simplified Petri nets and analysis uk/gnapn/

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1 Supplementary information S1 (table) Databases and tools Logical Booleannet GINsim 1 GNaPN 2 MetaReg 3-5 Continuous JigCell 6 Narrator 7 Oscill8 PET Modelling and analysis of RNs. Tools for editing and combining models Model creation and simulation using a graphical network representation, simulation with ODEs Analysis of the relation between rate parameters and network dynamics Estimation of rate constants for RNs according to experimental data edu/jigcell/ forge.net/ u/pet/ Linux, Mac PyBios Model creation, simulation, and analysis using ODEs n.mpg.de/ A suite of programs for Boolean networks and their extensions om/p/booleannet/ Source code Modelling and simulation of RNs using Petri nets Translation of logical RNs into simplified Petri nets and analysis uk/gnapn/ Creation of logical network models and detection of steady states il/metareg/applicati on.html Singlemolecule level BioNetS 8 Dizzy 9 E-Cell 10 StochKit 11 Simulation of networks that are affected by noise using discrete and continuous entities Simulation with SSA and different types of approximations including multi-step reactions Simulation, analysis and integration of biological networks. Supports combination of simulation algorithms from different classes Simulation using SSA and faster approximation methods. Contains analysis tools du/bionets/ msbiology.net/soft ware/dizzy/ ring.ucsb.edu/~cse/ StochKit Linux Linux; Contains A

2 STOCKS 12 Network inference tools Genenetwork 13 Genomica MetaReg 3-5 Physical Network Models 14 Simulation using SSA and approximations. Can model dividing cellular compartments and molecular pools; allows conversion between deterministic and stochastic rate constants pl/stocks/ Linux Inference of RN topology using time-series microarray data Analysis of gene modules; building of module networks Inference of regulatory information using steady state data Reconstruction of RNs using perturbation data sbl.bc.sinica.edu.tw /index.html zmann.ac.il/ il/metareg/applicati on.html du/yeang2005/plug in.shtml Windows ; requires Cytoscape Databases Content URL Comments AGRIS 15, 16 TFs AraC-XylS 17 BioModels 18 EcoCyc 19 and binding sites in Arabidopsis thaliana Transcriptional regulators in bacteria. Focuses on a specific TF family Annotations and online simulation of published models Metabolism and its regulation in E.coli ed.ohio-state.edu/ k/biomodels 20, 21 EPD Experimentally verified eukaryotic promoters GeneNet 22 RNs in prokaryotes and eukaryotes net.nsc.ru/mgs/gnw/ genenet/ JASPAR 23, 24 TF binding site profiles g.net/ mirna Registry 25 Reactome 26 Mature mirnas and precursors, search tool for mirna coding and regulatory sequences; a prediction tool for mirna targets in animals Signalling, metabolic and RNs in humans er.ac.uk/sequences/ e.org ; downloadable "Pathway tools" ; RNs can be queried via graphical representation ; downloadable A available Browsable graphical interface

3 TRANSCompel 27 Composite regulatory elements within specific genes in eukaryotes databases.html (requires registration) SKE 28 Signalling pathways in humans c.il/~spike/ TRANSFAC 27 TRRD 29 TFs in eukaryotes, binding sites and regulated genes Structural and functional organization of regulatory regions in eukaryotic genes databases.html net.nsc.ru/mgs/gnw/ trrd/ Downloadabl e tool; Includes visualization, analysis tools (requires registration) Abbreviations: ODE, ordinary differential equations;, platform independent; RN, regulatory network; SSA, stochastic simulation algorithm; TF, transcription factor;, web interface. In recent years the number of computational tools for systems biology has grown significantly. A large number of tools that support SBML are listed in the following website: References: 1. Simao, E., Remy, E., Thieffry, D. & Chaouiya, C. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli. Bioinformatics 21 Suppl 2, ii (2005). 2. Steggles, L.J., Banks, R., Shaw, O. & Wipat, A. Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinformatics 23, (2007). 3. Gat-Viks, I., Tanay, A. & Shamir, R. Modeling and analysis of heterogeneous regulation in biological networks. J. Comput. Biol. 11, (2004). 4. Gat-Viks, I., Tanay, A., Raijman, D. & Shamir, R. A probabilistic methodology for integrating knowledge and experiments on biological networks. J. Comput. Biol. 13, (2006). 5. Gat-Viks, I. & Shamir, R. Refinement and expansion of signaling pathways: the osmotic response network in yeast. Genome Res. 17, (2007). 6. Vass, M.T., Shaffer, C.A., Ramakrishnan, N., Watson, L.T. & Tyson, J.J. The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models. IEEE/ACM Trans. Comput. Biol. Bioinform. 3, (2006). 7. Mandel, J.J., Fuss, H., Palfreyman, N.M. & Dubitzky, W. Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 8, 103 (2007).

4 8. Adalsteinsson, D., McMillen, D. & Elston, T.C. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics 5, 24 (2004). 9. Ramsey, S., Orrell, D. & Bolouri, H. Dizzy: stochastic simulation of largescale genetic regulatory networks. J. Bioinform. Comput. Biol. 3, (2005). 10. Tomita, M. et al. E-CELL: software environment for whole-cell simulation. Bioinformatics 15, (1999). 11. Li, H., Cao, Y., Petzold, L.R. & Gillespie, D.T. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol. Prog. 24, (2008). 12. Kierzek, A.M. STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18, (2002). 13. Wu, C.C., Huang, H.C., Juan, H.F. & Chen, S.T. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics 20, (2004). 14. Yeang, C.H., Ideker, T. & Jaakkola, T. Physical network models. J. Comput. Biol. 11, (2004). 15. Palaniswamy, S.K. et al. AGRIS and AtRegNet. a platform to link cisregulatory elements and transcription factors into regulatory networks. Plant Physiol. 140, (2006). 16. Davuluri, R.V. et al. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4, 25 (2003). 17. Tobes, R. & Ramos, J.L. AraC-XylS database: a family of positive transcriptional regulators in bacteria. Nucleic Acids Res. 30, (2002). 18. Le Novere, N. et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D (2006). 19. Keseler, I.M. et al. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33, D (2005). 20. Schmid, C.D., Perier, R., Praz, V. & Bucher, P. EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res. 34, D82 85 (2006). 21. Schmid, C.D., Praz, V., Delorenzi, M., Perier, R. & Bucher, P. The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res 32, D82 85 (2004). 22. Ananko, E.A. et al. GeneNet: a database on structure and functional organisation of gene networks. Nucleic Acids Res. 30, (2002). 23. Bryne, J.C. et al. JASPAR, the open access database of transcription factorbinding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 36, D (2008). 24. Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. & Lenhard, B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91 94 (2004). 25. Griffiths-Jones, S. The microrna Registry. Nucleic Acids Res. 32, D (2004). 26. Vastrik, I. et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 8, R39 (2007).

5 27. Matys, V. et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D (2006). 28. Elkon, R. et al. SKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 9, 110 (2008). 29. Kolchanov, N.A. et al. Transcription Regulatory Regions Database (TRRD): its status in Nucleic Acids Res. 30, (2002).