diff --git a/CHANGELOG.md b/CHANGELOG.md
index 80cbdd7..8faf44f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,12 @@
# Changelog
+## 2.22 (OWL 2)
+- Added algorithms and paramters for XPP
+ - Maximum number of iterations for root finding
+ - Jacobian epsilon
+ - Second order backward method for Volterra equations
+ - Second order backward method for Volterra equations memory size
+
## 2.21 (OWL 2)
- Corrected ids for terms whose ids begin with `_`
- Corrected names and synonyms of terms to start with lowercase letters
diff --git a/kisao.owl b/kisao.owl
index 053561e..da26afe 100644
--- a/kisao.owl
+++ b/kisao.owl
@@ -19,7 +19,7 @@
Kinetic Simulation Algorithm Ontology (KiSAO)
http://co.mbine.org/standards/kisao
http://identifiers.org/pubmed/22027554
- 2.21
+ 2.22
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.
@@ -10932,6 +10932,7 @@ Levenberg first suggested an improvement to the Newton method in order to make i
VODE
https://identifiers.org/doi/10.1137/0910062
DVODE
+ Real-valued Variable-coefficient Ordinary Differential Equation solver, with fixed-leading-coefficient implementation
real-valued variable-coefficient ordinary differential equation solver, with fixed-leading-coefficient implementation
VODE provides implicit Adams method (for non-stiff problems) and a method based on backward differentiation formulas (BDF) (for stiff problems).
@@ -10988,6 +10989,7 @@ Levenberg first suggested an improvement to the Newton method in order to make i
https://identifiers.org/biosimulators/gillespy2
ZVODE
https://identifiers.org/doi/10.1137/0910062
+ Complex-valued Variable-coefficient Ordinary Differential Equation solver, with fixed-leading-coefficient implementation
complex-valued variable-coefficient ordinary differential equation solver, with fixed-leading-coefficient implementation
ZVODE provides implicit Adams method (for non-stiff problems) and a method based on backward differentiation formulas (BDF) (for stiff problems).
@@ -12222,6 +12224,7 @@ Global Newton method with error oriented convergence criterion; QR-decomposition
quadratic MOMA
https://identifiers.org/doi/10.1073/pnas.232349399
MOMA
+ Quadratic Minimization of Metabolic Adjustment
minimization of metabolic adjustment
quadratic minimization of metabolic adjustment
Minimization of metabolic adjustment (MOMA) is an extension of FBA for the prediction of flux distributions in gene knockouts. MOMA employs quadratic programming to identify the closest point (in terms of its Euclidean distance) in the permissible flux space of the knockout to the wild-type flux vector by solving the optimization problem
@@ -12311,6 +12314,7 @@ Min sum((fluxAi - fluxBi)^2) + sum(fluxAi)^(fluxMinimizationWeight) + sum(fluxBi
https://identifiers.org/biosimulators/optflux
linear MOMA
https://identifiers.org/doi/10.1038/ng.846
+ Linear Minimization of Metabolic Adjustment
linear minimization of metabolic adjustment
Linear minimization of metabolic adjustment (MOMA) is an extension of FBA for the prediction of flux distributions in gene knockouts. Linear MOMA employs linear programming to identify the closest point (in terms of its L1 norm) in the permissible flux space of the knockout to the wild-type flux vector by solving the optimization problem
@@ -12354,6 +12358,7 @@ Min sum(|fluxAi - fluxBi|)
https://identifiers.org/biosimulators/optflux
ROOM
https://identifiers.org/doi/10.1073/pnas.0406346102
+ Regulatory on/off minimization of metabolic flux changes
regulatory on/off minimization of metabolic flux changes
Constraint-based algorithm for predicting the metabolic steady state after gene knockouts which aims to minimize the number of significant flux changes (hence on/off) with respect to the wild type.
