Tuesday, March 2, 2010

“After 5 years, free systems biology markup language has proven popular - EurekAlert” plus 3 more

“After 5 years, free systems biology markup language has proven popular - EurekAlert” plus 3 more

After 5 years, free systems biology markup language has proven popular - EurekAlert

Posted: 01 Mar 2010 08:58 PM PST

[ Back to EurekAlert! ] Public release date: 2-Mar-2010
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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)


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Sigma-Aldrich(R) Focuses on Biology With Launch of New Life Science ... - Forbes

Posted: 01 Mar 2010 10:24 PM PST

ST. LOUIS, March 2 /PRNewswire-FirstCall/ -- Sigma-Aldrich(R) (NASDAQ: SIAL) today unveiled its new Sigma((R)) Life Science brand and website platform, designed to elevate the Company's current focus on biology and provide a single destination where researchers can access deep biological knowledge and market-leading products and technologies. The introduction of Sigma Life Science's 'Where Bio Begins' brand (www.wherebiobegins.com) brings attention to its biology focus by providing researchers with robust, unique, industry-leading technologies and biologically- focused products to help them explore, study and understand life.

The Sigma Life Science mission is expected to enable researchers to unravel the complex biomolecular interactions within cells, tissues, organs and organisms. The new brand and website are expected to generate awareness of Sigma Life Science's strengths in providing products and technologies that are intended to facilitate scientists' understanding of how diseases develop and how molecules function.

"Our new brand will help us tell our biology story - that Sigma holds what we believe is one of the largest portfolios of biologically rich products and technologies in the industry," said Dr. David Smoller, president of Sigma-Aldrich's Research Biotech business unit. "We have over $750 million worth of products in our portfolio and are fully committed to helping biologists. For over 50 years, life scientists around the world have depended upon our traditional foundation of bioessentials, including biochemicals, amino acids, antibodies, buffers, carbohydrates, enzymes, forensic tools, hematology, histology, nucleotides and cell culture media because of our quality, service and selection. Over the last few years we have built on this strong foundation to develop innovative products and technologies and become a true leader in the life science market."

Sigma Life Science is a leading biomolecule provider with:

-- The world's largest custom oligonucleotide service supplying customers around the globe with high quality DNA and RNA and, in many regions, same-day custom DNA synthesis; -- A growing portfolio of more than 25,000 monoclonal and polyclonal antibodies including Prestige Antibodies(R) Powered by Atlas Antibodies, the industry's most highly-validated antibodies; and -- The largest number of bioactive small molecules, peptides and proteins for cell biology and neuroscience research including GPCR and ion channel ligands, novel kinase inhibitors and cell cycle regulators, the gold-standard LOPAC(TM) library of pharmacologically active compounds and key signal transduction enzymes featuring Precisio(TM) kinases.


Sigma Life Science is also emerging as a leader in innovation with:

-- Cutting-edge gene silencing products, MISSION(R) siRNAs and the largest set of validated lentivirus based MISSION(R) shRNA clones; -- The award-winning CompoZr(TM) Zinc Finger Nucleases (ZFN) gene editing technology - the first technology to allow researchers to insert, delete or edit any region of the genome of a living cell or organism; -- SAGE(TM) Labs - the first knockout rat program designed to develop novel rodent models of human disease powered by the CompoZr(TM) ZFN technology; and -- Comprehensive and innovative sets of reagents for regenerative medicine including the Stemgent(TM) reprogramming kit to develop induced pluripotent stem (iPS) cells leveraging the Sigma Life Science lentivirus delivery expertise; HyStem(TM), a fully customizable synthetic extracellular matrix (ECM) to optimize stem cell proliferation and differentiation and a complete portfolio of zinc finger nuclease reagents, antibodies, shRNA/siRNAs for stem cell research.


All of these technologies are accessible through the 'Your Favorite Gene powered by Ingenuity' (http://sigma.com/yfg) search engine - the most dynamic, web-based biological search tool that delivers comprehensive gene-based content to model and evaluate experiments in the context of previously published scientific literature.

