CNApy Versions Save

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

v1.1.11

3 months ago

Main changes

This update provides a multitude of bug fixes, including the solution for a crash during plotting when it was installed using the Windows installer. Furthermore, one can now easily take a map screenshot under the respective options in the "Map" menu, EFMs can now be easily normalized and scenario-dependent annotations were added (e.g., for scenario-dependent variances or thermodynamic parameter values).

Installation Options

There are 4 alternative ways to install CNApy:

  1. If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
  2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see Assisted installation under Linux and MacOS X.
  3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section Install CNApy as conda package.
  4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.10...v1.1.11

v1.1.10

4 months ago

Important note for those who are using the cnapy-dev Anaconda environment: Since 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.

Main changes

This update provides a multitude of bug fixes and several small enhancements such as an improved Compute MCS dialog with a reaction auto-completion and the ability to use the "-" sign.

Installation Options

There are 4 alternative ways to install CNApy:

  1. If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
  2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see Assisted installation under Linux and MacOS X.
  3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section Install CNApy as conda package.
  4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.9...v1.1.10

v1.1.9

8 months ago

Main changes

This update provides a multitude of bug fixes and several small enhancements such as the new "Apply" button for calculated MCS (which directly sets them as a scenario) and the new ability to export an XLSX spreadsheet file with extensive in/out flux data for all metabolites of a model.

Installation Options

There are 4 alternative ways to install CNApy:

  1. If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
  2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see Assisted installation under Linux and MacOS X.
  3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section Install CNApy as conda package.
  4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.8...v1.1.9

v1.1.8

1 year ago

Important note if you're using the cnapy-dev Anaconda environment: Since 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.

Main changes

This updates provides an improved GUI experience including a history of viewed model items, a multitude of bug fixes and now officially supports the new easier way to install CNApy on Windows.

Installation Options

There are 4 alternative ways to install CNApy:

  1. If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
  2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see Assisted installation under Linux and MacOS X.
  3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section Install CNApy as conda package.
  4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelogs:

v1.1.7

1 year ago

Important note if you're using the cnapy-dev Anaconda environment: Since 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.

Main changes

This updates provides an improved GUI experience including a history of viewed model items, a multitude of bug fixes and now officially supports the new easier way to install CNApy on Windows.

Installation Options

There are 4 alternative ways to install CNApy:

  1. If you use Windows, the easiest way is to use our Windows installer, see section Using the Windows installer.
  2. If you use Linux or Apple MacOS X, the easiest installation producure is our assisted installation protocol, see Assisted installation under Linux and MacOS X.
  3. If you already have installed Anaconda or Miniconda on your computer, you can directly install CNApy as a conda package as described in section Install CNApy as conda package.
  4. If you want to develop CNApy, follow the instruction for the cloning and set-up of the CNApy repository using git and conda in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.6...v1.1.7

v1.1.6

1 year ago

Important note if you're using the cnapy-dev Anaconda environment: Since 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.

This is a major new release containing many new and novel features, as well as many important bug fixes:

New features

  • You can now set free linear constraints in scenarios and scenario-specific reactions in CNApy under the "Scenario" tab (#445). E.g., aside from many other new possibilities, you can now set linear constraints such that a minimal yield is reached or add import/export reactions for a specific scenario.
  • The thermodynamics-based method OptMDFpathway and a derived thermodynamic FBA as well as bottleneck reaction analysis are now integrated into CNApy (#441). You can find the functionality under the "Analysis" menu entry. To use OptMDFpathway, you have to provide dG'° values and metabolite concentration ranges, which can be manually added as annotations or loaded from a respective Excel XLSX or JSON file.
  • You can now perform the flux feasibility analysis with customizable biomass reaction modifications (#450).
  • You can now copy the content of the reaction (#438) and metabolite (#446) lists in an Excel or text file by right-clicking on the respective heading and copying it to the clipboard. For the reactions list, this is directly possible (as JSON or Excel XLSX) through the "Clipboard" menu tab (#449).
  • Added ability to set exact box positions in the interactive maps (#433).

Bug fixes

  • Circumvent "numpy.float is not defined" error (#442)
  • Fix parsing of annotation values which are Python list strings (#436)
  • Fix error message when multiple empty annotations are created (#440)

Installation Options

There are three ways to install CNApy:

  1. As the easiest way only under Windows, you can use the .exe installer attached to the assets at the bottom of CNApy's latest release.
  2. Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
  3. If you want to clone and/or develop CNApy, follow the instruction in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.4...v1.1.5 and Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.5...v1.1.6

v1.1.5

1 year ago

Important note if you're using the cnapy-dev Anaconda environment: Since 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.

This is a major new release containing many new and novel features, as well as many important bug fixes:

New features

  • You can now set free linear constraints in scenarios and scenario-specific reactions in CNApy under the "Scenario" tab (#445). E.g., aside from many other new possibilities, you can now set linear constraints such that a minimal yield is reached or add import/export reactions for a specific scenario.
  • The thermodynamics-based method OptMDFpathway is now integrated into CNApy (#441). You can find the functionality under the "Analysis" menu entry. To use OptMDFpathway, you have to provide dG'° values and metabolite concentration ranges, which can be manually added as annotations or loaded from a respective Excel XLSX or JSON file.
  • You can now perform the flux feasibility analysis with customizable biomass reaction modifications (#450).
  • You can now copy the content of the reaction (#438) and metabolite (#446) lists in an Excel or text file by right-clicking on the respective heading and copying it to the clipboard. For the reactions list, this is directly possible (as JSON or Excel XLSX) throuch the "Clipboard" menu tab (#449).
  • Added ability to set exact box positions in the interactive maps (#433).

Bug fixes

  • Circumvent "numpy.float is not defined" error (#442)
  • Fix parsing of annotation values which are Python list strings (#436)
  • Fix error message when multiple empty annotations are created (#440)

Installation Options

There are three ways to install CNApy:

  1. As the easiest way only under Windows, you can use the .exe installer attached to the assets at the bottom of CNApy's latest release.
  2. Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
  3. If you want to clone and/or develop CNApy, follow the instruction in section Setup the CNApy development environment.

If you have questions or suggestions regarding CNApy, you can use either of the CNApy GitHub issues, the CNApy GitHub discussions or the CNApy Gitter chat room.

What's Changed

Full Changelog: https://github.com/cnapy-org/CNApy/compare/v1.1.4...v1.1.5

v1.1.4

1 year ago

CNApy has got a Gitter chat room where you can talk to CNApy's developers and stay informed about new releases

This is primarily a maintenance release with some new small features and many bug fixes.

New features

  • Annotation values can now be searched in the search bar if selected (#412).
  • Annotations can now be deleted using a "-" button and can be directly opened in the web browser by using identifiers.org (#412)
  • Gene annotations are now shown and can be edited (#412)

Bug fixes

  • Fix model saving problem (#427).
  • Fix error when editing scenario using backspace (#424).
  • Various error messages when opening files and performing calculations are now catched (#413, #414)

Further changes

  • Reactions selected in the reaction list are now automatically highlighted in the map (#418).
  • The most recent opened .cna files are now shown as a File menu entry (#415, #419).

Installation Options

There are three ways to install CNApy:

  1. As the easiest installation way which only works under Windows, you can use the .exe installer attached to the assets at the bottom of CNApy's latest release.
  2. Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
  3. If you want to develop CNApy, follow the instruction for the successful cloning of CNApy in section Setup the CNApy development environment.

v1.1.3

1 year ago

CNApy has got a new Gitter chat room where you can talk to CNApy's developers and stay informed about new releases

Major new feature

  • CNApy can now use interactive Escher maps, including the ability to load, save and edit them thanks to @axelvonkamp's integration of the Escher in CNApy. From now on, Escher maps are the 2nd type of possible interactive metabolic model maps in CNApy, together with the "traditional" CNApy maps (#401). If you encounter any problems with Escher maps in CNApy, please let us know through our GitHub issues.

Bug fixes

  • Editing a GPR rule does not create many new orphaned genes anymore (#329)
  • CNApy now always downloads the latest CNApy projects version (#398)
  • Scenario objectives are not deleted when using flux history values (#404)
  • StrainDesign now comes in version 1.9, fixing some crashes with GLPK.
  • Escher also works within cobra packages and the .exe installer version (#406)

Further changes

  • Again, some vertical space is saved by rearranging the reaction view's content, making it more readable with smaller screens (#402)
  • Various optimizing refactorings (#396, #400)

Installation Options

There are three ways to install CNApy:

  1. As the easiest installation way which only works under Windows, you can use the .exe installer attached to the assets at the bottom of CNApy's latest release.
  2. Under any operating system, you can install CNApy as a conda package as described in section Install CNApy as conda package.
  3. If you want to develop CNApy, follow the instruction for the successful cloning of CNApy in section Setup the CNApy development environment.

v1.1.2

1 year ago

Beta release