@@ -12412,6 +12417,7 @@ Min sum(|fluxAi - fluxBi|)
https://identifiers.org/biosimulators/maboss
BKMC
https://identifiers.org/doi/10.1186/1752-0509-6-116
+ Boolean Kinetic Monte-Carlo
Boolean kinetic Monte-Carlo
The Boolean kinetic Monte Carlo method (BKMC) is a natural generalization of the asynchronous Boolean simulation method, with a direct probabilistic interpretation. In the BKMC framework, the dynamics is parameterized by a biological time and the order of update is noisy, which is less strict than priority classes introduced in GINsin. A BKMC model is specified by logical rules as in regular Boolean models but with a more precise information: a numerical rate is added for each transition of each node.
@@ -12564,6 +12570,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
https://identifiers.org/biosimulators/biouml
IMEX
+ Implicit-Explicit Runge-Kutta method
implicit-explicit Runge-Kutta method
Method for solving stiff and imaginary ODE problems
@@ -12605,6 +12612,7 @@ Min sum(|fluxAi - fluxBi|)
https://identifiers.org/biosimulators/cobratoolbox
ACB flux sampling method
https://identifiers.org/doi/10.1038/s41596-018-0098-2
+ Artificial centering boundary flux sampling method
artificial centering boundary flux sampling method
@@ -12732,6 +12740,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
true
MOMA
+ Minimization of Metabolic Adjustment
minimization of metabolic adjustment
minimization of metabolic adjustment (MOMA) is an extension of FBA for the prediction of flux distributions in gene knockouts. MOMA identifies the closest point in the permissible flux space of the knockout to the wild-type flux vector by solving an optimization problem.
@@ -12959,6 +12968,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
MLB
minimum species threshold for continuous approximation
+ Epsilon
epsilon
Minimum number of molecules of both reactant and product species required for approximation as a continuous Markov process.
@@ -12979,6 +12989,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
MLB
minimum reaction rate for continuous approximation
+ Lambda
lambda
Minimum reaction rate required for approximation as a continuous Markov process.
@@ -12999,6 +13010,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
MLB
MSR tolerance
+ Multiple slow reactions tolerance
multiple slow reactions tolerance
Maximum allowed effect of executing multiple slow reactions per numerical integration of the SDEs.
@@ -13019,6 +13031,7 @@ Min sum(|fluxAi - fluxBi|)
JRK
MLB
SDE tolerance
+ Maximum allowed value of the drift and diffusion errors.
maximum allowed value of the drift and diffusion errors.
Stochastic differential equation tolerance
@@ -13095,9 +13108,9 @@ Min sum(|fluxAi - fluxBi|)
https://identifiers.org/biosimulators/ibiosim
hierarchical Fehlberg method
https://identifiers.org/doi/10.3389/fbioe.2014.00055
+ hODE
hierarchical ODE integration method
hierarchical ordinary differential equation integration method
- hODE
Method for continuous simulation of hierarchically organized models, such as a model of a cellular population where each cell in the population is represented by the same species and reactions.
@@ -13130,8 +13143,9 @@ Min sum(|fluxAi - fluxBi|)
https://identifiers.org/biosimulators/ibiosim
hierarchical flux balance analysis
https://identifiers.org/doi/10.3389/fbioe.2014.00055
- hierarchical FBA
+ Hierarchical FBA
hFBA
+ hierarchical FBA
Method for constraint-based simulation of hierarchically organized models, such as a model of a cellular population where each cell in the population is represented by the same species and reactions.
@@ -13933,8 +13947,8 @@ This method only involves evaluations of f. This method is suitable for non-stif
2021-06-04
JRK
- rate of a process in extensive/absolute units such as reactions per second.
amount rate
+ rate of a process in extensive/absolute units such as reactions per second.
@@ -14098,218 +14112,322 @@ This method only involves evaluations of f. This method is suitable for non-stif
-
+
-
-
- 06-03-2021
- LPS
- link matrix
- The link matrix of a model.
+
+
+ 2021-08-07
+ JRK
+ http://identifiers.org/biosimulators/xpp
+ Second order backward implicit product Euler scheme
+ https://doi.org/10.1137/1.9781611970852
+ Method for solving Volterra equations.
