Projects

DVD

The Deafness Variation Database (DVD) is part of the AudioGene project. The DVD lists genes associated with deafness, all variations observed from ClinVar and dbSNP, and the clinically relevant variations as tested by the Otoscope screening panel of deafness causing genes. The DVD also shows pathogenicity prediction scores and allele frequencies derived from EVS and the 1000's genome project.

Cordova

Cordova is an open source, web-based content management system for building and maintaining a database of genetic variations. It provides an interface for researchers to review and manually or computationally curate data prior to public release. Cordova offers a platform to share reliable genetic variation data for clinical diagnostics and the advancement of research. Production examples of Cordova include The Deafness Variation Database and The Vision Variation Database.

Kafeen

TrAPSS stands for Transcript and Annotation Prioritization Screening System. It is a system comprised of several tools written by researchers at the Coordinated Lab for Computational Genomics in the University of Iowa. The system aims to aid scientists who are searching for the genetic mutation or mutations that are linked to expression of a disease phentotype. The system offers support for almost all areas of a mutation discovery project from the creation and prioritization of a large candidate gene list, to the selection, ordering, and managing of primer pairs, and even support for SSCP assay results. TrAPSS is a currently deployed and often used tool for several laboratories here at the University of Iowa in the College of Medicine. The system is composed of several Java applications, many web-based PHP tools, and a local MySQL database. Even the Java applications are available through a web browser due to Sun's Java Web Start. Director of the CLCG, Professor Terry A. Braun, heads the project along with Dr. Todd Scheetz and Prof. Thomas L. Casavant. Eight developers create and maintain the software: Bartley Brown , Steven Davis and Jason Grundstad; along with four graduate students, Hakeem Abdulkaway, Brian O'Leary, Michael Smith, and John Ritchison; and one undergraduate student, Matthew Kemp.

TrAPSS

TrAPSS stands for Transcript and Annotation Prioritization Screening System. It is a system comprised of several tools written by researchers at the Coordinated Lab for Computational Genomics in the University of Iowa. The system aims to aid scientists who are searching for the genetic mutation or mutations that are linked to expression of a disease phentotype. The system offers support for almost all areas of a mutation discovery project from the creation and prioritization of a large candidate gene list, to the selection, ordering, and managing of primer pairs, and even support for SSCP assay results. TrAPSS is a currently deployed and often used tool for several laboratories here at the University of Iowa in the College of Medicine. The system is composed of several Java applications, many web-based PHP tools, and a local MySQL database. Even the Java applications are available through a web browser due to Sun's Java Web Start. Director of the CLCG, Professor Terry A. Braun, heads the project along with Dr. Todd Scheetz and Prof. Thomas L. Casavant. Eight developers create and maintain the software: Bartley Brown , Steven Davis and Jason Grundstad; along with four graduate students, Hakeem Abdulkaway, Brian O'Leary, Michael Smith, and John Ritchison; and one undergraduate student, Matthew Kemp.

Iowa Pseudogenes

This site serves as a repository for all pseudogenes in the human genome. It also provides a ranked list of human pseudogenes that have been identified as candidates for gene conversion.

Software

A list of software produced by this lab which is being made available for use by the genomics community.