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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'.
  • The characteristics 'differential-algebraic equation problem' and ''ordinary differential equation problem' are no longer disjoint (and in fact the former are a complete subset of the latter).

2.33 (OWL 2)

  • Reorganized the steady state algorithms: moved flux balance and steady state to 'general steady state method' (KISAO_0000630), and others to the 'steady state root-finding method' (KISAO_0000407)

2.32 (OWL 2)

  • Added algorithm concepts for eQuilibrator.
  • Added organizational 'ODE solver' (KISAO_0000694) for noting in SED-ML that some solver should be used, but which is not important.
  • Added 'parameters for' (KISAO_0000695) to indicate that the children parameters of this term are applied when the parent general term is implented as the more-specific value of this term.

2.31 (OWL 2)

  • Added concepts for Metabolic Pathway Analysis
  • Added top-level algorithm concept for network optimization methods and nested the Metabolic Pathway Analysis methods, flux balance methods, and resource balance analysis under this

2.30 (OWL 2)

  • Added and unified aggregation functions for SED-ML L1V4
    • maximum ignoring NaN (KISAO_0000828)
    • minimum ignoring NaN (KISAO_0000829)
    • mean ignoring NaN (KISAO_0000825)
    • standard deviation ignoring NaN (KISAO_0000826)
    • standard error ignoring NaN (KISAO_0000827)
    • maximum (KISAO_0000830)
    • minimum (KISAO_0000840)
    • mean (KISAO_0000841)
    • standard deviation (KISAO_0000842)
    • standard error (KISAO_0000843)
    • sum ignoring NaN (KISAO_0000844)
    • sum (KISAO_0000845)
    • product ignoring NaN (KISAO_0000846)
    • product (KISAO_0000847)
    • cumulative sum (KISAO_0000848)
    • cumulative sum ignoring NaN (KISAO_0000849)
    • cumulative product ignoring NaN (KISAO_0000850)
    • cumulative product (KISAO_0000851)
    • count ignoring NaN (KISAO_0000852): number of non-zero elements, ignoring NaN entries
    • count (KISAO_0000853): number of non-zero elements, ignoring NaN entries
    • length ignoring NaN (KISAO_0000854): number of elements, ignoring NaN entries
    • length (KISAO_0000855): number of elements, ignoring NaN entries
    • median ignoring NaN (KISAO_0000856)
    • median (KISAO_0000857)
    • variance ignoring NaN (KISAO_0000858)
    • varianc (KISAO_0000859)

2.29 (OWL 2)

  • Added term for number of simulation steps per simulation output needed by BioNetGen

2.28 (OWL 2)

  • Improved performance of algorithm substitution in Python library

2.27 (OWL 2)

  • Added algorithm parameters for Gillespie and NLEQ2 in RoadRunner

2.26 (OWL 2)

  • Added RKQS method in XPP
  • Added documentation for XPP methods

2.25 (OWL 2)

  • Added algorithm parameters for libRoadRunner/CVODE

2.24 (OWL 2)

  • Added algorithm for Resource Balance Analysis
  • Aligned Identifiers.org URIs to http:// rather than https://

2.23 (OWL 2)

  • Added algorithms and paramters for XPP
    • Gear-like method for stiff ODE systems

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
  • Started guidelines for conventions such as the rules above
  • Added tests
    • URIs of terms follow the above pattern
    • URIs of terms are unique
    • Terms have names
    • Names start with lower case letters (warning)

2.20 (OWL 2)

  • Generalized label and description of KISAO_0000216
  • Added label for citation for KISAO_0000216

2.19 (OWL 2)

  • Added algorithms for logical modeling
    • Sequential simulation
    • Stable state search
    • Trap space identification

2.18 (OWL 2)

  • Added parameter for adaptive time steps

2.17 (OWL 2)

  • Added terms for simulation outputs (formerly urn:sed:symbol)
  • Added method for getting the type of a KiSAO term

2.16 (OWL 2)

  • Added terms for sub-methods of CVODE

2.15.3 (OWL 2)

