Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update doc for copasi import and github installation #158

Merged
merged 1 commit into from
Dec 2, 2019
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 15 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,10 @@ for example:
Where PEtab is used / supported:

- Within the systems biology optimization
[benchmark problem collection](https://github.com/LoosC/Benchmark-Models)
[benchmark problem collection](https://github.com/LeonardSchmiester/Benchmark-Models)

- A PEtab -> [COPASI](http://copasi.org/)
[converter](https://github.com/copasi/python-petab-importer)

- [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)

Expand Down Expand Up @@ -85,15 +88,24 @@ it is running

It will require Python3.6 to run.

Development versions of the PEtab library can be installed using

pip3 install https://github.com/ICB-DCM/PEtab/archive/develop.zip

(replace `develop` by the branch or commit you would like to install).

When setting up a new parameter estimation problem, the most useful tools will
be:

- The PEtab validator, which is now automatically installed using Python entrypoints to
be available as a shell command from anywhere called `petablint`
- The **PEtab validator**, which is now automatically installed using Python
entrypoints to be available as a shell command from anywhere called
`petablint`

- `petab.core.create_parameter_df` to create the parameter table, once you
have set up the model, condition table and measurement table

- Functions in `petab.sbml` to define observables and error model parameters
in the SBML model

## Extending PEtab

Expand Down