"Over the past couple of years we have been working very hard in an attempt to gather the most talented people who are passionate about helping life scientists around the world understand the secrets of life and address the main challenges in biology." said Dr. Helge Bastian, Vice President of Sigma-Aldrich's Research Biotech business unit. "These efforts have transformed our life science business into what we believe is an innovation powerhouse that surprises the market with genuine product innovations. Our award-winning, dynamic web-based biological search tool, 'Your Favorite Gene', our Prestige antibody collection, our ground-breaking CompoZr ZFN technology and the novel, ZFN-enabled knockout rat models generated by our SAGE((TM)) Labs business are proof of the things that researchers can expect from Sigma's Life Science business now and in the future: technologies and products that help advance life science and provide deeper insight into biology leading to better medicines and cures. We are committed more than ever to support life science researchers on their way to new discoveries for a healthier and better life. For researchers, Sigma Life Science is the destination where the new biology begins."

To support the 'Where Bio Begins' launch, eight information portals have been specifically tailored to serve the biology community. Themed around the Company's core biological capabilities in targeted genome editing (bioediting), transgenics (SAGE Labs), functional genomics (biosilencing), stem cell research and epigenetics (bioreprogramming), molecular biology (biomapping), biomolecules, oligonucleotides/custom products (bionucleics), customer education and training programs (biouniversity) and bioinformatic resource (Your Favorite Gene) these sites can be accessed at www.wherebiobegins.com.

The Sigma Life Science blog at http://sigmabioblogs.com serves as a resource for new techniques, improvements to old techniques, exciting applications, and information about scientists from every spectrum of the biological community. We plan to extend our presence via the Where Bio Begins Facebook(R) Fan page and Where Bio Begins Twitter account at http://twitter.com/WhereBioBegins to engage the biology community. Our existing Social Media presence as SAGE Research Models (http://twitter.com/ResearchModels or the SAGE Research Models Facebook(R) Fan page), Your Favorite Gene (http://twitter.com/YourFaveGene or the YFG Facebook(R) Fan ), and CompoZr ZFN Facebook(R) fan page are intended to communicate with the biocommunity around topics more directly related to using Sigma Life Science tools and techniques.

Cautionary statement: The foregoing release contains forward-looking statements that can be identified by terminology such as "designed to elevate," "is expected to generate," " emerging as a leader in innovation," "most dynamic, web-based biological search tool," or similar expressions, or by express or implied discussions regarding potential future revenues from products derived therefrom. You should not place undue reliance on these statements. Such forward-looking statements reflect the current views of management regarding future events, and involve known and unknown risks, uncertainties and other factors that may cause actual results to be materially different from any future results, performance or achievements expressed or implied by such statements. There can be no guarantee that Sigma Life Science products will continue to meet the demands of the marketplace. Nor can there be any guarantee that any of these products will achieve any particular levels of revenue in the future. In particular, management's expectations regarding these products could be affected by, among other things, unexpected regulatory actions or delays or government regulation generally; the company's ability to obtain or maintain patent or other proprietary intellectual property protection; competition in general; government, industry and general public pricing pressures; the impact that the foregoing factors could have on the values attributed to the Company's assets and liabilities as recorded in its consolidated balance sheet, and other risks and factors referred to in Sigma-Aldrich's current Form 10-K on file with the US Securities and Exchange Commission. Should one or more of these risks or uncertainties materialize, or should underlying assumptions prove incorrect, actual results may vary materially from those anticipated, believed, estimated or expected. Sigma-Aldrich is providing the information in this press release as of this date and does not undertake any obligation to update any forward-looking statements contained in this press release as a result of new information, future events or otherwise.

About Sigma Life Science: Sigma Life Science is a Sigma-Aldrich brand that represents Sigma's leadership in innovative biological products and services for the global life science market and offers an array of biologically-rich products and reagents that researchers use in scientific investigation. Product areas include biomolecules, genomics and functional genomics, cells and cell-based assays, transgenics, protein assays, stem cell research, epigenetics and custom services/oligonucleotides. Sigma Life Science also provides an extensive range critical bioessentials like biochemicals, antibiotics, buffers, carbohydrates, enzymes, forensic tools, hematology and histology, nucleotides, amino acids and their derivatives, and cell culture media.

About Sigma-Aldrich:Sigma-Aldrich is a leading Life Science and High Technology company. Its biochemical and organic chemical products and kits are used in scientific research, including genomic and proteomic research, biotechnology, pharmaceutical development and as key components in pharmaceutical, diagnostic and other high technology manufacturing. Sigma-Aldrich has customers in life science companies, university and government institutions, hospitals, and in industry. Over one million scientists and technologists use its products. Sigma-Aldrich operates in 38 countries and has 7,700 employees providing excellent service worldwide. Sigma-Aldrich is committed to Accelerating Customer Success through Innovation and Leadership in Life Science, High Technology and Service. For more information about Sigma-Aldrich, please visit its award-winning website at http://www.sigma-aldrich.com.

Sigma-Aldrich, Sigma, Prestige Antibodies, CompoZr, Precisio, MISSION, SAGE and LOPAC are trademarks of Sigma-Aldrich Biotechnology L.P. and Sigma-Aldrich Co.Stemgent is a trademark of Stemgent, Inc. Hystem is a trademark of Glycosan BioSystems, Inc.Facebook is a registered trademark of Facebook, Inc.

SOURCE Sigma-Aldrich


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Lecture: 'Bare bones info: What skulls and skeletons tell us about ... - Battle Creek Enquirer

Posted: 02 Mar 2010 07:06 AM PST

On March 2, 2010 at 6:30 p.m. Kingman Museum welcomes Dr. Dale Kennedy for "Bare Bones Info: What Skulls and Skeletons Tell us About Mammals." The lecture is Free to the public and is held in the Community Planetarium. The lecture last approximate 45 minutes and is followed by a question answer period. Local teachers receive professional development credit for attending.

Installations of new exhibitions on Kingman Museum's mezzanine level are scheduled for completion in summer 2010. Inspiration for all First Tuesday lectures in 2010 comes from the new exhibit themes. Kingman is currently working on exhibits in the Biological Science Hall. In addition to human health exhibits there are several focusing on our animal relatives including a skeleton exhibit, which serves as inspiration for Kingman's March lecture. Kingman's March 2, 2010 lecture, "Bare bones info: What skulls and skeletons tell us about mammals," will be all about the study of animal skeletons.

Dr. Dale Kennedy is the A. Merton Chickering Professor of Biology and Chair of the Biology Department at Albion College. Dr. Kennedy will teach us about the forensics side of biology and all of the interesting information that can be gained by studying an animal's skeletal remains. How old was the animal? What did it eat? Was it sick? How did it die? All of these questions can be answered by studying the animal's skeleton and Dr. Kennedy will tell us how.

Dr. Kennedy is a behavioral ecologist whose research focuses primarily on factors that affect clutch size (number of eggs laid) and breeding success in birds. She carries out field studies on mating and feeding behaviors, clutch size, hatching and fledgling success, and nestling growth rates of a variety of cavity-nesting birds. In recent years she and her students have examined sex ratios of nestling House Wrens and Tree Swallows, patterns and variation in songs of House Wrens and other birds, effects of nest box microclimate on breeding success of wrens and swallows, and dominance and movements of local Black-capped Chickadees. Almost all her work is done in the Whitehouse Nature Center at Albion College.

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Giant Snake Preyed on Baby Dinosaurs - Democratic Underground.com

Posted: 02 Mar 2010 07:42 AM PST

Remains of an enormous snake have been discovered in a 67-million-year-old dinosaur nest, according to a new study. The snake was found coiled around a crushed dinosaur egg and next to what was left of a hatchling titanosaur.

This preserved moment in Cretaceous time provides the first direct evidence of the feeding behavior of a primitive snake, co-author Jason Head told Discovery News. Aside from this discovery, two other similar snake-egg pairings were also found at the site, located in what is now Gujarat in western India.

The 11.5-foot-long snake, described in the latest PLoS Biology, represents a new species, Sanajeh indicus, meaning "ancient-gaped one from the Indian subcontinent."

"It was not necessarily a specialized constrictor, but it clearly grabbed dinosaur hatchlings and gobbled them down," said Head, a paleontologist and assistant professor in the Department of Biology at the University of Toronto Mississauga.

"Sauropods laid their eggs in nests covering several hundred miles, so the newly hatched dinosaurs would have been like meatballs on a smorgasbord for the snakes," he added.

http://news.discovery.com/animals/snakes-baby-dinosaurs...

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