SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Publikováno v: Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi

Externí odkaz: https://doaj.org/article/86e517962df24b21af078b7f951f7487

Estimating Attractor Reachability in Asynchronous Logical Models

Autor: Nuno D. Mendes, Rui Henriques, Elisabeth Remy, Jorge Carneiro, Pedro T. Monteiro, Claudine Chaouiya

Publikováno v: Frontiers in Physiology, Vol 9 (2018)

Logical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are associated with model attractors (stable states or cyclic attractors) whose identification and

Externí odkaz: https://doaj.org/article/7e91480e5d1c48e3acf5398053c08e72

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Autor: Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

Publikováno v: Frontiers in Physiology, Vol 9 (2018)

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps. The accessibility and reproducibility of such workflows i

Externí odkaz: https://doaj.org/article/9a2d4dac80934cea9cb3c36fd1316bdf

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Autor: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

Publikováno v: Standards in Genomic Sciences, Vol 13, Iss 1, Pp 1-1 (2018)

Following publication of the original article [1], the author requested this addition to the ‘Acknowledgements’ section of the article: “DW is funded by the German Federal Ministry of Education and Research (e: Bio program SEMS, FKZ 031 6194)�

Externí odkaz: https://doaj.org/article/03d3844ffcec4f9a9421ab83a89b530d

Majority rules with random tie-breaking in Boolean gene regulatory networks.

Autor: Claudine Chaouiya, Ouerdia Ourrad, Ricardo Lima

Publikováno v: PLoS ONE, Vol 8, Iss 7, p e69626 (2013)

We consider threshold boolean gene regulatory networks, where the update function of each gene is described as a majority rule evaluated among the regulators of that gene: it is turned ON when the sum of its regulator contributions is positive (activ

Externí odkaz: https://doaj.org/article/6279e382280149e2a2de756b27e09a07