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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: boolnet
version: 2.1.5
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BoolNet/8ed5223de07383db0e4b38a66c2d175faac98dd7/biosimulators.json
specificationsPa…
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---
id: tellurium
version: 2.2.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_tellurium/6eb72cb20bdd04dc80c702d203f8da2925d75d85/biosimulators.json
specificationsPa…
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---
id: gillespy2
version: 1.5.11
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/bd1af429cf9188adf60744948c7df7dd9fad0728/biosimulators.json
specificationsP…
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From KiSAO SurveyMonkey
Q1: Which type of term would you like to suggest?
Algorithm parameter
Q10: Parameter name (e.g. absolute tolerance):
maximum step size
Q11: Parameter type:…
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As of version 2.6 the CVODES solver by SUNDIALS supports the sparse linear solver KLU from SuiteSparse (http://faculty.cse.tamu.edu/davis/suitesparse.html). Especially for large scale systems with spa…
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---
id: cobrapy
version: 0.21.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/8f1039fb83a2c976e89c47bf179560aa38baaeee/biosimulators.json
specificationsPatch…
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---
id: gillespy2
version: 1.5.7
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_GillesPy2/99c498ba36ee5b6807b236991e7e9a92c0154b93/biosimulators.json
specificationsPa…
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name: Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method
definition: Combines a deterministic numerical integration of ODEs with a stochastic simulation algorithm. The whole biochemi…
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# Issue
* Talked about how to get things like eigenvalues, jacobian, etc.
* Decided that adding new tasks for these is the way to go
* These tasks will make various vectors and matrices available t…