Navigation Links
TopCoder's Open Community Challenge Process Yields 970 Fold Increase in Speed for Big Data Genomics Sequencing Algorithm
Date:2/7/2013

em where the limitations of existing tools had severely constrained the ability to pioneer new advances in medical knowledge.

The researchers offered TopCoder what they thought would be an impossible goal: to develop a predictive algorithm that was an order of magnitude better than either a custom solution developed by Arnaout or the NIH's standard approach (MegaBLAST) and that could scale up to mounting data demands. To do this, they had to first reframe the problem, translating it so that it could be accessible to individuals not trained in computational biology. Among the 84 solutions produced by the TopCoder Community, 16 were an improvement over MegaBLAST with one over 970 times faster than either and was produced during a two week long competition costing just $6,000.

"This is a proof-of-concept demonstration that we can bring people together not only from different schools and different disciplines, but from entirely different economic sectors, to solve problems that are bigger than one person, department or institution," said Eva Guinan , HMS associate professor of radiation oncology at Dana-Farber Cancer Institute and director of the Harvard Catalyst Linkages Program. "Given how complicated the immune system is, this has been a particularly formidable biological problem, and building tools for solving it has been hard and time-consuming. We were stunned by the power of these results and their potential application."

"In a way, the immune system is really the dark matter of biology," said Ramy Arnaout, assistant professor of pathology at Beth Israel Deaconess Medical Center. "We have all this sequence data, and there's no good way to figure out what it's doing. Not only did the best entries achieve truly superior performance, but also this kind of crowdsourcing has the potential to be a general solution for a whole class of problems in biology. No single university or institution has the bandwidth and reso
'/>"/>

SOURCE TopCoder, Inc.
Copyright©2012 PR Newswire.
All rights reserved

Page: 1 2 3 4 5

Related biology technology :

