Software Tools

Software Tools

Software Tools

Software Tools developed by IDSC include:


BioAssay Ontology

BAO Search logo The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BioAssay Ontology hosts a trio of portals:  NCBO BioPortal, BioAssayOntology, and OntoloBridge. OntoloBridge API specification includes implemented functionality. To test a Simplified Web interface for API, visit: OntoloBridge API client.



Human Genome Clinical Annotation Tool (h-GCAT)

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.



LAND: Land Access for Neighborhood Development

LAND: Land Access for Neighborhood DevelopmentThe Land Access Neighborhood Development (LAND) mapping tool visualizes the distribution of local institutional and government-owned vacant, as well as underused properties. Developed by the University of Miami (UM)’s Office of Civic and Community Engagement (CCE), in collaboration with the UM Center for Computational Science, and with support from Citi Community Development, LAND will enable policymakers and community-based organizations to identify potential development opportunities for affordable housing in transit-served areas.


LIFE LINCS Information Framework

LIFE search logo
The LIFE search engine contains data generated from the LINCS Pilot Phase, to integrate 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 and other LINCS centers, who provide more information including experimental conditions and raw data. (NIH Project #1U01HL111561)


LINCS Data Portal

LINCS data portal logoThe 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: Datasets, Small Molecules, Cells, Genes, Proteins and Peptide Probes, and Antibodies.


MAP: Miami Affordability Project

MAP sample Miami Affordability ProjectThe Miami Affordability Project (MAP) is an interactive online map centered on the distribution of affordable housing and housing needs in greater Miami. The intent is to provide an open-access tool for planners, developers, community groups, and scholars of urban issues to better understand local housing needs and encourage data-driven affordable housing planning and analysis. This technical documentation is for the second phase of MAP, and will be updated as we complete future releases of MAP with expanded functionality and additional and updated data. MAP is led by the University of Miami’s Office of Civic and Community Engagement and supported by JPMorgan Chase, with additional support from the Jesse Ball duPont Fund.


SNP evaluation tool

GENA was SNPThe Genomic Oligoarray and SNP array evaluation tool was originally 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.  [Note:  This tool has been moved to SIVOTEC Bioinformatics with new features and functionalities, and is now called GENA.™]



URIDE logoThe University Research Informatics Data Environment, also known as URIDE, is a web-based platform empowering clinical research investigators with translational research tools and platforms to aggregate and visualize de-identified EMR data. URIDE can easily explore demographics, diagnoses, procedures, vitals, medications, labs, notes, allergies, comorbidities, locations, physicians, and much more.

Medical School faculty with a Cane ID already have access to URIDE. An investigator may request access to URIDE for a member of his/her study team. Request access by emailing