Comments (1)
Given that you are already using AMICI, PEtab and pyPESTO, I agree that encoding the benchmark problems via PEtab is the way to go. Unfortunately it seems that in the repository you linked, not all formats provide the entire information, in particular the COPASI format provides the dynamics, but not the parameter estimation problem, which needs to be defined manually on the GUI. However e.g. the AMIGO one seems to do so. It should yet be straightforward to take e.g. the SBML model definition, and the parameter bounds from COPASI, and the objective function definition from wherever that is defined, and combine it to a PEtab problem.
BTW: If you are looking for benchmark problems, these here may be of interest to you -- a larger set of models already in PEtab format. https://github.com/Benchmarking-Initiative
from pypesto.
Related Issues (20)
- Waterfall plot error: `order_by_id` and `start_indices` do not work together
- Optimization with conditions specific for observables fails HOT 4
- Frequent timeouts for `mac (3.11)` workflow runs HOT 3
- Check pypesto/sample/geweke_test.py calculate_zscore/spectrum0/spectrum
- Frequent readthedocs timeout HOT 1
- `pyjulia` is no longer maintained
- Roadrunner petab test case 0018 fails on Mac HOT 3
- Lazy loading of optimization results from HDF5
- Aggregated Objective does not return expected outputs using `return_dict` HOT 7
- NegLogParameterPriors evaluates prior density also on fixed parameters HOT 6
- AmiciObjective: For sensi_orders>0, check that sensitivities wrt all relevant parameters are computed
- PetabImporter does not respect estimate=0 HOT 3
- KeyError for parameter with amici prefix HOT 2
- Lots of warnings in test suite HOT 2
- Using PyPesto with jax HOT 11
- Roadrunner does not correctly handle estimated noise parameters
- objective.FD does not inherit the PrePostProcessor
- How to set `fill_fixed_parameters`=True for petab parameter mappings?
- Fitting reduced kinetic data (without time) HOT 3
- Publications using pyPESTO
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pypesto.