“MIT receives funding to start new Center for Cancer Systems Biology - MIT News” plus 3 more

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• MIT receives funding to start new Center for Cancer Systems Biology - MIT News
• NCSU selects 6 Park Scholars from area - Raleigh News & Observer
• PETA seeks end to ASU using animals in biology labs - AZCentral.com
• After 5 years, free systems biology markup language has proven popular - EurekAlert

MIT receives funding to start new Center for Cancer Systems Biology - MIT News Posted: 04 Mar 2010 10:46 AM PST This past week, the David H. Koch Institute for Integrative Cancer Research at MIT received funding from the National Cancer Institute (NCI) to become a Center for Cancer Systems Biology (CCSB). These centers are part of NCI's Integrative Cancer Biology Program (ICBP), which is the NCI's primary effort in cancer systems biology, a field that is rapidly seen as an essential component in the future of cancer research.  "These centers represent a unique multidisciplinary union of outstanding scientists and clinicians who will work to unravel the complexities of cancer through the novel application of technology and mathematical modeling. Their discoveries and models will be critical to our continued success in understanding and treating this disease," said Dan Gallahan, program director for the Integrative Cancer Biology Program.   Douglas Lauffenburger, member of the Koch Institute and head of the Department of Biological Engineering, will be the principal investigator for the new center. In addition to the funding received by MIT, 10 other outstanding centers nationwide will share NCI's commitment to this area of research. Selection of MIT as part of NCI's Integrative Cancer Biology Program underscores and reflects the Institute's leadership within the community. These new centers and the research that evolves from them should enable scientists to gain a better understanding, and therefore better treatment and prevention, for the disease.  "This program is part of the next generation of cancer research, in that it will approach the disease from a holistic or comprehensive viewpoint in order to understand how all of the components of the disease fit together," said John E. Niederhuber, M.D., NCI Director. This approach to cancer research is made possible by advances in technology and computational modeling. These centers will not only explore new insights in the areas of cancer systems biology, but will generate computational and mathematical models for application in the lab and the clinic. The centers will work closely with all aspects of the research community and rely heavily on data and insight from other prominent NCI efforts. Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

NCSU selects 6 Park Scholars from area - Raleigh News & Observer Posted: 05 Mar 2010 02:52 AM PST The Park Scholarship is valued at $80,000 for North Carolina residents and $135,000 for out-of-state students. It covers expenses for four years of study at NCSU and includes a computer stipend and money for academic enrichment activities. The Park Scholarships are named for the late Roy H. Park, a 1931 NCSU graduate who created the Park Foundation, based in Ithaca, N.Y. Here are the Triangle winners: Nicole Doris Roscoe of Bear Creek, who will graduate from Chatham Central High School and plans to major in biology. Ansilta Zulima De Luca-Westrate of Durham, who will graduate from Durham Academy and plans to major in elementary education. Madhulika Vulimiri of Morrisville, who will graduate from Enloe High School and plans to major in biology or public health. Alex Jin-Wei Chin ofCary, who will graduate from Broughton High School and plans to major in mathematics and physics. William Hampton Coe of Raleigh, who will graduate from Sanderson High School and plans to major in philosophy. Stephen Thomas West of Raleigh, who will graduate from Trinity Academy and plans to major in aerospace engineering. Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

PETA seeks end to ASU using animals in biology labs - AZCentral.com Posted: 04 Mar 2010 01:02 PM PST The animal-rights group PETA wants Arizona State University to stop using animals in its biology labs. "There is no sound scientific or educational justification for dissection and classroom experiments on live animals," said Justin Goodman, research associate supervisor with PETA. He spoke Tuesday in ASU's Memorial Union. His visit was sponsored by an ASU group, Students Taking Action for Animal Rights or STAAR. At any one time, 5,000 animals are being used on campus, he said, including rats, rabbits, dogs, cats and monkeys. Most are used in research, but one-fifth are used - unnecessarily -- for educational purposes, he said. In a general biology lab, Bio 188, a total of 864 frogs were used in three years, Goodman said. Live frogs are anesthetized and cut so students can watch their hearts beat, and watch the effects on their bodies of the application of hormones. Then the frogs are killed by having a pin stabbed in their brain or they're decapitated, he said. Citing figures he obtained from ASU through a public records request, he said that in three years, the class Bio 201 used 120 pregnant rats, Bio 352 used 400 mice and Bio 361 used 216 frogs, 41 pregnant rats and 295 rabbits. Students learn as well or better with non-animal alternatives, he said, including computer software, DVDs, models, virtual reality and lifelike mannequins. Skip Derra, an ASU spokesman, said ASU had responded to two public records requests from PETA. "We also reviewed our procedures when PETA presented alternatives and found that the PETA suggestions did not provide the educational experience of the present method," he said. "ASU communicated that to PETA." Derra provided a statement from ASU that said the university supports the responsible study and humane care and treatment of animals in teaching. "ASU believes that alternatives to the use of live animals should be developed and the university should employ them whenever possible," it said. In fact, most labs use non-animal alternatives, the university said. The goal of ASU's Institutional Animal Care and Use Committee is to not only ensure that ASU meets all regulatory requirments, but also to ensure that there is a strategic balance between the quality of teaching and the use of animals, the ASU statement said. "Animals are never treated cruelly or inhumanely at ASU," the university said. Goodman cited an article in the journal Nature that said 93 percent of U.S. medical schools do not use live animals in labs to train students. "Today you can become a brain surgeon or a trauma surgeon without touching an animal, dead or alive," he said. "Nearly all medical students learn by human simulators. . . . When you deal with a rabbit, you get a rabbit response; that's not telling you about humans." Places are still using animals because of lack of information about alternatives or because of "institutional inertia" and faculty resistance to calls for change from outside parties, he said. "ASU can do better," he said. If the university replaced animals in labs, it would save lives, enhance education, save money and create a more inclusive learning environment by not discouraging those who have ethical beliefs against using animals, Goodman said. PETA first contacted ASU nearly a year and a half ago after PETA was contacted by some ASU students. Goodman said ASU had been "very unresponsive" in his requests to open a dialogue. "I contrast that to UC-Irvine, where we had ongoing discussions, and they were responsive and communicative. ASU hasn't been. It's disappointing." Goodman encouraged his audience to sign petitions, write letters to ASU and to newspapers, work with student government to pass resolutions against animal use and to speak to the Board of Regents. Petitions signed by 1,500 students were previously delivered to ASU Provost Betty Capaldi. Kirby Mauro, vice president of STAAR, said the petitions were accompanied by a letter inviting ASU to debate, but that there had been no response. Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

