diff --git a/CHANGELOG.md b/CHANGELOG.md index 5714ef8..16aa7f5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,8 @@ # Changelog +## 2.35 (OWL 2) +- Added algorithms and characteristics for attractor methods in mpbn + ## 2.34 (OWL 2) - Added organizational 'DAE solver' (`KISAO_0000699`) for collecting solvers that can solve DAE problems. - Removed 'has characteristic' some 'differential-algebraic equation problem' from KINSOL and from 'method for solving a system of linear equations'. diff --git a/kisao.owl b/kisao.owl index 174b10e..70dd2ee 100644 --- a/kisao.owl +++ b/kisao.owl @@ -14027,7 +14027,13 @@ This method only involves evaluations of f. This method is suitable for non-stif - + + + + + + + 2021-07-08 @@ -14063,6 +14069,12 @@ This method only involves evaluations of f. This method is suitable for non-stif + + + + + + 2021-07-08 JRK true @@ -14076,6 +14088,12 @@ This method only involves evaluations of f. This method is suitable for non-stif + + + + + + 2021-07-08 JRK true @@ -15081,6 +15099,258 @@ This method only involves evaluations of f. This method is suitable for non-stif + + + + + 2022-01-20 + JRK + LP + logical network + A network of logical-valued (an enumeration, such as a set of integers) variables. + + + + + + + + + 2022-01-20 + JRK + LP + boolean network + A network of Boolean-valued variables. + + + + + + + + + 2022-01-20 + JRK + LP + locally-monotone Boolean network + Boolean network where each regulator is either an activator or an inhibitor, but cannot be both. + + + + + + + + + 2022-01-20 + JRK + logical variable + A variable whose value can be one of an enumerated set of possible values such as ON/OFF, HIGH/MEDIUM/LOW, or a set integers (e.g., 0, 1, 2). + + + + + + + + + 2022-01-20 + JRK + Boolean variable + A variable whose value can be TRUE/FALSE (e.g., ON/OFF, YES/NO, 1/0). + + + + + + + + + 2022-01-20 + JRK + LP + most permissive updating policy + http://identifiers.org/doi:10.1038/s41467-020-18112-5 + The most permissive updating policy captures behaviors of any compatible quantitative model. + + + + + http://identifiers.org/doi:10.1038/s41467-020-18112-5 + Loïc Paulevé, Juraj Kolčák, Thomas Chatain, Stefan Haar. Reconciling qualitative, abstract, and scalable modeling of biological networks. Nat Commun 11(1):4256 (2020). + + + + + + + + + + + + + + + + + + + + + 2022-01-20 + JRK + LP + http://identifiers.org/biosimulators/mpbn + Paulevé ASP-based fixed point identification + + + + + http://identifiers.org/biosimulators/mpbn + mpbn + + + + + + + + + + + + + + + + + + + + + 2022-01-20 + JRK + LP + http://identifiers.org/biosimulators/mpbn + Paulevé ASP-based minimal trap space identification + + + + + http://identifiers.org/biosimulators/mpbn + mpbn + + + + + + + + + + + + + + + 2022-01-20 + JRK + LP + http://identifiers.org/biosimulators/mpbn + logical model attractor identification method + + + + + http://identifiers.org/biosimulators/mpbn + mpbn + + + + + + + + + + + + + + + + + + + + + + + + + + + 2022-01-20 + JRK + LP + http://identifiers.org/biosimulators/mpbn + Paulevé ASP-based most permissive attractor identification + + + + + http://identifiers.org/biosimulators/mpbn + mpbn + + + + + + + + + 2022-01-20 + JRK + trap space + + + + + + + + + 2022-01-20 + JRK + stable state + steady state + + + + + + + + + 2022-01-20 + JRK + minimal trap space + + + + + + + + + 2022-01-20 + JRK + attractor + + + + @@ -16671,7 +16941,5 @@ This method only involves evaluations of f. This method is suitable for non-stif - - diff --git a/kisao_full.owl b/kisao_full.owl index 62c4a6c..4ed1127 100644 --- a/kisao_full.owl +++ b/kisao_full.owl @@ -19,7 +19,7 @@ Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes) http://co.mbine.org/standards/kisao http://identifiers.org/pubmed/22027554 - 2.34 + 2.35 The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.