  • Added more functionality to Python package

2.15.2 (OWL 2)

  • Debugged CI action

2.15.1 (OWL 2)

  • Added Python package for getting sets of similar algorithms
  • Added unit tests for the above
  • Added unit tests to CI action

2.15 (OWL 2)

Improved organization and relationships to facilitate the inference of similar simulation algorithms

  • Nested dynamic flux balance (KISAO_0000499) analysis under hybrid method (KISAO_0000352)
  • Moved 'has characteristic' some 'ordinary differential equation problem' from DA-DFBA (KISAO_0000502) to parent (dynamic flux balance analysis (KISAO_0000499))
  • Corrected relationship for stochastic Runge-Kutta method (KISAO_0000564) 'has characteristic' max 1 'stochastic differential equation problem' to 'has characteristic' some 'stochastic differential equation problem'`
  • Added relationship for stochastic Runge-Kutta method (KISAO_0000564) 'has characteristic' some 'stochastic system behaviour' (KISAO_0000104)
  • Added relationship for stochastic Runge-Kutta method (KISAO_0000564) not ('has characteristic' some 'ordinary differential equation problem') (KISAO_0000374)
  • Added is hybrid of relationships for VCell hybrid methods (KISAO_0000598, KISAO_0000599, KISAO_0000600)
  • Added more detail to is hybrid of relationships for Pahle hybrid methods (children of KISAO_0000231)
  • Added 'is hybrid of' some (LSODA and LSODAR) to hybrid LSODA/LSODAR method (KISAO_0000560)
  • Relabeled hybrid LSODA/LSODAR method (KISAO_0000560)
  • Added alt label Gillespie's algorithm to Gillespie direct algorithm (KISAO_0000029)
  • Added relationship 'has characteristic' some hybridity to BKMC (KISAO_0000581)
  • Nested Composite-rejection stochastic simulation algorithm (KISAO_0000610) under accelerated SSA (KISAO_0000333)
  • Added updating policy chacteristics to logical simulation methods (children of KISAO_0000448)
  • Added parent term for parsimonious FBA methods (children of KISAO_0000620)
  • Nested methods under generalized SSA (KISA_0000335)
    • bunker (KISAO_0000618)
    • EMC (KISAO_0000619)
    • iSSA (KISAO_0000611)
    • NMC (KISAO_0000613)
    • Bortz-Kalos-Lebowitz algorithm (KISAO_0000051)
    • Gillespie multi-particle method (KISAO_0000075)
  • Added organizational term for stochastic simulation leaping methods (KISAO_0000621)
  • Added missing exact (KISAO_0000236) vs approximate (KISAO_0000237) characteristics for non-generalized Gillespie-like methods
  • Added organizational term for flux balance methods (KISAO_0000622)
  • Added 'flux balance problem' (KISAO_0000623)

2.14 (OWL 2)

  • Added algorithms for iBioSim bunker and emc-sim methods
  • Added algorithms for VCell finite volume methods and VCell hybrid IDA/CVODE method

2.13 (OWL 2)

  • Added algorithm and parameter terms for iBioSim methods

2.12 (OWL 2)

  • Added missing subclass annotation for KISAO_0000435 of KISAO_0000302

2.11 (OWL 2)

  • Added algorithm and parameter terms for Salis hybrid methods implemented in VCell

2.10 (OWL 2)

  • Corrected capitalization of OptFlux to Optflux
  • Added BioSimulators identifiers for simulation tools

2.9 (OWL 2)

  • added term suggested in ticket 85
  • added algorithm and parameter terms for COBRA Toolbox, Optflux, RAVEN, The Cell Collective, MaBoSS, E-Cell 4, JSim, SBSCL, BioUML, COBRApy
  • organized order and tolerance parameter terms
  • fixed data types of created dates

2.8 (OWL 2)

  • added terms suggested in tickets 45-83

2.7 (OWL 2)

  • added gFBA, pFBA, FVA and related parameters (tickets 37-44)

2.6 (OWL 2)

