Insilicos - Biomarker Discovery Software | Insilicos and The Institute for Systems Biology Announce Cloud Computing System |

April 19, 2009, Seattle - The Trans-Proteomics Pipeline (TPP), a free, open-source software suite for high-throughput proteomic analysis developed by researchers in the Seattle Proteome Center at the Institute for Systems Biology (ISB), is now “cloud computing” ready.

These changes, implemented by Insilicos as part of a grant-funded collaboration with ISB, make it possible for scientists from smaller institutes to use the TPP to conduct large-scale research, without making the capital investment necessary to build server facilities necessary to process massive amounts of data generated by high volume proteomics experiments. Changes to the TPP now allow the software to function remotely with data processed and stored on off-site processing “farms” available for rent from commercial organizations.

“We’re really enthusiastic about the modification because it has the potential to significantly expand the number of scientists and institutions that can cost-effectively conduct leading edge proteomics research,” said Natalie Tasman, proteomics software developer in the lab of ISB Co-founder and Professor Ruedi Aebersold, PhD.

The TPP was developed in Aebersold lab at ISB’s Seattle Proteome Center (funded by the National Heart, Lung and Blood Institute (NHLBI), part of the National Institutes of Health). The TPP includes the well-known PeptideProphet and ProteinProphet statistical proteomics tools, which are available at http://tools.proteomecenter.org/TPP.php.

Brian Pratt, Insilicos’ VP Informatics, was the primary developer behind the recent TPP cloud modifications. In addition to enabling cloud computing, Pratt identified several places in the TPP for implementing optimizations, including the introduction of industry-standard “gz” compression, enabling the TPP to automatically process and produce compressed files.

“Even if you're just running the TPP on your own server, the gz compression will really save disk space-- which is increasingly important with the huge files coming off the new instruments,” said Pratt.

Dr. Aebersold describes this effort as a successful example of commercializing publicly funded research and development. “This collaboration allows us to make the tools developed by the NHLBI-supported proteome center widely accessible and to sustain them long-term without the need for continued public funding”.

Users are encouraged to visit the TPP's support and discussion mailing list at http://groups.google.com/group/spctools-discuss for information and assistance with installing and using the freely-available software.

Insilicos LLC develops life science software for pharmaceutical development, biological research and clinical diagnostics.
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