Navigation Links
SDSC, Calit2 awarded $1.4 million NSF grant for new bioinformatics tools
Date:10/18/2011

Researchers at the San Diego Supercomputer Center (SDSC) and the California Institute for Telecommunications and Information Technology (Calit2) at the University of California, San Diego, have been awarded a three-year, $1.4 million grant from the National Science Foundation (NSF) to create a Kepler Scientific Workflow System module. Researchers will develop new tools to help manage ever-growing data sets used in next-generation DNA sequencing.

"Next-generation DNA sequencing is now creating such a large amount of sequence data that it is overwhelming current computational tools and resources," said Ilkay Altintas, director of the Scientific Workflow Automation Technologies (SWAT) Lab within SDSC's Cyberinfrastructure Research, Education And Development (CI-RED) group, and Principal Investigator for the project. "New computational techniques and efficient implementation mechanisms for this data-intensive workload are needed to enable rapid analysis of these next-generation sequence data."

The project receiving the NSF award is called Advances in Biological Informatics Development: bioKepler: A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data. Bioinformatics refers to a field of science that combines biology, information technology, computers and statistical techniques to create research-driven solutions such as customized medications and treatments to help prevent disease, three-dimensional models of genomes and proteins, and advanced agricultural technologies.

"The enormous growth in data-intensive research means that as these data sets get larger, moving data over the network becomes more complicated, error-prone and costly to maintain," said Altintas, who also serves as SDSC's deputy coordinator for research.

The bioKepler project is motivated by the following three challenges that remain unsolved:

  • How can large-scale sequencing data be analyzed systematically in a way that incorporates and enables reuse of best practices by the scientific community?
  • How can such analysis be easily configured or programmed by end-users with various skill levels to formulate actual bioinformatics workflows?
  • How can such workflows be executed in computing resources available to scientists in an efficient and intuitive manner?

To create such an environment, the bioKepler project will create scientific workflow components to develop an array of bioinformatics tools using distributed execution techniques. Once customized, these components will be used on multiple distributed platforms, including various cloud and grid computing platforms. The tools will be selected to meet the diverse needs of researchers, and organized into eight groups covering most aspects of bioinformatics applications: sequence database searches; mapping; sequence assembly; gene prediction; clustering; multiple sequence alignment, phylogeny and taxonomy; protein annotation; and other miscellaneous utilities such as data format transformation and parsing.

Training Next-Generation Scientists

"These tools will be applicable to a wide range of bioinformatics and computational biology problems," said Altintas, noting that "a key part of this project will also focus on education and outreach efforts, underscoring the importance of training next-generation scientists, as well as the need to narrow the gap between bioinformatics and technology."

All the resources, materials, and open-source software products produced by the bioKepler project will be integrated with Calit2's Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA), a data repository and a bioinformatics resource for metagenomic analysis.

"The Kepler workflow system has already been used comprehensively in the CAMERA project," said project co-investigator Weizhong Li, a research scientist at Calit2 and the Center for Research in Biological Systems (CRBS), and Bioinformatics group leader for CAMERA. "With the proposed developments in bioKepler, the CAMERA project and its large user communities will benefit from a larger set of next generation sequence analysis tools with much better scalability and flexibility. Other projects that heavily rely on next-generation sequencing, such as various microbiome projects, can also take advantage of the bioKepler software."

Moreover, bioKepler will be packaged to be installed on diverse, distributed execution environments (e.g., as a Web service and as virtual machines tuned for various Grid and Cloud systems), which in turn will enable deployment of bioKepler on public and private clusters and clouds.


'/>"/>

Contact: Jan Zverina
jzverina@sdsc.edu
858-534-5111
University of California - San Diego
Source:Eurekalert

Related biology news :

1. UofL researcher awarded $2.6 million NIH grant renewal
2. Danforth Plant Science Center awarded major bioenergy grant from US Department of Energy
3. UCSB awarded $15 million by Dow to establish collaborative institute for materials research and education
4. National Museum of the American Indian awarded prestigious LEED Green Building Certification
5. Tobin Marks awarded Dreyfus Prize in the Chemical Sciences
6. University of Texas marine scientists awarded $5.6 million for study of critical Arctic environment
7. Contract awarded for equipment to support on-going fish studies in the West
8. Harvard School of Public Health awarded $20 million CDC grant to study HIV prevention in Botswana
9. BMC awarded NIH grant to study brain abnormalities in former ELGANS patients
10. Louisville researcher awarded $12.8 million NIH grant renewal for adult stem cell project
11. Mass. Eye and Ear awarded largest NIH grant in hospital’s history
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:12/7/2016)... , Dec. 7, 2016   Veridium , ... the appointment of new CEO James Stickland ... with decades of experience, has served in senior ... where he specialized in expanding a pipeline of ... portfolios. He most recently served as managing director ...
(Date:12/2/2016)... , December 1, 2016 ... (Fingerprint, Voice), Future Technology (Iris Recognition System), Vehicle ... - Global Forecast to 2021", published by MarketsandMarkets, ... Million in 2016, and is projected to grow ... CAGR of 14.06%.      (Logo: http://photos.prnewswire.com/prnh/20160303/792302) ...
(Date:11/29/2016)... 29, 2016   Neurotechnology , a ... recognition technologies, today released FingerCell 3.0, a ... solutions that run on low-power, low-memory microcontrollers. ... less than 128KB of memory, enabling it ... have limited on-board resources, such as: mobile ...
Breaking Biology News(10 mins):
(Date:12/8/2016)...  Anaconda BioMed S.L., a pre-clinical stage medical device ... neuro-thrombectomy system for the treatment of Acute Ischemic Stroke ... to join its Scientific Advisory Board (SAB). The SAB ... scientific and clinical experts to Anaconda BioMed S.L., as ... ® to its clinical phase. The SAB is ...
(Date:12/8/2016)... ... December 08, 2016 , ... ... the World Technology Awards. uBiome is one of just six company finalists in ... , In addition to uBiome, companies nominated as finalists in this year’s awards ...
(Date:12/8/2016)... , Dec. 8, 2016 Soligenix, Inc. ... company focused on developing and commercializing products to treat ... announced today that it will be hosting an Investor ... ET on the origins of innate defense regulators (IDRs) ... review of oral mucositis and the recently announced and ...
(Date:12/8/2016)... , Dec. 8, 2016 Eutilex Co. ... billion KRW (US $18.9M) Series A financing. This financing ... G.N. Tech Venture and SNU Bio Angel. This new ... 30.5 billion KRW (US $27.7M) since its founding in ... to bolster the development and commercialization of its immuno-oncology ...
Breaking Biology Technology: