Cnapy

Latest version: v1.2.3

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1.0.6

*Important note if you're using the CNApy-dev Anaconda environment: Since the CNApy's Anaconda environment requirements are changed with this release, it is recommended to create CNApy's Anaconda enviroment again, e.g. by deleting the old environment and creating a new one.*

New features
* Auto-FBA now also works when a reaction's flux bounds are changed (344)
* Whenever a new metabolite is going to be created after a reaction equation is changed, the user is now asked if this should happen or not

Bug fixes
* Add instructional error message when CellNetAnalyzer is not up-to-date or incorrectly configured (348)
* A rare MCS computation error with optlang under Windows is now solved (341)
* Fixed error on SBML export (321)
* Fixed error by clicking on a metabolite in a reaction navigation text line (345)

Install

There are two ways to install CNApy:

1. Under any operating system, by installing CNApy as a conda package (see [https://github.com/cnapy-org/CNApy#install-cnapy-with-conda](https://github.com/cnapy-org/CNApy#install-cnapy-with-conda))
2. As an alternative installation way under Windows, by using the .exe installer attached to [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).

1.0.5

New features
* Added a Genes tab which shows all genes of the currently loaded model. Once a gene is selcted, the user can change the name (not the ID) of the shown gene. In addition, all gene-associated reactions and their reaction strings are shown.
* In the Reaction list view, an editable "scenario" column is added where one can directly enter a scenario value, even if the reaction doesn't occur on any map.
* Added the "Auto FBA" mode which allows one to automatically perform an FBA whenever the current scenario is changed.
* Added a QLP FBA which makes a currently infeasible scenario feasible using a quadratic linear programming approach.

Bug fixes
* Fixed further potential errors when opening the MCS calculation window.

Install

There are two ways to install CNApy:

1. Under any operating system, by installing CNApy as a conda package (see [https://github.com/cnapy-org/CNApy#install-cnapy-with-conda](https://github.com/cnapy-org/CNApy#install-cnapy-with-conda))
2. As an alternative installation way under Windows, by using the .exe installer attached to [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).

1.0.4

*Note if you're using the CNApy-dev Anaconda environment: Since the CNApy's Anaconda environment requirements are changed with this release, it is recommended to create CNApy's Anaconda enviroment again, e.g. by deleting the old environment and creating a new one.*

New features
* In the reactions view, lower and upper bounds are now shown in respective columns. After performing an FVA, the FVA results are shown in these columns.
* In a metabolite's view, the metabolite-associated reactions are now listed with their full reaction string. By double-clicking on any metabolite in the reaction string, the view automatically switches to the metabolite. By double-clicking on the reaction name, the view switches to the reaction.
* Reaction and metabolite identifiers can now be checked using the identifiers.org API. If a key or an identifier is invalid according to identifiers.org, it is marked red. Note: Sometimes, identifiers.org's API marks obviously invalid IDs as valid.
* Scenarios can now be merged using the "Merge scenario..." option in the Scenario menu tab.

Bug fixes
* Fixed a potential error when opening the MCS calculation window.
* Fixed issues with multi-reaction selection.

Further changes
* optlang is now the default solver interface for MCS calculations

Install

There are two ways to install CNApy:

1. Under any operating system, by installing CNApy as a conda package (see [https://github.com/cnapy-org/CNApy#install-cnapy-with-conda](https://github.com/cnapy-org/CNApy#install-cnapy-with-conda))
2. As an alternative installation way under Windows, by using the .exe installer attached to [CNApy's latest release](https://github.com/cnapy-org/CNApy/releases/latest).

1.0.3

New features
* The README is extended and now including the setting of the PYTHONNOUSERSITE variable
* Errors in written target/desired regions of MCS will now be printed to the user in a pop-up window with a detailed error description

Bug fixes for the following issues
311, 310, 307 and 305

1.0.2

* Better Elementary Mode and Minimal Cut Set navigation (as described in the manual)
* Added abort option for EFMtool computation
* New metabolic models
* Fix reaction bound setting bug
* Fix MCS window setting bug
* Several further bug fixes

1.0.1

*Beta release*

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