Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks

2 code implementations • 3 May 2023 • Sara Riva, Jean-Marie Lagniez, Gustavo Magaña López, Loïc Paulevé

In this paper, we address the logical reasoning on universal properties of MTSs in the scope of two problems: the reprogramming of Boolean networks for identifying the permanent freeze of Boolean variables that enforce a given property on all the MTSs, and the synthesis of Boolean networks from universal properties on their MTSs.

Logical Reasoning

Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis

2 code implementations • 27 Jul 2022 • Loïc Paulevé

In this paper, we demonstrate how the software BoNesis can be employed to exhaustively identify combinations of perturbations which enforce properties on their fixed points and attractors.

Variable-Depth Simulation of Most Permissive Boolean Networks

no code implementations • 25 Jun 2022 • Théo Roncalli, Loïc Paulevé

This permissive depth reflects the potential concentration and time scales heterogeneity along the abstracted quantitative process.

BioSimulators: a central registry of simulation engines and services for recommending specific tools

no code implementations • 13 Mar 2022 • Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurelien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators. org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool.

SAT Heritage: a community-driven effort for archiving, building and running more than thousand SAT solvers

1 code implementation • 2 Jun 2020 • Gilles Audemard, Loïc Paulevé, Laurent Simon

However, since every cycle of competitions has its own set of rules and an adhoc way of publishing source code and binaries, compiling or even running any solver may be harder than what it seems.

Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming

no code implementations • 10 Sep 2019 • Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Zinovyev

Boolean networks model finite discrete dynamical systems with complex behaviours.

Most Permissive Semantics of Boolean Networks

2 code implementations • 30 Aug 2018 • Thomas Chatain, Stefan Haar, Loïc Paulevé

In brief, the most permissive semantics of BNs enables a correct abstract reasoning on dynamics of BNs, with a greater tractability than previously introduced update modes.

Formal Languages and Automata Theory Logic in Computer Science Quantitative Methods