+
+
+
+ http://identifiers.org/biosimulators/xpp
+ XPP
+
+
+
+
+ https://doi.org/10.1137/1.9781611970852
+ Peter Linz. Analytical and Numerical Methods for Volterra Equations. 1985.
+
-
+
-
-
+
+
+ 2021-08-07
+ JRK
+ https://identifiers.org/biosimulators/xpp
+ Maximum number of iterations for root finding
+
+
+
+
+ https://identifiers.org/biosimulators/xpp
+ XPP
+
+
+
+
+
+
+
+
+ 2021-08-07
+ JRK
+ https://identifiers.org/biosimulators/xpp
+ Jacobian epsilon
+
+
+
+
+ https://identifiers.org/biosimulators/xpp
+ XPP
+
+
+
+
+
+
+
+
+ 2021-08-07
+ JRK
+ https://identifiers.org/biosimulators/xpp
+ Memory size
+ Maximum number of points to store in memory, such as in the second order backward implicit product Euler scheme.
+
+
+
+
+ https://identifiers.org/biosimulators/xpp
+ XPP
+
+
+
+
+
+
+
+
06-03-2021
LPS
- kernel matrix
- The Kernel matrix of a model.
+ true
+ systems property
+ A systems-level property of an entire model or simulation.
-
+
-
+
+
+
+
+
+
+
06-03-2021
LPS
- L0 matrix
- The L0 matrix of a model.
+ concentration control coefficient matrix (unscaled)
+ The unscaled concentration control coefficient matrix. The dimensions are species by reactions.
-
+
-
+
+
+
+
+
+
+
06-03-2021
LPS
- Nr matrix
- The Nr matrix of a model.
+ control coefficient (scaled)
+ A scaled control coefficient of any dependent element (such as a reaction or a floating species) with respect to an independent element (such as a global parameter or boundary species).
-
+
-
+
+
+
+
+
+
+
+
06-03-2021
LPS
- true
- model and simulation property characteristic
- A property of a variable of a model or simulation.
+ control coefficient (unscaled)
+ An unscaled control coefficient of any dependent element (such as a reaction or a floating species) with respect to an independent element (such as a global parameter or boundary species).
-
+
-
-
+
+
+
+
+
+
+
+
06-03-2021
LPS
- true
- intensive property
- https://en.wikipedia.org/wiki/Intensive_and_extensive_properties
- An intensive variable such as a concentration or temperature.
+ elasticity matrix (unscaled)
+ The unscaled elasticity matrix. The dimensions are reactions by species.
-
+
-
-
+
+
+
+
+
+
+
+
06-03-2021
LPS
- extensive property
- https://en.wikipedia.org/wiki/Intensive_and_extensive_properties
- An extensive variable such as an amount, particle number, or mass.
+ elasticity coefficient (unscaled)
+ An unscaled elasticity coefficient of any reaction with respect to an independent element (such as a global parameter or boundary species).
-
+
-
-
+
+
+
+
+
+
+
+
06-03-2021
LPS
- true
- aggregation function
- A function that aggregates a set of results, reducing its dimension(s). Examples include functions that compute minima or maxima of sets of values.
+ elasticity matrix (scaled)
+ The scaled elasticity matrix. The dimensions are reactions by species.
-
+
-
-
+
+
+
+
+
+
+
+
06-03-2021
LPS
- mean
- The mean (average) of a set of values, ignoring NaN entries.
+ elasticity coefficient (scaled)
+ A scaled elasticity coefficient of any reaction with respect to an independent element (such as a global parameter or boundary species).
-
+
-
-
+
+
06-03-2021
LPS
- standard deviation
- The standard deviation of a set of values, ignoring NaN entries.
+ reduced stoichiometry matrix
+ The reduced stoichiometry matrix. The dimensions are species by reactions.
-
+
-
-
+
+
06-03-2021
LPS
- standard error
- The standard error of a set of values, ignoring NaN entries.
