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Meeting Report COMBINE 4 Standards in Genomic Sciences (2014) 9:1285-1301 DOI:10.4056/sigs.5279417 Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Dagmar Waltemath1*, Frank T. Bergmann2, Claudine Chaouiya4, Tobias Czauderna3, Padraig Gleeson5, Carole Goble6, Martin Golebiewski7, Michael Hucka2, Nick Juty8, Olga Krebs7, Nicolas Le Novère8,14, Huaiyu Mi9, Ion I. Moraru10, Chris J. Myers11, David Nickerson12, Brett G. Olivier13, Nicolas Rodriguez14, Falk Schreiber3,15,16, Lucian Smith2, Fengkai Zhang17, Eric Bonnet18,19,20*. 1 Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Ger- many 2 Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California, USA 3 IPK Gatersleben, Gatersleben, Germany 4 Instituto Gulbenkian de Ciência - IGC, Rua da Quinta Grande, Oeiras, Portugal 5 Department of Neuroscience, Physiology and Pharmacology, University College London, United Kingdom 6 School of Computer Science, The University of Manchester, Manchester, UK 7 Heidelberg Institute for Theoretical Studies, Heidelberg, Germany 8 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom 9 Department of preventive medicine, Keck School of Medicine, University of Southern Cal- ifornia, Los Angeles, CA, USA 10 Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farming- ton, CT, USA 11 Department of Electrical and Computer Engineering, University of Utah, USA 12 Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand 13 Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands 14 The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom 15 Martin Luther University Halle-Wittenberg, Halle, Germany 16 Monash University, Melbourne, Australia 17 Computational Biology Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA. 18 Institut Curie, Paris, France 19 INSERM U900, 75248 Paris, France 20 Mines ParisTech, 77300 Fontainebleau, France *Correspondence: Dagmar Waltemath ([email protected]), Eric Bonnet (er- [email protected]) The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the an- nual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. Dur- ing subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between dif- ferent standards in computational systems biology. The Genomic Standards Consortium Meeting report COMBINE 4 Introduction The Computational Modeling in Biology Network [16], which are again actively being evolved by the (COMBINE) [1] coordinates the development of community. open standards and file formats in computational Unfortunately, many of these standards were orig- systems biology and related fields. Recent decades inally developed independently, with poor coordi- have witnessed a major shift in biological science, nation and consequently little or no integration with massive amounts of quantitative data in- between the different efforts. As a result, redun- creasingly being generated at high speed. Multiple dancies in topic coverage and efforts arose, wast- sources of data, such as measurements of the ac- ing scarce sources of funding and time. The COM- tivity and states of various components of cells BINE initiative was created to help avoid these ob- and tissues, are being integrated into computa- structions to smooth progress. It was inspired by tional models that today help researchers investi- the way in which the World Wide Web Consorti- gate the dynamic properties of living systems. Var- um (W3C [17]) develops standards for the web. ious online resources disseminate curated infor- COMBINE has succeeded in creating a number of mation related to pathways (e.g., WikiPathways community events aimed at coordinating and [2], PANTHER pathways [3], KEGG [4], Reactome promoting the development of open and interop- [5], Pathway Interaction Database [6]) and com- erable standards for computational systems biol- putational models (e.g., BioModels Database [7], ogy [18]. Physiome Model Repository [8]). The growth of these resources has led to the creation of open The COMBINE Forum is an open event that offers standards to facilitate the exchange and interop- the opportunity to discuss new developments and erability of models and data, as well as the devel- features in the different standards, address cross- opment of computational software tools. The Sys- standard interoperability issues, and to hear about tems Biology Markup Language (SBML) [9] covers implementation and scientific work that benefits computational models of biological processes, de- (or can benefit) from the use of the standards. scribing variables, their relationships and initial This meeting is attended predominantly by devel- conditions. BioPAX, the Biological Pathway opers of (proposed) standards, software develop- eXchange format [10], focuses on the representa- ers who implement support for these standards, tion of biological pathways at the molecular and and interested end users of COMBINE standards. cellular levels. The Systems Biology Graphical No- The COMBINE Forum was launched three years tation (SBGN) [11] is a set of visual languages en- ago and has since has been accepted as the cross- abling the graphical representation of biological standard community meeting. It first took place in processes. Additional standardization efforts un- 2010, organized by the center for integrative sys- der the COMBINE umbrella include CellML [12], tems biology at the University of Edinburgh, Unit- aimed at storing and exchanging computer-based ed Kingdom, as a joint event with the 10th SBML th mathematical models; NeuroML [13], a language Anniversary and a satellite of the 11 ICSB [19]. for the description of detailed models of neural Since then, the meetings have taken place in Hei- systems; and the Simulation Experiment Descrip- delberg (2011, organized by the Heidelberg Insti- tion Markup Language (SED-ML) [14], an XML- tute for Theoretical Studies, Germany) and in To- based format for encoding the configurations and ronto (2012, organized by the Donnelly Centre in procedures necessary to reproduce computational Toronto, Canada). experiments on models. All efforts use a common The second type of annual meeting organized by development approach in which the community is the COMBINE initiative is HARMONY, the the central driver: community participation is ac- Hackathon on Resources for Modeling in Biology. As tively pursued not only to identify and suggest the name indicates, it is organized as a hackathon novel features to include in the standards, but also and is targeted towards software developers, fa- to choose the editorial board members and make voring hands-on sessions instead of presentations. other technical decisions democratically. Finally, A number of outreach activities have been imple- the COMBINE standards incorporate a number of mented throughout the past several years to pro- related resources, including ontologies such as the mote open computational standards for biology. Systems Biology Ontology (SBO) [15], and Mini- Joint tutorials took place as 1-day satellite work- mum Information Guidelines such as MIRIAM shops of the International Conferences on Systems Biology (ICSB) 2012 in Toronto, Canada [20] and 1286 Standards in Genomic Sciences Waltemath et al. 2013 in Copenhagen, Denmark [21]. At the core of devoted the first day of the meeting to general these workshops, an international team of tutors presentations on modeling approaches in biology. introduced the most widely used computer tools, The focus was on approaches that either are not model databases and data management platforms yet covered by COMBINE efforts, or that are being in the field of systems biology and provided in- used in new or innovative ways. No fee was structions in how these tools support COMBINE charged for attending this first day and the audi- standards. Both tutorials were well attended with ence reached 96, including many students. Days 2 80-100 participants. through 5 were then dedicated to recent devel- In September 2013, the members of the communi- opments in COMBINE standards, and discussion ty gathered in Paris for their annual forum meet- on future evolutions. As with previous COMBINE ing (Fig. 1). The COMBINE Forum was hosted by events, slides and video recordings of all presenta- the Computational Systems Biology of Cancer tions are available on the meeting website [23]. group of the Institut Curie [22]. The organizers Figure 1. Group picture of the participants to COMBINE 2013 (photo courtesy of Mike Hucka). Modeling approaches in biology (Day 1) The COMBINE 2013
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