1. BioSpace Spotlights Northwests Life Science Community
2. BioSpace Spotlights Leading Life Science Community
3. Number of Ion Community Users Triples, Spurred by Open Access to DNA Sequencing Protocols and Analysis Software
4. ELISAlink.com ELISA Marketplace and Community Site Coming Soon
5. Bunker Hill Community College Holds Biomedical Careers Graduation Ceremony
6. WHEATON® Introduces a New Web Community for Scientists, Researchers, and Biopharmaceutical Packagers
7. Bunker Hill Community College Student Speaks at 2012 BIO International Convention
8. Aquatic Habitats Donates Research Equipment to Gadsden State Community College
9. BioSpace Spotlights the growing Midwest Life Science Community
10. BioSpace Spotlights Thriving Bay Area Life Science Community
11. BioSpace Spotlights Northwests Life Science Community
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:7/10/2014)... 2014 Unraveling life’s mysteries can intrigue, ... Archer Family purchased a DNA test to ... up with a lifetime of memories, sharing, and closeness. ... members’ DNA genuinely brought the family closer together. ... into genetic history and prior to taking the ...
(Date:7/10/2014)... 2014 EvoDerma ’s NOOME Anti-Aging Motion ... device now comes with a second treatment cup to help ... The new cup is thinner on the edges for a ... rough, thin and uneven surfaces on the face, neck and ... stimulating treatment on areas such as the cheeks and neck, ...
(Date:7/10/2014)... 2014 On July 9 Prime ... presented Russia,s first national "Industry" ... Company is developing a unique project called MabNext ... a number of innovative drugs based on monoclonal antibodies ... took place at the International Exhibition "Innoprom 2014" in ...
(Date:7/10/2014)... , July 10, 2014 Research ... addition of the "International Photonic Integrated Circuit ... Forecasts to 2019" report to their offering. ... The concept of photonic integration traces its ... century. The promise of photonic integration went unexplored ...
Breaking Biology Technology:Ancestry DNA Test Reveals a Controversial and Undiscovered Family History 2Ancestry DNA Test Reveals a Controversial and Undiscovered Family History 3Ancestry DNA Test Reveals a Controversial and Undiscovered Family History 4Ancestry DNA Test Reveals a Controversial and Undiscovered Family History 5Introducing a New Bonus Treatment Cup for EvoDerma’s NOOME Anti-Aging Motion 2Dmitry Medvedev Presented BIOCAD the First National "Industry" Award 2International Photonic Integrated Circuit (Monolithic Integration, Hybrid Integration, Module Integration) Market - Forecasts to 2019 2
... Md. - Engineers at the University of Idaho have ... upcoming NASA missions that will study the Earth and ... a grant technical officer Pen-Shu Yeh, a senior engineer ... engineering team at the University of Idaho,s ...
... sensitive microscopy developed by researchers at Harvard University could ... scientists to track the location of minuscule metabolites and ... of any kind of fluorescent labeling. , The technique, ... the vibrations in chemical bonds between atoms. SRS microscopy ...
... iPods to those who test their knowledge at www.synbioproject.org ... Among the 75 people Esquire magazine recently chose as ... an emerging discipline that combines science and engineering in order to ... as synthetic biology. , , ...
Cached Biology Technology:New one-of-a-kind technology will fly on 2 NASA missions 2New one-of-a-kind technology will fly on 2 NASA missions 3New label-free method tracks molecules and drugs in live cells 2Synthetic Biology Importance in the 21st Century 2Synthetic Biology Importance in the 21st Century 3
(Date:7/11/2014)... with other group members to reduce aggression and gain ... strategy for grooming activities shows a certain pattern across ... scientific journal Biology Letters . , Grooming between ... without ulterior motives. To be groomed has hygienic benefits ... another individual can provide access to infants, mating opportunities ...
(Date:7/11/2014)... kidney injury related to the use of hydroxyethyl starch ... molecules, according to a report in Anesthesia & ... Society (IARS). , The "total mass of HES molecules" ... renal proximal tubule cells (PTCs), concludes the laboratory study ... Wrzburg, Austria. Other factorssuch as differences in the ...
(Date:7/11/2014)... Evidence exists that cannabinoid receptor type 1 ... Ca2+ influx, and reduce neurotransmitter release. However, ... 1 can increase extracellular Ca2+ influx and ... his team, Tongji Hospital Affiliated to Tongji ... Technology, China used whole cell voltage-clamp and ...
Breaking Biology News(10 mins):Baboons groom early in the day to get benefits later 2In lab studies, hydroxyethyl starch has direct harmful effects on kidney cells 2
... ways to automate the production of DNA and proteins, making ... complex carbohydrates, it,s been a different story. Until now, ... study has been slow and tedious. In what may change ... Georgia has created a method for the rapid chemical synthesis ...
... MADISON The "mineral-breathing" bacteria found in many ... or anaerobic, environments contain microbes sometimes described as "mineral-breathing" ... the same way we use oxygen. According to a ... Nature Geoscience , this bacterial respiration may be accelerated ...
... microbicide based on a new type of anti-HIV drug found ... similar to HIV, according to a study reported at the ... is the first of a gel with an integrase inhibitor, ... for the treatment of HIV but just one of the ...
Cached Biology News:New method for producing 'libraries' of important carbohydrate molecules 2New method for producing 'libraries' of important carbohydrate molecules 3Organic solids in soil may speed up bacterial breathing 2Vaginal gel with integrase inhibitor shows promise in monkeys 2Vaginal gel with integrase inhibitor shows promise in monkeys 3Vaginal gel with integrase inhibitor shows promise in monkeys 4Vaginal gel with integrase inhibitor shows promise in monkeys 5Vaginal gel with integrase inhibitor shows promise in monkeys 6
... Digital Sight DS-L2 imaging controller is a ... DS-L1, and allows users to comfortably observe, ... DS-L2 controller features an 8.4 inch LCD ... variety of Nikon cameras including the DS-Fi1 ...
... a premium quality recombinant form of Thermus ... suitable for a wide range of PCR ... reproducible performance, each preparation is extensively tested ... NovaTaq DNA Polymerase possesses an integral 5′→3′ ...
Mouse polyclonal antibody raised against a partial recombinant TSEN2. NCBI Entrez Gene ID = 80746...
Mouse polyclonal antibody raised against a partial recombinant NCLN. NCBI Entrez Gene ID = 56926...
Biology Products: