NewsByteswhat the nucleosome core wouldlook like.” Schlick says.Regardless of which of the four foldingmodels they started their simulationwith, they found that their virtualchromatin always folded into an irregularzig-zag conformation after enoughcomputational steps. They also pinpointedthe key electrostatic attractionsand repulsions that drive chromatinfolding and unfolding.“This is not the first attempt tomodel the chromatin fiber, but this onemakes the fewest artificial assumptions,”says Sergei Grigoryev, PhD,assistant professor of biochemistry andmolecular biology at Penn StateUniversity College of Medicine.Their findings agree with the experimentaldata he has collected on chromatinfolding using electron microscopy.“I really admire their paper,” he says.“For the first time it produced a nucleosomearray model that really matchesbiological observations.”A graphical depiction of the private BioModels submission (1), checking (2),and annotation (3) steps (above) and the public access steps (below).Courtesy of Nicolas Le Novere.Reliable ModelsNow AvailableAs systems biologists develop modelsthat attempt to simulate life, theyneed a good way to make them accessibleto others as well as a good way toaccess other peoples’ models—and toknow they can be trusted to work. Aninternational collaboration known asBioModels intends to provide just that;in April they released an initial set offully annotated models for public use.“We are storing quantitative, peerreviewedmodels so that people canuse them,” says Nicolas Le Novere,PhD, a computational neurobiologistwith the European BioinformaticsInstitute (EBI) in the UnitedKingdom. “We want it to be a kind ofgolden resource.” BioModels is t<strong>here</strong>sult of a collaboration led by EBIand the SBML Team, an internationalgroup that develops open-source standardsto describe biological systems.The project staff only accepts modelsthat have been published in peerreviewedliterature. Curators thencheck to make sure that, when downloadedand run in the appropriate simulationsoftware, the model will dowhat it’s supposed to do. Next, annotatorsadd model descriptions and crosslinksto related modelsand papers. At thatpoint, the model isreleased for public use.The systems biologycommunity is wageringthat this collectionof models willprove extremely valuable.According to aneditorial in Nature,“It is hoped thatBioModels will formthe basis of a universallyaccepted repositorythat can do forsystems biology whatGenBank and theProtein Data Bankhave done for geneticsand structuralbiology.” Nature 435,1 (5 May 2005)The majority of early submissionsto the database deal with signalingpathways or metabolic networks, butthey are quantitative and dynamicmodels—not just pathways. “You canimport these models into a simulator,click ‘run,’ and see things happen, see“We wantit to be akind of goldenresource,” saysPhilip La Novereof theBioModelsproject.values updated,” says Le Novere.Formalized, realistic models of subcellularparts or even muscles can alsobe stored in BioModels. And althoughmodels of that typehaven’t arrived yet,Le Novere says theproject already has abacklog of submissions.“We have somany good modelsarriving that we haveto prioritize.”BioModels initialusers are primarily thepeople who’ve createdthe models, says LeNovere, but he anticipatesthat will soonchange. The siteshould prove extremelyvaluable to experimentalbiologists whowant to have an ideaof how a system worksbefore designing anexperiment. Andpharmaceutical companies could turnto it as well, in order to test the likelyeffect of enhancing or inhibiting a moleculeor doing things that affect severalparts of a network at the same time.For more information, visithttp://www.ebi.ac.uk/biomodels/ ■6 BIOMEDICAL COMPUTATION REVIEW Fall 2005 www.biomedicalcomputationreview.org
PACKING ITALL IN:Curricula for<strong>Biomedical</strong>ComputingThe last decade saw a proliferationof training programs atthe intersection of life scienceand computation,with more than 60 newdegree and certificate programs launchedin the U.S. alone—and a similar number worldwide.Most appeared within the last five years. 1The number and variety of programs aregrowing, in step with the complexity ofmodern biomedical challenges.It’s the evolution of biological researchthat’s driving educational change. “We’renot just sequencing DNA or looking at agap junction,” says John Wooley, PhD,Associate Vice Chancellor of Research atUC San Diego and an active advocatefor education in biomedical computation.“We’re putting together thetotal cardiovascular system fromthe heart to the microcirculation, orthe brain from neuron junctions allthe way up to cognition.” This workrequires interdisciplinary education,says Wooley, who is also Senior Fellowof the San Diego Supercomputer Center.“It’s going to be the next generationwho actually accomplish these goals—studentswho understand both biology andcomputing, and can listen to experimentalbiologists and mathematicians.” >BY SHAWNE NEEPERwww.biomedicalcomputationreview.orgFall 2005 BIOMEDICAL COMPUTATION REVIEW 7
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