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it 3/2006 Schwerpunktthema Computational Systems Biology Platforms Computergestützte Systembiologieplattformen Ivayla Vacheva, Roland Eils, German Cancer Research Center, Heidelberg Summary Numerous software platforms in Computational Systems Biology have been developed in the past decade. Each program has its own strengths but their functionality often overlaps significantly. In this article, we review nu- merous aspects related to the functionality and infrastruc- ture of existing platforms in the context of a selected set of tools. We discuss the biological

From Genomes to Ecosystems

addition, complete specificity of therapeutic molecules is rarely obtained, and “off target” effects must be understood to assess both efficacy and potential toxicity. Indeed, the challenge in finding efficient and safe drug treatments for complex diseases requires building an integrative model of human physiology and disease. This strategy supports a systems biology approach involving the integration and the modeling of biological components and phenotypes that vary considerably via factors of time and space from patients to chemical and reverse (iterative process

it 3/2006 Schwerpunktthema Information Technology in Systems Biology Informationstechnologien in der Systembiologie Henning Schmidt, Mats Jirstrand, Fraunhofer-Chalmers Research Centre, Gothenburg, Sweden, Olaf Wolkenhauer, University of Rostock, Germany Summary Information technology is an important part within the highly interdisciplinary scientific field of systems biol- ogy. In this paper we are presenting an overview over systems biology, focusing on the information technological aspects, cur- rent developments, and future challenges. Zusammenfassung

References Albert, Réka. 2007. Network inference, analysis, and modeling in systems biology. The Plant Cell 19: 3327–38. Bansal, Mukesh; Belcastro, Vincenzo; Ambesi-Impiombato, Alberto; and di Bernardo, Diego. 2007. How to infer gene networks from expression profiles. Molecular Systems Biology 3: 1–10. Braillard, Pierre-Alain. 2010. Systems biology and the mechanistic framework. History and Philosophy of Life Sciences 32: 43–62. Cartwright, Nancy. 1993. Mark and probabilities: two ways to find causal structure. In Scientific Philosophy: Origins and

Biol. Chem., Vol. 391, pp. 731–735, July 2010 • Copyright by Walter de Gruyter • Berlin • New York. DOI 10.1515/BC.2010.094 2010/116 Article in press - uncorrected proof Minireview Towards molecular systems biology of gene transcription and regulation Patrick Cramer Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig Maximilians University, Feodor-Lynen-Straße 25, D-81377 Munich, Germany e-mail: Abstract Ten years after the determination of the RNA polymerase II structure, the basic mechanism

Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov and Augustin Luna* Systems biology graphical notation markup language (SBGNML) version 0.3 Received April 1, 2020; accepted April 16, 2020 Abstract: This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, mod- elers, and computer scientists. SBGN aims at

Lucian P. Smith*, Stuart L. Moodie, Frank T. Bergmann, Colin Gillespie, SarahM. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson and Michael Hucka Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1 Received April 4, 2020; accepted April 17, 2020; published online July 20, 2020 Abstract: Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty

Au to m at ica lly ge ne ra te d ro ug h PD Fb yP ro of Ch ec kf ro m Ri ve rV al le yT ec hn ol og ie sL td DE GRUYTER Journal of Integrative Bioinformatics. 2019; 20190021 Michael Hucka1 / Frank T. Bergmann1 / Claudine Chaouiya2 / Andreas Dräger3,4,5 / Stefan Hoops6 / Sarah M. Keating7 / Matthias König8 / Nicolas Le Novère9 / Chris J. Myers10 / Brett G. Olivier11 / Sven Sahle12 / James C. Schaff13 / Rahuman Sheriff7 / Lucian P. Smith14 / Dagmar Waltemath15 / Darren J. Wilkinson16 / Fengkai Zhang17 The Systems Biology Markup Language (SBML): Language

Au to m at ica lly ge ne ra te d ro ug h PD Fb yP ro of Ch ec kf ro m Ri ve rV al le yT ec hn ol og ie sL td DE GRUYTER Journal of Integrative Bioinformatics. 2018; 20170081 Michael Hucka1 / Frank T. Bergmann2 / Andreas Dräger3 / Stefan Hoops4 / Sarah M. Keating5 / Nicolas Le Novère6 / Chris J. Myers7 / Brett G. Olivier8 / Sven Sahle9 / James C. Schaff10 / Lucian P. Smith11 / Dagmar Waltemath12 / Darren J. Wilkinson13 The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core 1 California Institute of Technology, Pasadena, CA