  • added patitioned leaping (KISAO_0000524) and stop condition (KISAO_0000525) (tickets 35-36)

2.5 (OWL 2)

  • added optimisation methods (ticket 33)

2.4 (OWL 2)

  • added dynamic FBA methods (ticket 32)

2.3.113 (OWL 2)

  • 'number of runs' added (ticket 31)

2.3.12 (OWL 2)

  • KLU added (ticket 30)

2.3.12 (OWL 2)

  • KLU added (ticket 30)

2.3.11 (OWL 2)

  • several terms updated (tickets 21-29)

2.3.10 (OWL 2)

  • several algorithm parameters updated (ticket 20)

2.3.9 (OWL 2)

  • several algorithm parameters added (tickets 15-19)

2.3.8 (OWL 2)

  • several algorithm parameters added (tickets 12-13)

2.3.7 (OWL 2)

  • 'optimization algorithm' branch added (ticket 6) including 2 child terms: -- 'local optimization algorithm' added (ticket 7) -- 'global optimization algorithm' added (ticket 8)
  • 'bayesian inference algorithm' added (ticket 9)

2.3.6 (OWL 2)

  • 'maximal timestep method' added

2.3.5 (encoded in OWL 2)

  • 'maximum step size' parameter is added
  • hierarchical relationships for 'Newton-type method' is updated

2.3.4 (encoded in OWL 2)

  • COAST method is added
  • 'logical model simulation method' sub-branch is added
  • 'type of updating policy' sub-brach is added to characteristics

2.3.3 (encoded in OWL 2)

  • 'flux balance analysis' is added.

2.3.2 (encoded in OWL 2)

  • 'Embedded Runge-Kutta method' branch is updated: 'Dormand-Prince 8(5,3) method' and 'Higham-Hall method' are added.

2.3.1 (encoded in OWL 2)

  • KINSOL and IDA solvers are moved to the 'Newton-type method' subbranch of the algorithm hierarchy tree.
  • MIRIAM URNs in 'seeAlso' annotations are replaced with corresponding identifiers.org URLs.

2.3 (encoded in OWL 2)

  • steady state method branch is added
  • PLSR method branch is added
  • 'kinetic simulation algorithm' term is renamed to 'modeling and simulation algorithm'.

2.2 (encoded in OWL 2)

  • more Krylov subspace projection methods
  • 'type of problem' characteristic is added
  • skos:definition annotation is now used to represent definitions (instead of rdfs:comment)
  • skos:altLabel annotation is now used to represent synonyms (instead of oboInOwl:Synonym)
  • consists of two parts: -- kisao.owl: the core version containing all but deprecated terms -- kisao_full.owl: the full version which imports the core KiSAO and also contains deprecated terms.

2.1 (encoded in OWL 2)

  • two times more simulation algorithms, than in the previous versions
  • characteristic and parameter branches, linked to the algorithms which possess them, e.g. 'tau-leaping method' 'has parameter' 'tau-leaping epsilon'
  • both hierarchical relations between simulation methods, e.g. 'Poisson tau-leaping method' subClassOf 'tau-leaping method', and ones representing a complex method switching between several algorithms, e.g. 'LSODA' uses 'backward differentiation formula'
  • consists of two parts: -- kisao.owl: the core version containing all but deprecated terms -- kisao_full.owl: the full version which imports the core KiSAO and also contains deprecated terms.

2.0 (encoded in OWL 2)

  • the first of the KiSAO versions representing algorithm characteristics as a separate branch of OWL class hierarchy
  • algorithms are linked to the characteristics they possess using 'has property' relationship, e.g. 'Gillespie direct method' 'has property' 'stochastic system behaviour'

1.0 (encoded in OBO, OWL export is provided)

  • an old version of KiSAO
  • algorithm parameters are not covered
  • algorithm subclassing is based on algorithm types, derivation (algorithm derived from another pre-existing one), and characteristics.
  • characteristics are represented as subsumptions in algorithm branch, e.g. 'algorithm using adaptive time steps'
  • multiple inheritance of algorithms (subsumptions as parents)