News

Insilcos Releases GPU-based Linear Modeling tool for R

Plone Site Administrator — 2012-03-09T08:00:00Z

Insilicos today announced the release of the WideLM package for the R language. WideLM includes a GPU-based method to perform linear modeling at rates 150 times faster than CPU-based implementations. Insilicos developed WideLM for bioinformatics research, but the package is useful more generally for analysis of "wide" data sets, or those involving many more predictor variables than actual observations.

"We wrote WideLM because no available method achieves the throughput necessary to handle the large number of models we are testing," said Mark Seligman, Senior Scientist at Insilicos and lead developer of WideLM. "Our research involves extensive resampling of data in order to estimate the false-discovery rates of gene-interaction statistics. On microarray data involving the yeast genome, for example, WideLM allows us to test well over 1 million submodels per second using NVIDIA Tesla-series GPUs."

WideLM is available from Insilicos at www.insilicos.com/products/widelm

Insilicos specializes in biomarker analysis for diagnostic medicine and other applications. Seligman's research at Insilicos is to identify candidates for gene-gene interactions, or "epistasis." Because epistasis potentially exists between any two or more genes, a combinatorial explosion results in literally billions of possible epistasis candidates. Even after standard data-reduction techniques are applied, the potential number of tests to perform can grow unwieldy. Besides the enormous number of possibilities to check, some combinations will falsely look like epistasis, simply by chance. To estimate the number of such false instances, the data is resampled iteratively and wide linear modelling is applied to each resampled data set. A false-discovery rate is thus approximated by iteratively modelling numerous pairs of genes. The result is a large computation task, even for a supercomputer. Insilicos developed WideLM to allow this computation to be completed using a GPU-enabled desktop computer on a whole genome in literally seconds. Insilicos' work on epistasis is funded in part by NIH grant HG005936. Details of the work to accelerate these algorithms using the GPU will be presented at NVIDIA's upcoming GTC 2012 conference.

Insilicos Publishes Paper on Cloud-based Peptide Search

Erik Nilsson — 2012-01-18T06:00:00Z

Seattle, 18 January 2011 - Seattle biotech company Insilicos today announced that the journal Bioinformatics has published a paper on Insilicos' development of MR-Tandem, a cloud-based version of the popular, open-source X!Tandem peptide search engine. MR-Tandem uses the Hadoop Map-Reduce framework to create large virtual clusters, allowing researchers to quickly and inexpensively analyze large proteomics studies, even when many post-translational modifications must be considered.

"Up 'til now, proteomics researchers have either had to have an expensive computer cluster, or else confine themselves to small experiments," explains lead paper author and Insilicos VP of Informatics Brian Pratt. "What the community needed was an open-source peptide search engine that runs well in the cloud. So that's what we did."

"We just took a big capital expense out of large-scale proteomics," noted Insilicos President Erik Nilsson. "Don't have a million-dollar compute cluster at your beck and call? Now that isn't a problem."

The paper "MR-Tandem: Parallel X!Tandem using Hadoop MapReduce on Amazon Web Services" is available at http://bioinformatics.oxfordjournals.org/content/early/2011/11/08/bioinformatics.btr615.abstract

MR-Tandem, full documentation, and a windows installer are available as part of the Insilicos Cloud Army project here.

MR-Tandem source code is available as part of the Sashimi project here. This work is funded in part by grant HG006091 from the National Human Genome Research Institute, part of the National Institutes of Health.

Insilicos LLC is a Seattle-based biomarker analytics and diagnostic development company. For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos,' 'PreClue,' 'Life Science Software,' and 'Cloud Army' are trademarks of Insilicos LLC.

Insilicos begins prospective heart attack study

Erik Nilsson — 2011-09-13T17:40:00Z

Seattle, 14 September 2011 - Insilicos announced today that the Seattle life sciences company has begun enrolling clinical subjects in a diagnostic study to predict heart attacks up to two years before they occur.

The study will evaluate Insilicos’ PreClue diagnostic test by collecting blood samples from 400 persons who visit a Seattle-area emergency room with chest pain. Those who agree to participate in the study will provide a blood sample. The PreClue diagnostic will be used on the samples to predict each person’s risk of a heart attack.

“This prospective study is a milestone for PreClue and for Insilicos,” said Insilicos Chief Scientist Dr. Bryan Prazen. “PreClue has previously shown powerful results on banked samples. We’re now building on that work with this large study of a group of patients --patients who frankly need better information about the risks they face. The prospect of being able to help such people is exciting –as is the opportunity to create a valuable sample set.”

Insilicos is collaborating with researchers at the University of Washington in the study. The work is funded in part by the National Heart, Lung, a Blood Institute, a part of the National Institutes of Health.

Insilicos Awarded Grant for Proteomics Supercomputing

Erik Nilsson — 2011-08-12T21:27:51Z

Seattle, 15 August 2011 - Insilicos today announced that Brian Pratt has received an SBIR grant from the National Human Genome Research Institute, a part of the National Institutes of Health (NIH).

