SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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Add terms for all algorithms supported by GSL #5

Closed jonrkarr closed 3 years ago

jonrkarr commented 13 years ago

To go through the list:

Explicit embedded Runge-Kutta (2, 3) => No term yet Explicit 4th order (classical) Runge-Kutta => Already KISAO_0000032 Explicit embedded Runge-Kutta-Fehlberg (4, 5) method => Already KISAO_0000086 Explicit embedded Runge-Kutta Cash-Karp (4, 5) method => No term yet Explicit embedded Runge-Kutta Prince-Dormand (8, 9) method => No term yet. Implicit Gaussian first order Runge-Kutta => No term yet. Implicit Gaussian second order Runge-Kutta => No term yet. Implicit Gaussian 4th order Runge-Kutta => No term yet. Implicit Bulirsch-Stoer method of Bader and Deuflhard => No term yet. A variable-coefficient linear multistep Adams method in Nordsieck form. This stepper uses explicit Adams-Bashforth (predictor) and implicit Adams-Moulton (corrector) methods in P(EC)^m functional iteration mode. Method order varies dynamically between 1 and 12 => No term yet. A variable-coefficient linear multistep backward differentiation formula (BDF) method in Nordsieck form => KISAO_0000030 is vague but that term could describe this algorithm.

Reported by: a1kmm

jonrkarr commented 13 years ago

Fixed in revision 163. Below are the KiSAO identifiers for the suggested methods:

Explicit embedded Runge-Kutta (2, 3) => KISAO_0000302 and 'has characteristic' some 'explicit method type' and 'uses' some (Runge-Kutta based method' and 'has Runge-Kutta method order' value 2) and 'uses' some ('Runge-Kutta based method' and 'has Runge-Kutta method order' value 3) Explicit 4th order (classical) Runge-Kutta => KISAO_0000032 Explicit embedded Runge-Kutta-Fehlberg (4, 5) method => KISAO_0000086 Explicit embedded Runge-Kutta Cash-Karp (4, 5) method => KISAO_0000321 Explicit embedded Runge-Kutta Prince-Dormand (8, 9) method => KISAO_0000087 Implicit Gaussian first order Runge-Kutta (implicit Euler) => KISAO_0000031 Implicit Gaussian second order Runge-Kutta (implicit mid-point rule) => KISAO_0000378 Implicit Gaussian 4th order Runge-Kutta => KISAO_0000302 and 'has characteristic' some 'implicit method type' Implicit Bulirsch-Stoer method of Bader and Deuflhard => KISAO_0000383 A variable-coefficient linear multistep Adams method in Nordsieck form. This stepper uses explicit Adams-Bashforth (predictor) and implicit Adams-Moulton (corrector) methods in P(EC)^m functional iteration mode. Method order varies dynamically between 1 and 12 => KISAO_0000364 A variable-coefficient linear multistep backward differentiation formula (BDF) method in Nordsieck form => KISAO_0000288

Original comment by: annazhukova

jonrkarr commented 13 years ago

Original comment by: annazhukova