TrAPSS2 -- CLCG @ UIowa

Neccessary Components

Modules
Mysql JDBC Driver
Java 1.4.2
Java Web Start

Download
WebStart

Here are some of the beta versions of programs for TrAPSS2. These are meant for testing only, no important data should be entered with any of these programs because it may disappear at any time. But we would like testing of all of the functionality of these programs, so use them as thorough as possible. Thanks!

- CLCG TrAPSS Team

What is 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.

The Usefulness of TrAPSS

The true usefulness of TrAPSS is that it is based upon a novel way to examine a large candidate list of genes. Rather than sequentially examining full genes, the scheme often followed in current projects, TrAPSS provides tools that offer the user the opportunity to screen certain small parts of several genes from the candidate list at once. The current method will be referred to as the serial method and the new idea will be called the parallel method. This parallel screening idea was envisioned by researchers here at the University including Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate student Steven Davis has demonstrated the advantage of the parallel screening method.

Quick Overview of the Different Approaches to Mutation Screening

Serial methods look at one gene at a time: One gene is picked, a decision often based on incomplete or inaccurate information, and that gene is fully screened until the next gene is chosen to be examined.
Graphical Representation:

This is an imaginary candidate list with genes labelled 1 through 4. The gene structure is represented by dark blue for exons and light blue for introns (portions of the introns are not shown). Each arrow represents a primer pair. The pairs are picked in order of heir color from red (first) to green (last).
An alternative method, parallel screening, involves determining the most important parts of a gene and screening those areas first.
One drawback is that identifying those important regions of genes requires the examination of loads of information as well as performing several complex calculations.
Graphical Representation:

This is the same imaginary candidate list as shown above. The selection of primer pairs occurs in a different order, however. Primer pairs are still selected in order of their color, red being first, but as shown all genes have at least some portion examined.

The Programs Integrated into TrAPSS

Program Name	Program Use	Developers
TrAPSS CGI Web Interface	Candidate List Management / Overview	Bart Brown, Hakeem Abdulkaway
GrEEN	Java Application Candidate List Management / Overview	John Ritchison
PrimerViewer	Java Application Primer pair selection	Steven Davis
PrimerManager	Java Application Primer pair management / ordering	John Ritchison, Steven Davis, and Mike Smith
Assay Viewer	Java Application Storing / Reviewing SSCP results	John Ritchison

To learn more about TrAPSS, go to bioneos.com, a startup bioinformatics company that will be furthering development on TrAPSS.

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