v0.5.0-snapshot1

Use control library without Z3.

0.4.1

This version fixes issue #9 (attractor visualization problems) and adds a new binary which is similar to experiment, but outputs the sink states of the analyzed model.

Also, manual is now part of the repository and for the first time, we are including the experiment and sink-state-enumerator binaries as part of the release bundle.

0.4.0

Stabilisation of 0.4.0-beta.1 with some extra bugfixes.

0.4.0-beta.1

Beta release of 0.4.0 with all the functionality of the final version in place. Compared to alpha-3, this includes:

• A more sophisticated stability analysis toolbox (we can now filter based on attractor behaviour type).
• Auto-expand button with variable depth.
• Tree rendering with precision, meaning that mixed/decision nodes with sufficient majority class are collapsed to leafs.
• Attribute sorting and shadowing.

Edition 2019.1

First release of our "edition" builds. These are stand-alone applications that are running the client in an embedded webview. Edition 2019 is loosely based on the 0.1.0 versions, but with a few additional bugfixes from newer versions.

• For Windows, simply download Aeon-2019.exe and run it.
• For MacOS, download Aeon-2019.dmg which contains the corresponding .app. However, note that the app is not digitally signed by Apple, so you'll have to enable it in security preferences when you first run it.
• For Linux installations, there is a provided .deb package. It only depends on Gtk and GtkWebKit, so please make sure you have webkit2gtk-4.0 installed.
• If you (for any reason) don't want to use a pre-compiled binary, you can always download the source and run cargo run --release --bin biodivine-aeon-server.

0.4.0-alpha.3

Compared to alpha.2, there is now an option to display detailed stability analysis of sink states with witness generator.

0.4.0-alpha.2

Compared to the previous alpha, this version adds and API endpoint to display stability analysis data.

0.3.0

This release focuses on stability and performance improvements. Specifically:

• We now use the stable version 0.1.0 of biodivine-lib-param-bn. This brings additional improvements (compared to 0.2.0) in the SBML parser, as well as other bugfixes and API improvements.
• This is the first version to use fully symbolic representation of asynchronous graphs.
• Internal algorithms have been significantly improved to a point where we can handle any fully instantiated real-world network that we know of. Large parameterized models (20+ variables) can expect several orders of magnitude speed-up as well.
• Progress tracking and cancellation support during computation have been reworked and should be more reliable.
• We show a two-state approximation for large attractors that cannot be otherwise visualized.
• Adding Github Actions build check. In the future we should really consider the option to automatically build artifacts for releases using Github Actions.
• We incorporate a large (125+) collection of real world models that can be used for testing (already used in biodivine-lib-param-bn for differential SBML testing) and benchmarking (includes simple python scripts to run such benchmakrs). The integrity of the benchmark set is validated using a custom rust executable.

0.4.0-alpha.1

This is the first preview of the decision tree visualisation for bifurcation functions. Aside from some small bug-fixes in the main GUI, the essential change is the new bifurcation function explorer. This explorer allows to dynamically create decision trees showing necessary conditions to reach different BN phenotypes.

0.3.0-beta.1

First working stable version with uses fully symbolic analysis.