The grant is to apply massively-parallel GPGPU computing technology to proteomics. GPGPU technology uses highly-parallel processors originally developed for graphics processing to perform many computations at once, making computations run as much as 1,000 times faster. Peptide search is used to identify proteins in biological samples. Peptide search requires extensive computations, and is usually the bottleneck in proteomics data analysis. A prototype search engine suggests that GPGPU technology can be used to greatly accelerate peptide search.

"Advances in lab technology have brought proteomics within reach of many researchers," said Pratt. "Yet, analysis of results often requires access to a computer cluster costing millions of dollars. At Insilicos, our strategy is to put proteomics analysis into the hands of researchers who don't have the resources for a computer cluster. This grant will allow researchers to use the computer sitting on their desk right now as a peptide search supercomputer. We think that's pretty cool."

Insilicos releases peptide search engine

Plone Site Administrator — 2011-03-30T08:00:00Z

Seattle, 30 March, 2011 - Insilicos today announced the first official release of MR-Tandem, a highly-scalable peptide search engine based on the popular X!Tandem program. MR-Tandem is available for free at insilicos.com/products/mr-tandem

Peptide search engines are used in proteomics research with mass spectrometry data, to identify proteins in biological samples. X!Tandem is one of the leading peptide search engines, and the most popular open-source peptide search tool.

"Peptide search typically requires a computer cluster costing hundreds of thousands or even millions of dollars," said Insilicos VP of Informatics Brian Pratt. "As the cost of lab work falls, computation becomes the cost and time bottleneck. We developed MR-Tandem to allow researchers who don't have their own computer cluster to do proteomics computational analysis inexpensively, using cloud computing."

MR-Tandem employs the Hadoop framework to use literally hundreds of inexpensive cloud computing instances, allowing results to be obtained both quickly and inexpensively. This efficiency is particularly important when many post-translational modifications must be considered. "Post-translational modifications make the search task so much bigger," said Insilicos President Erik Nilsson. "We think biologists may be under-searching their data, simply because they lack the resources for a more thorough search. By making search more accessible, MR-Tandem will help us find out if there are valuable discoveries hidden in the proteomics data researchers have already collected."

Insilicos LLC is a biomarker analytics company based in Seattle.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Announces Appointment of Jeff Howbert as Senior Scientist

Plone Site Administrator — 2010-12-15T08:00:00Z

Seattle, 15 December 2010 - Insilicos announced today the company has appointed Dr. Jeff Howbert to the role of Senior Scientist. Dr. Howbert is a computer scientist and chemist, with particular interests in statistics, machine learning, and predictive models. He has a longstanding association with Insilicos, working with the company on several research projects. Dr. Howbert brings over 25 years experience in drug discovery and gene discovery in multiple therapeutic areas, in both large pharmaceutical and biotech environments.

"Dr. Howbert is an accomplished and imaginative reearcher," said Insilicos President Erik Nilsson. "It is my pleasure to announce this role for Jeff, a capable scientist whose research interests are well-aligned with Insilicos' direction."

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Wins Therapeutic Discovery Award for Cardiovascular Diagnostic

Plone Site Administrator — 2010-11-01T07:00:00Z

Seattle, 1 November 2010 - Insilios announced today the company has been awarded a $244,000 Therapeutic Discovery grant for Insilicos' cardiovascular diagnostic PreClue^TM.

"This award comes at a particularly opportune time for us, at the start of a key clinical study," said Insilicos president Erik Nilsson.

The award was part of the program known officially as the Qualifying Therapeutic Discovery Project program. This program was created by Congress as part of the Patient Protection and Affordable Care Act, and provides a tax credit or grant equal to a portion of eligible 2009 and 2010 research and development expenditures.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Awarded Grant Applying GPU Computing to Epistasis

Plone Site Administrator — 2010-10-02T07:00:00Z

Seattle, 2 October 2010 - Insilicos today announced the company has received a grant applying GPU computing to the genomic phenomenon called epistasis. The grant is from the National Human Genome Research Institute, part of the National Institutes of Health. This is the third research grant Insilicos has received in 2010.

Epistasis occurs when the effects of one gene are modified by one or more other genes. GPU computing uses graphics accelerator cards as parallel computation engines for a "desktop supercomputer."

"This research requires extensive computation," said Insilicos researcher Mark Seligman, principal investigator on the grant. "Our goal is to use new statistical methods with GPU computing to make such research practical on a desktop computer."

The research will compare data on eQTLs (expression quantitative trait loci, SNPs which are associated with the expression of a gene) to GWAS (genome-wide association studies) data. GPU computing will quickly perform the necessary computations on an inexpensive desktop computer.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Announces Trial of Cardiovascular Diagnostic

Plone Site Administrator — 2010-09-06T07:00:00Z

Seattle, 6 September 2010 - Insilicos today announced that the company has been awarded a $1.2 million grant to evaluate Insilicos' PreClue diagnostic test for cardiovascular disease. The test will be given to 400 subjects with suspected cardiovascular disease, to predict future heart attacks in advance.

