come down to a manageable gene list from the huge dataset.



The Genomic Oligoarray and SNP array evaluation tool was developed by Zhijie Jiang and Nicholas Tsinoremas in the collaboration with Klaas Wierenga at University of Oklahoma. The tool can spot disease causative genes on runs of homozygosity detected by SNP arrays. Currently the tool has 1000 registered users across the world.



BAO Search logoBAOSearch is a web-based application for querying, viewing, browsing and downloading small molecule biological screening results including high-throughput (HTS) data.  BAOSearch has been developed as part of the National Institutes of Health (NIH) funded Bioassay Ontology (BAO) project.   (NIH Project #1RC2HG005668)



LIFE-LINCS logoThe LIFE Search Engine integrates all LINCS content leveraging a semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to the Harvard Medical School and Broad Institute LINCS centers, which provide more information including experimental conditions and raw data. (NIH Project #1U01HL111561)



BD2K LINCS Data Coordination and Integration CenterThe LINCS Data Portal is the unified resource for the Library of Network-Based Cellular Signatures (LINCS) Program which aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents.

The LINCS Data Portal is composed of a suite of applications:

  • LINCS Dataset Data Portal (  The LINCS entry resource to access LINCS data.  It is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay.
  • The dataset group comprises datasets for the same experiment but with different data level results (data processed at a different level).
  • LINCS Small Molecule Data Portal (  The LINCS entry resource to access LINCS small molecules; approved drugs, small molecules under clinical phase and chemical probes.



URIDE starburstThe University Research Informatics Data Environment, also known as URIDE, is a large scale data services atmosphere where de-identified data from multiple clinical and research sciences systems can be explored preparatory to research, prospective and retrospective analysis. The goal of URIDE is to provide a single, secure, exploratory environment for all clinically and scientifically derived data for research at the University. It does not contain data from Jackson Memorial Hospital.

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