As translational medicine efforts evolve, institutions are looking to build "virtual" biorepository management systems that combine open source tools from the National Cancer Institute's Cancer Biomedical Informatics Grid with commercial software development and support.
In March, 5AM Solutions was awarded a three-year contract worth $1.2 million to develop a centralized, Web-based biological specimen tracking software system based on caBIG's ca¬Tissue Suite for the Arizona Biomedical Research Commission. The system will provide users a view of tissue samples stored in repositories in a number of Arizona hospitals and research facilities, according to 5AM Solutions CEO Brent Gendleman.
In addition, caTissue developers at Washington University recently worked with Persistent Systems software developers to create a new version of caTissue that takes advantage of grid computing, as well as the ca¬Tissue KnowledgeCenter, an online portal that helps ca¬Tissue users adapt the suite for their needs.
In its contract with ABRC, 5AM Solutions is developing a virtual biobank for five Arizona institutions: St. Joseph's Hospital, Phoenix Children's Hospital, Maricopa Medical Center, Sun Health, and Scottsdale Healthcare.
Gendleman says the company plans to customize, extend, and host the ca¬Tissue Suite for the project. "This is neat; the federal government invested in software, architecture, and environment; a state government will take advantage of said software; and a small company is able to be involved as well," he says.
James Matthews, deputy director of ABRC, says that Arizona has embarked upon several efforts during the last four years to support translational research in the areas of cancer, neurological diseases, bioimaging, and bioengineering, but scientists reported "difficulty obtaining tissue for research purposes." With a virtual biobanking portal, scientists will be able to see which institution holds which type of tissue and whether there is enough tissue for a given experiment, he said.
— Vivien Marx
Software developer Persistent Systems is partnering with Indiana University's School of Informatics to create a research and development center in the nearly completed incubator on the Bloomington campus.
The American Museum of Natural History in New York City has licensed data-management software from software firm Biomatters. The museum's Sackler Institute for Comparative Genomics will use the Geneious software for gene sequence visualization, assembly, primer design, and Blast searching.
Stanford University licensed Rosetta Biosoftware's Syllego platform system to manage and analyze genetic data produced by the Genetics of Insulin Sensitivity, or GENESIS, consortium.
Amount of NSF grant to Seattle's Northwest Association for Biomedical Research to promote bioinformatics education.
Translational Bioinformatics for Human Developmental Genomics
Grantee: Donna Slonim, Tufts University
Began: Dec. 2, 2008; Ends: Nov. 30, 2012
Slonim will use this grant to develop a method for discovering new, statistically validated gene sets from expression data. Along with literature mining, she will develop new systems biology annotation specific to fetal development and a new computational paradigm for sample classification that can identify and determine the nature of rare abnormal developmental profiles.
Computational Framework for Analysis of Microarray Gene Expression Data
Grantee: Dariusz Wroblewski, Bioformatix
Began: Jan. 1, 2009; Ends: Dec. 31, 2010
With this grant, Wroblewski plans to develop and validate a novel numerical framework to identify differentially expressed transcripts, with an emphasis on the analysis of experiments with a small number of replicates and genes with moderate levels of expression. The approach is based on a non-parametric method for assessment of noise distributions in microarray data.