+ reduced Jacobian matrix
+ The reduced Jacobian matrix. The dimensions are species by species.
-
+
-
-
+
+
06-03-2021
LPS
- maximum
- The maximum value of a set of values, ignoring NaN entries.
+ reduced eigenvalue matrix
+ The reduced eigenvalue matrix of a model. The dimensions are species by two, where the first column is the real part of the eigenvalues, and the second column is the imaginary part of the eigenvalues.
-
+
-
-
+
+
06-03-2021
LPS
- minimum
- The minimum value of a set of values, ignoring NaN entries.
+ stoichiometry matrix
+ full stochiometry matrix
+ The (full) stoichiometry matrix. The dimensions are species by reactions.
-
+
-
+
+
06-03-2021
LPS
- true
- model and simulation property
- A variable of a model or simulation.
+ Jacobian matrix
+ full Jacobian matrix
+ The (full) Jacobian matrix. The dimensions are species by species.
-
+
-
-
+
+
06-03-2021
LPS
- time
- The implied time variable of the model state.
+ Eigenvalue matrix
+ full eigenvalue matrix
+ The (full) eigenvalue matrix of a model. The dimensions are species by two, where the first column is the real part of the eigenvalues, and the second column is the imaginary part of the eigenvalues.
-
+
-
-
-
-
-
-
-
-
+
+
-
+
06-03-2021
LPS
- rate of change
- rate
- The rate of change of one variable with respect to a second variable.
+ flux control coefficient matrix (unscaled)
+ The unscaled flux control coefficient matrix. The dimensions are reactions by reactions.
-
+
-
+
@@ -14319,330 +14437,307 @@ This method only involves evaluations of f. This method is suitable for non-stif
06-03-2021
LPS
- concentration control coefficient matrix (scaled)
- The scaled concentration control coefficient matrix. The dimensions are species by reactions.
+ flux control coefficient matrix (scaled)
+ The scaled flux control coefficient matrix. The dimensions are reactions by reactions.
-
+
-
-
-
-
-
-
-
-
- 06-03-2021
- LPS
- amount
- The extensive quantity amount.
+
+
+ 06-03-2021
+ LPS
+ link matrix
+ The link matrix of a model.
-
+
-
-
-
-
-
-
-
-
- 06-03-2021
- LPS
- particle number
- The extensive quantity particle number, or, the molar amount of the entity multiplied by Avogadro's number.
+
+
+ 06-03-2021
+ LPS
+ kernel matrix
+ The Kernel matrix of a model.
-
+
-
-
-
-
-
-
-
-
- 06-03-2021
- LPS
- concentration
- The intensive quantity concentration, or, the amount of the entity with respect to the entity in which it resides.
+
+
+ 06-03-2021
+ LPS
+ L0 matrix
+ The L0 matrix of a model.
-
+
-
-
-
-
-
-
-
-
- 06-03-2021
- LPS
- temperature
- The intensive quantity temperature.
+
+
+ 06-03-2021
+ LPS
+ Nr matrix
+ The Nr matrix of a model.
-
+
-
-
+
06-03-2021
LPS
true
- systems property
- A systems-level property of an entire model or simulation.
+ model and simulation property characteristic
+ A property of a variable of a model or simulation.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- concentration control coefficient matrix (unscaled)
- The unscaled concentration control coefficient matrix. The dimensions are species by reactions.
+ true
+ intensive property
+ https://en.wikipedia.org/wiki/Intensive_and_extensive_properties
+ An intensive variable such as a concentration or temperature.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- control coefficient (scaled)
- A scaled control coefficient of any dependent element (such as a reaction or a floating species) with respect to an independent element (such as a global parameter or boundary species).
+ extensive property
+ https://en.wikipedia.org/wiki/Intensive_and_extensive_properties
+ An extensive variable such as an amount, particle number, or mass.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- control coefficient (unscaled)
- An unscaled control coefficient of any dependent element (such as a reaction or a floating species) with respect to an independent element (such as a global parameter or boundary species).
