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Ahead of Full System Launch, Intrepid Seeks Ag-Bio Test Drivers for 'Private Beta'


By Uduak Grace Thomas

With about a month left before the official launch of its flagship product, Intrepid Bioinformatics is seeking beta testers for a final run of its web-based data repository and software system.

The company plans to recruit 10 groups at the Plant and Animal Genomes Conference in San Diego, Calif., next week, who will receive full access to the genomic data management system with the option to test its tools on their own datasets or to run them on publicly available data stored in the repository.

The system, which was originally called GeneSentry, has been renamed the Intrepid Bioinformatics Solution and incorporates new features aimed at making the commercial version of the tool more user friendly, Intrepid CEO Tom McMahon told BioInform this week

Although the data repository hasn’t changed, the company has added a user interface; provided users with the ability to upload, download, and share their data; and added open application programming interfaces that allow users to adapt the system to their specific needs, all of which did not exist in the previous incarnation of the tool, McMahon said.

He said that the company has conducted internal assessments of the product and is now looking for input from community members that are looking to test-drive new tools for their research projects.

Specifically, the company is targeting ag-bio academic researchers that have genomic data on cattle, sheep, and pigs, McMahon said. Currently, Intrepid's data repository contains fully annotated human, horse, mouse, and cattle genomic datasets as well as partially annotated genomes on gorilla, chimpanzee, rat, sheep, and pigs.

GeneSentry, first developed by Ted Kalbfleisch, associate director of bioinformatics at the University of Louisville Center for Genetic and Molecular Medicine, includes software that lets users visualize and track their data as well as design assays, and provides some storage space for the data (BI 10/15/2010).

Kalbfleisch told BioInform that the tool now lets users create a network of collaborators and includes a two-step process to ensure that data sharing mistakes can be corrected. Furthermore, the system has capabilities that let researchers stratify populations based on criteria like phenotype and race, scrutinize data at the level of particular loci within populations or individuals, and browse datasets by subject sample and experimental sample.

The genome browser lets users perform searches based on genes, polymorphisms, genomic regions, and by samples, and shows mappings of the results. Users can identify trends in populations by comparing datasets placed side by side

Additionally, single nucleotide polymorphism and genotype data can be uploaded and download to and from the system in Illumina SNP Chip, .ab1 and .scf formats or as Plink or tab-delimited files by dragging and dropping the files into the browser. Once the data is in the system, the platform uses a series of parsers to "break it into its constituent pieces" and stores the results of the analysis in the repository.

Intrepid plans to offer its customers a pay-as-you-go model for data uploading, along with monthly subscription options, when the system goes online next month.

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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