"We're excited to be moving into the clinic," said Insilicos Chief Scientist Bryan Prazen. "Our human results to date have been extremely encouraging. Now we'll get to see performance under more realistic clinical conditions."

"This is an important day for Insilicos," said president Erik Nilsson. "Our test has the potential to revolutionize the way cardiovascular patients are evaluated and treated. We look forward to this project with great enthusiasm."

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos President Erik Nilsson Speaks on Health Information Panel

Plone Site Administrator — 2010-08-30T07:00:00Z

Seattle, 30 August 2010 - Xconomy reported today on a Health Information Technology (HIT) panel held August 25th at the Microsoft Conference Center in Redmond.

The panel was moderated by Pacific Biosciences chief scientist Eric Schadt. Panelists included Insilicos president Erik Nilsson, Sage Bionetworks president Stephen Friend, senior director of Microsoft’s applied research and technology division Jim Karkanias, Swedish Medical Center chief executive Rod Hochman, and Beacon Community of the Inland Northwest director Jac Davies.

Nilsson's remarks focused on the concept of Pervasive Healthcare, and how cloud computing can support a nexus of healthcare, epidemiology, research, and product development.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Awarded Grant to Develop Cloud Computing Biomarker Search System

Plone Site Administrator — 2010-08-23T07:00:00Z

Seattle, 23 August 2010 - Insilicos announced today that the company has been awarded a grant to develop a highly-scalable, cloud computing-based system to search protein databases. The system is intended for use in mass spectrometry proteomics.

Insilicos will be modifying the open-source X!Tandem protein search engine for use with large cloud-based computer clusters, to search for post-translational modifications to proteins. Post-translationally modified proteins can be important biomarkers for understanding human health and disease.

This work is supported by funding from the National Human Genome Research Institute, part of the National Institutes of Health.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos President Erik Nilsson Writes on Cloud Computing

Plone Site Administrator — 2010-08-03T07:00:00Z

Seattle, 3 August 2010 - Xconomy today carried an op ed by Insilicos president Erik Nilsson on Seattle's unique confluence of biotech and cloud computing.

Nilsson concludes that, even though biotech is not the largest cloud customer, cloud computing companies court biotech. This is probably because biotech's time flexibility makes it a disproportionately profitable cloud customer.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Awarded Grant to Improve Bioinformatics Software

Plone Site Administrator — 2010-08-02T07:00:00Z

Seattle, 2 August 2010 - Insilicos announced today that the company has won a Federal stimulus grant to improve the user interface of a popular open-source system for analyzing biological data.

The grant is for enhancements to the Trans-proteomic Pipeline (TPP), a software system developed at the Institute for Systems Biology (ISB) in Seattle. Insilicos and the ISB have collaborated for several years on improvements to the TPP software. For this grant, Insilicos will add security and data sharing features to the TPP to enable collaborators to more easily share experimental data.

Insilicos received the grant from the National Human Genome Research Institute, part of the National Institutes of Health. The grant was made as part of the American Reinvestment and Recovery Act.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos, Collaborators Publish Results of Human Cardiovascular Study

Plone Site Administrator — 2010-07-12T07:00:00Z

Seattle, 12 July 2010 - Insilicos and collaborators at the University of Washington have published results showing that the company's biomarker platform is a rich source of information on human cardiovascular health. The paper correlates changes in high-density lipoprotein (HDL) particles with cardiovascular disease.

The paper in the journal Clinica Chimica Acta is authored by Insilicos chief scientiest Dr. Bryan Prazen, UW scientist Dr. Tomas Vaisar, and others. The paper describes changes in the protein composition of HDL particles that correlate with cardiovascular disease, as well as responses to treatment.

"We are excited to share this work with the research community," said Dr. Prazen. "These results demonstrate the potential of lipoprotein complexes as a rich source of biomarkers and diagnostic insight."

The article is cited as Clin Chim Acta. 2010 Jul 4;411(13-14):972-9), Pubmed 20307520

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.

Insilicos Moves to New offices

Plone Site Administrator — 2009-12-07T08:00:00Z

Seattle, 7 December 2009 - Insilicos today announced that it has moved to larger offices in the Uptown neighborhood of Seattle. Insilicos' new address is 111 Queen Anne Avenue North, #500, Seattle, WA.

"Our new headquarters accomodate recent expansion of the company and gives us room for frther growth," said Insilicos president Erik Nilsson.

Insilicos LLC is a biomarker discovery and diagnostic development company, concentrating on cardiovascular disease.

For more information, visit the Insilicos web site www.insilicos.com or contact Insilicos at info@insilicos.com. 'Insilicos' 'PreClue," and 'Life Science Software' are trademarks of Insilicos LLC.