Comments (3)
jonrkarr
commented on June 23, 2024
Closing because this is the same issue as #45.
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fbergmann
commented on June 23, 2024
i dont think it is the same issue, even basic steady state computation, loading a model simulating to steady state, retrieveing the report. or scan over a parameter, bringing the model to steady state, plotting the result. Would be supported by COPASI on import right now, but is not available through BioSimulation.
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jonrkarr
commented on June 23, 2024
These functions aren't supported for the reasons outlined in #45. #45 outlines what needs to be done to make this work through runBioSimulations. This includes the subset of things needed to advertise these capabilities through BioSimulators.
This advertising in BioSimulators also utilizes KiSAO. This is important for connecting the capabilities of tools to the requirements to execute specific SED-ML documents. The advertising can be expanded separately from expanding the capabilities of the docker image. The specifications of tools are structured to be able to capture the different capabilities of different interfaces (ui, api, docker, etc).
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Related Issues (20)
- COPASI or wrapper should support KISAO terms for algorithms and algorithm parameters HOT 1
- Apply new KISAO terms for algorithms and parameters HOT 2
- Add citation for Stochastic Runge-Kutta Method HOT 1
- What are the user-configurable parameters of the hybrid LSODA algorithm? HOT 1
- Support hybrid RK45 method HOT 2
- Improve messages for COPASI errors HOT 2
- Expose static and steady-state analyses through SED-ML HOT 1
- Get values of non-constant parameters HOT 8
- Internalize functionality into COPASI itself (obviating the need for this repository) HOT 7
- Setup cron job to pull COPASI releases from PyPi HOT 1
- Substitute algorithm when Radau5 requested for model with events HOT 1
- Substitute hybrid runge kutta and LSODA methods to hybrid RK-45 for models with events HOT 1
- copasi_model_obj_common_name needs to be a string HOT 4
- biosimulators no longer working on macOS HOT 4
- Lowering Cognitive complexity as per SonarCloud
- Docker run command returning "is not a file" error on omex path HOT 1
- Documentation discrepancies between repo and website. HOT 1
- Incorrectly raised Exception regarding number of time points HOT 1
- Biosimulators copasi gives incorrect results that normal copasi doesn't HOT 3
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