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name: linear convex optimization
definition: optimization of a linear convex problem
subClassOf: convex optimization
isImplementedIn: CPLEX, GLPK, Gurobi
Reported by: jonrkarr
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name: quadratic convex optimization
definition: optimization of a quadratic convex problem
subClassOf: convex optimization
isImplementedIn: CPLEX, Gurobi
Reported by: jonrkarr
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- algorithms
- KISAO_0000407: parsimonius FBA (minimum number of active fluxes) --> KISAO_0000554
- parameters:
- KISAO_0000201: solver (e.g., CPLEX, GPLK) --> KISAO_0000553
- KISAO_0000243:…
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For any algorithm with variable step size, sometimes it is helpful to be able to set the minimum step size instead of just the maximum step size.
Reported by: luciansmith
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This should indicate the number of runs that a simulation should perform. It would typically be used to specify the number of runs for a stochastic simulation.
Reported by: cjmyers
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For any stochastic algorithm, being able to set the seed means you can reproduce your results if you run the same algorithm on the same computer.
Reported by: luciansmith
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The dampening factor is a variable for at least some steady state algorithms: roadrunner allows you to set the minimum value for this.
Reported by: luciansmith
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Some solver algorithms and implementations are specifically designed for solving ODE problems \(y\(0\) = y0, y' = f\(y, t\) \) while others solve more general DAE problems like y\(0\) = 0, F\(x, y, y'…
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It is valid to run simulations from a negative start time (start is only how the value is called which corresponds to the the start of the simulation). I.e. if I want a plot from -20 to 0 this is comp…
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---
id: cbmpy
version: 0.7.25
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_CBMPy/a7be1736fedd9a1d0bfd78f11e6300a2f52c098d/biosimulators.json
specificationsPatch…