CNApy 1.1.5

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

• Fix #432 by @Paulocracy in #433
• set Qt version to 5.15 (LTS) by @axelvonkamp in #431
• parse lists of annotation values as lists by @axelvonkamp in #436
• Copy reaction table to UI clipboard by @axelvonkamp in #438
• Scenario constraints by @axelvonkamp in #445
• Visual OptMDFpathway by @Paulocracy in #441
• Fix #439 (error with multiple empty annotations) by @Paulocracy in #440
• Add automatic blank background with reaction addition by @Paulocracy in #447
• Add free linear constraints to OptMDFpathway and thermodynamic bottleneck analysis by @Paulocracy in #446
• Scenario tab updates by @axelvonkamp in #448
• Add menu entry for storing reaction list content by @Paulocracy in #449
• Move website data to master branch by @sthiele in #444
• In out fluxes additions by @Paulocracy in #451
• Flux feasibility with biomass modification by @axelvonkamp in #450
• Bump to 1.1.5 by @Paulocracy in #452

Full Changelog: v1.1.4...v1.1.5

CNApy 1.1.4

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.

CNApy 1.1.3

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.

CNApy 1.1.2

Beta release

CNApy 1.1.1

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

• Scenarios can now get an optional objective and description (#388)
• Separate objective tab added (#388)
• Scenario-bound reactions can now be pinned in the reaction list (#388)
• The flux feasibility routine now shows all made changes for feasibility in the iPython console (#385)
• New first start-up routine specifically asking for the download of CNApy's example projects (#388)

Bug fixes

• Resolve CNApy installer issue, which led to no CNApy start-up, by using @sthiele's JVM-searching routine (#386)
• Resolve CNApy installer issue in common folders (#386)
• Resolve update_item() error when changing reaction elements (#390)
• Resolve error with in/out metabolite fluxes on some devices (#389)

Further changes

• Reordered Scenario menu tab for more consistency (#388)
• Some vertical space is saved by rearranging the reaction view's content (#388), making it more readable with smaller screens
• @VonAlphaBisZulu's StrainDesign package was updated to its latest version 1.6

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)
2. As an alternative installation way under Windows, by using the .exe installer attached to CNApy's latest release.

CNApy 1.1.0

Beta release

CNApy 1.0.9

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.

This is a major update which contains many significant changes and additional features:

New features

• @VonAlphaBisZulu's StrainDesign package is now integrated within CNApy. You can access it under CNApy's GUI under the "Analysis" menu entry. By using StrainDesign's GUI and functions, one can easily create powerful combinations of several strain design methods such as OptKnock, RobustKnock and generalized Minimal Cut Sets (MCS). StrainDesign makes use of state-of-the-art model compression algorithms in order to minimize the computational complexity of all calculations as much as currently possible, thus making calculations faster and less memory-intensive. Further major features are: One can also define knock-ins instead of knock-outs; Aside of reaction-based knock-outs, one can also define gene-based knock-outs.
• Right now only for the StrainDesign features, the open-source solver SCIP is now usable with CNApy. You still have to install and configure SCIP by yourself. In the future, this will be facilitated and SCIP will be usable with all CNApy functions.
• Since almost all legacy functions are now programmed in Python, all CellNetAnalyzer legacy bindings are now removed, so that no MATLAB or Octave is needed for them anymore.
• The community versions of IBM CPLEX and Gurobi are now installed by default. These community versions are restricted to models up to 1000 variables. In order to facilitate the integration of both solver's full versions (usable for big versions), wizards were added to CNApy which you may find under the "Config" menu entry.
• The standard CNApy projects can now be downloaded under the respective field in the "Projects" menu entry even after the first start.

Bug fixes

• GLPK is now the standard solver in order to prevent typical IBM CPLEX or Gurobi errors (#376)
• Numerous potential IBM CPLEX and Gurobi errors are now catched (#368, #373)
• WIth the newest CNApy projects release, a map resolution error under Linux affecting the map's text was resolved (#377)
• An error while using the Escher SVG integration was resolved (#355)
• Maps are now automatically zoomed in the start-up such that no scroll bars have to appear (#354)

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)
2. As an alternative installation way under Windows, by using the .exe installer attached to CNApy's latest release.

CNApy 1.0.8

Beta release

CNApy 1.0.7

Beta release

CNApy 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)
2. As an alternative installation way under Windows, by using the .exe installer attached to CNApy's latest release.