+ true
+ aggregation function
+ A function that aggregates a set of results, reducing its dimension(s). Examples include functions that compute minima or maxima of sets of values.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- elasticity matrix (unscaled)
- The unscaled elasticity matrix. The dimensions are reactions by species.
+ mean
+ The mean (average) of a set of values, ignoring NaN entries.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- elasticity coefficient (unscaled)
- An unscaled elasticity coefficient of any reaction with respect to an independent element (such as a global parameter or boundary species).
+ standard deviation
+ The standard deviation of a set of values, ignoring NaN entries.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- elasticity matrix (scaled)
- The scaled elasticity matrix. The dimensions are reactions by species.
+ standard error
+ The standard error of a set of values, ignoring NaN entries.
-
+
-
-
-
-
-
-
-
-
+
+
06-03-2021
LPS
- elasticity coefficient (scaled)
- A scaled elasticity coefficient of any reaction with respect to an independent element (such as a global parameter or boundary species).
+ maximum
+ The maximum value of a set of values, ignoring NaN entries.
-
+
-
-
+
+
06-03-2021
LPS
- reduced stoichiometry matrix
- The reduced stoichiometry matrix. The dimensions are species by reactions.
+ minimum
+ The minimum value of a set of values, ignoring NaN entries.
-
+
-
-
+
06-03-2021
LPS
- reduced Jacobian matrix
- The reduced Jacobian matrix. The dimensions are species by species.
+ true
+ model and simulation property
+ A variable of a model or simulation.
-
+
-
-
+
+
06-03-2021
LPS
- reduced eigenvalue matrix
- The reduced eigenvalue matrix of a model. The dimensions are species by two, where the first column is the real part of the eigenvalues, and the second column is the imaginary part of the eigenvalues.
+ time
+ The implied time variable of the model state.
-
+
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
06-03-2021
LPS
- stoichiometry matrix
- full stochiometry matrix
- The (full) stoichiometry matrix. The dimensions are species by reactions.
+ rate of change
+ rate
+ The rate of change of one variable with respect to a second variable.
-
+
-
+
+
+
+
+
+
+
06-03-2021
LPS
- Jacobian matrix
- full Jacobian matrix
- The (full) Jacobian matrix. The dimensions are species by species.
+ concentration control coefficient matrix (scaled)
+ The scaled concentration control coefficient matrix. The dimensions are species by reactions.
-
+
-
-
- 06-03-2021
- LPS
- Eigenvalue matrix
- full eigenvalue matrix
- The (full) eigenvalue matrix of a model. The dimensions are species by two, where the first column is the real part of the eigenvalues, and the second column is the imaginary part of the eigenvalues.
+
+
+
+
+
+
+
+
+ 06-03-2021
+ LPS
+ amount
+ The extensive quantity amount.
-
+
-
-
+
+
-
+
- 06-03-2021
- LPS
- flux control coefficient matrix (unscaled)
- The unscaled flux control coefficient matrix. The dimensions are reactions by reactions.
+ 06-03-2021
+ LPS
+ particle number
+ The extensive quantity particle number, or, the molar amount of the entity multiplied by Avogadro's number.
-
+
-
-
+
+
-
+
- 06-03-2021
- LPS
- flux control coefficient matrix (scaled)
- The scaled flux control coefficient matrix. The dimensions are reactions by reactions.
+ 06-03-2021
+ LPS
+ concentration
+ The intensive quantity concentration, or, the amount of the entity with respect to the entity in which it resides.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 06-03-2021
+ LPS
+ temperature
+ The intensive quantity temperature.
EXACT
diff --git a/kisao_full.owl b/kisao_full.owl
index edade33..e05b10e 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
- 2.21
+ 2.22
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.
diff --git a/libkisao/python/kisao/_version.py b/libkisao/python/kisao/_version.py
index 1498ad4..0d7140a 100644
--- a/libkisao/python/kisao/_version.py
+++ b/libkisao/python/kisao/_version.py
@@ -1 +1 @@
-__version__ = '2.21'
+__version__ = '2.22'