Activity for Jonathan Karr
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Jonathan Karr created ticket #23
Conversion of SBML to PDF sometimes fails with no error
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Conversion of SBML to SVG sometimes fails with no error
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New modeling framework for particle-based discrete spatial simulation
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Added to SBO
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New terms for hybrid frameworks
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Added to SBO
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population-based discrete non-spatial simulation
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Added to SBO
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population-based discrete spatial simulation
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Added to SBO
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New term for deterministic non-spatial continuous framework
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Added to SBO
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New term for stochastic non-spatial continuous framework
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Added to SBO
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Added to SBO
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New term for deterministic non-spatial continuous framework
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stochastic non-spatial continuous framework
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Added to SBO
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New modeling framework for particle-based discrete spatial simulation
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Added to SBO
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Added to SBO
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Summary of tickets 137-145
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Revised request: (a) name: hybrid framework parent: SBO_0000004 description: Modelling approach which combines multiple canonical modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations....
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Summary of tickets 137-145
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stochastic non-spatial continuous framework
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New term for deterministic non-spatial continuous framework
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New modeling framework for particle-based discrete spatial simulation
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New modeling framework for particle-based discrete spatial simulation
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Conversion of SBML to Octave often generates empty files with no error
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SBML URN conversion creates invalid SBML when the layout package is used
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sbfConverter.sh contains paths specific to the developer
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sbfConverter.sh cannot handle spaces in filenames
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Converter generates invalid XPP for some models
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Added algorithms for iBioSim bunker and emc-sim methods, VCell finite volume methods, and VCell hybrid IDA/CVODE method
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Added algorithm and parameter terms for iBioSim methods:
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Added missing subclass annotation for KISAO_0000435 of KISAO_0000302
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added links to BioSimulators for VCell
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Added algorithm and parameter terms for Salis hybrid methods implemented in VCell
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Some recently added terms are not visibile in the Ontology Lookup Service
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This appears to be fixed
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Version 2.10: Corrected capitalization of OptFlux to Optflux, Added BioSimulators identifiers for simulation tools
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adding directory for v2.9 files
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creating tag for version 2.9
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New algorithm for GillesPy2 Hybrid Tau-Leaping Method
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adding algorithms and parameters for COBRA Toolbox, Optflux, RAVEN, The Cell Collective, MaBoSS, E-Cell 4, JSim, SBSCL, BioUML, COBRApy; organizing order and tolerance parameters; fixing data types of created dates; bumping to version 2.9
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Will be added as KISAO_0000575
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New algorithm for GillesPy2 Hybrid Tau-Leaping Method
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New parameter for IDAS Error control strategy
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incorporated as KISAO_0000545
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New parameter for species transition probabilities for asynchonrous logical model simulation method
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incorporated as KISAO_0000574
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New algorithm for probabilistic logical model simulation method
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incorporated as KISAO_0000573
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New parameter for noise level
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incorporated as KISAO_0000572
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New parameter for absolute tolerance adjustment factor for CVODE
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incorporated as KISAO_0000571
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New parameter for auto reduce tolerances
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incorporated as KISAO_0000570
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New algorithm for Stochastic second order Runge-Kutta method
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incorporated as KISAO_0000566
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New algorithm for nleq2
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incorporated as KISAO_0000569
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New algorithm for Stochastic differential equation method
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New parameter for force physical correctness
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incorporated as KISAO_0000567
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New parameter for absolute tolerance for root finding
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incorporated as KISAO_0000565
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New algorithm for stochastic Runge-Kutta method
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incorporated as KISAO_0000564
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New algorithm for Pahle hybrid Gibson-Bruck Next Reaction method/LSODA method
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incorporated as KISAO_0000562
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Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 method
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incorporated as KISAO_0000563
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New algorithm for Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta metho
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incorporated as KISAO_0000561
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New algorithm for LSODA or LSODAR
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incorporated as KISAO_0000560
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New parameter for initial step size
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incorporated as KISAO_0000559
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Parameter for relative steady-state tolerance for CVODES
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incorporated as KISAO_0000558
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Parameter for relative quadrature tolerance for CVODES
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incorporated as KISAO_0000556
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Parameter for absolute steady-state tolerance for CVODES
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incorporated as KISAO_0000557
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Parameter for absolute quadrature tolerance for CVODES
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incorporated as KISAO_0000555
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New algorithm for parsimonious FBA (min number of active fluxes)
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incorporated as KISAO_0000554
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New algorithm for quadratic convex optimization
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incorporated as KISAO_0000548
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New algorithm for linear convex optimization
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incorporated as KISAO_0000547
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New parameter for optimization solver
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incorporated as KISAO_0000553
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New parameter for optimization method
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incorporated as KISAO_0000552
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New algorithm for convex optimization
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incorporated as KISAO_0000546
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