After 5 years, free systems biology markup language has proven popular - EurekAlert Posted: 01 Mar 2010 08:58 PM PST Public release date: 2-Mar-2010 [ | E-mail | Share ] Contact: Barry Whyte whyte@vbi.vt.edu 540-231-1767 Virginia Tech Blacksburg, Va. A scientific paper that describes a file format used by scientists to represent models of biological processes has exceeded 500 citations in the ISI Web of Knowledge, an online academic database that documents the impact of scientific publications. The Systems Biology Markup Language (SBML) is designed to enable the exchange of quantitative models of biochemical networks between different computer software packages, allowing the models to be shared and published in a form other researchers can use in various software environments. Information standards are needed by the systems biology community to help share, evaluate, and develop models of biological processes. Over the years, many scientists and computer specialists have contributed their time and expertise to the development of SBML as part of the international consortium known as the SBML Forum. The paper that first described the SBML information standard and which has exceeded the 500-citation milestone appeared in the journal Bioinformatics in 2003 and is entitled "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models." Michael Hucka, a Senior Research Fellow at the California Institute of Technology (Caltech) in Pasadena, and first author of the paper, has chaired the SBML Editors and SBML Team by community consensus since 2003. Today he works on all aspects of SBML and is involved with BioModels.net http://biomodels.net/> consortium efforts such as the BioModels Database http://www.ebi.ac.uk/biomodels>. Said Hucka, "We're all really pleased by this outcome. The number of citations for our original paper is a validation of the usefulness of the SBML language to the scientific community. The development of SBML continues at pace thanks to the efforts of both a team of dedicated developers and an international community of volunteers and researchers, who act as SBML users and fellow developers. SBML is a free and open community resource that extends beyond the interests of any single group of researchers." Back in 1999, when the SBML team was coming together, some of the early members of the group included Hamid Bolouri, John Doyle, Andrew Finney, Hiroaki Kitano, Herbert Sauro, and Hucka.* Hiroaki Kitano, the principal investigator who started the SBML project, is director of Sony Computer Science Laboratories, Inc., and director of the Systems Biology Institute in Tokyo, Japan. Commented Kitano, "Systems biology has triggered a revolution in biology that in time will hugely impact scientific and medical practice. The idea of SBML came from the vision that compatibility and interoperability were going to be the issue once systems biology took-off. In 1999, the group that eventually became the SBML Team at Caltech and I organized a workshop to discuss issues in software platforms and how to solve them. This is when we decided to initiate the project. Since then, many people have found value in the project and the community has grown beyond critical mass. At the time, I was fortunate to be the recipient of Japanese Exploratory Research for Advanced Technology (ERATO) funding. ERATO funding is a large-scale, extremely flexible funding that helped me to support the initiative at an early stage, make the initiative happen, and assist in making the project self-sustainable. Breaking 500 in the citation index is a sure sign that SBML is coming of age." SBML is a computer-readable format for describing qualitative and quantitative models of biochemical reaction networks. It can also be used to express gene regulatory networks and other phenomena of interest in systems biology. Stefan Hoops, computational systems biologist at the Virginia Bioinformatics Institute (VBI) at Virginia Tech, served as an SBML Editor for three years. He helped to develop the latest edition of SBML, which is called Level 3, from 2007 until the end of 2009. Said Hoops, "SBML continues to develop in new directions. For example, the new Level 3 specification will allow a much more detailed description of biological models. As a modular solution, it is also becoming very easy to incorporate SBML into a wide range of software packages." Pedro Mendes, associate professor at VBI and professor in the School of Computer Science, University of Manchester, England, commented, "The community-led and community-maintained initiative described in this paper set out to address a fundamental need in the systems biology community, namely to develop a computer language that facilitates communication and research for scientists interested in studying biochemical pathways and networks. SBML has been a focal point for the computational systems biology community and a catalyst for new developments in this area of research. This citation milestone affirms that SBML is the main standard in the growing field of systems biology." Read the original paper: * Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531. www.ncbi.nlm.nih.gov/pubmed/12611808?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=7> [PMID: 12611808] Visit the SBML web site at http://sbml.org/Main_Page The new SBML Level 3 Core specification is described in the following publication: Hucka, Michael, Bergmann, Frank, Hoops, Stefan, Keating, Sarah, Sahle, Sven, and Wilkinson, Darren. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate). Available from Nature Precedings http://dx.doi.org/10.1038/npre.2010.4123.1 (2010) [ | E-mail | Share ]   Five Filters featured article: Chilcot Inquiry. Available tools: PDF Newspaper, Full Text RSS, Term Extraction.

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