Medusa
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opencobra
Analysis of ensembles of metabolic network reconstructions
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Bumps [notebook](http://jupyter.org) from 6.4.1 to 6.4.12. [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a...
Bumps [ipython](https://github.com/ipython/ipython) from 7.1.1 to 7.16.3. Commits d43c7c7 release 7.16.3 5fa1e40 Merge pull request from GHSA-pq7m-3gw7-gq5x 8df8971 back to dev 9f477b7 release 7.16.2 138f266 bring back release helper from master...
Bumps [ipython](https://github.com/ipython/ipython) from 7.1.1 to 7.16.3. Commits d43c7c7 release 7.16.3 5fa1e40 Merge pull request from GHSA-pq7m-3gw7-gq5x 8df8971 back to dev 9f477b7 release 7.16.2 138f266 bring back release helper from master...
Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 0.35.4 to 1.2.21. Changelog Sourced from jupyterlab's changelog. github_url: 'https://github.com/jupyterlab/jupyterlab/blob/master/CHANGELOG.md' JupyterLab Changelog 4.0 4.0.0a4 (Full Changelog) Enhancements made Don't sort context menu items by selector #10666 (@fcollonval)...
Bumps [jupyterlab](https://github.com/jupyterlab/jupyterlab) from 0.35.4 to 1.2.21. Changelog Sourced from jupyterlab's changelog. github_url: 'https://github.com/jupyterlab/jupyterlab/blob/master/CHANGELOG.md' JupyterLab Changelog 4.0 4.0.0a4 (Full Changelog) Enhancements made Don't sort context menu items by selector #10666 (@fcollonval)...
This is the code that added to generate a metabolite probability-based gap-filling and generate ensembles of models based on some noise to the penalty The new medusa with continuous gap-filling...
Some utility functions that have come up as potentially useful so far: * getting a list of all reactions that vary across an ensemble, rather than iterating over all features...
There is a problem with the base_model attribute of the medusa module. It generates the following error when I try to call base_model method on the loaded ensembles. This is...
The docstrings and variable names for the batch_load_from_files function suggest that only json files are accepted as input, rather than both json and SBML. The function currently checks whether the...