Release notes from BioModelAnalyzer

v14 Architecture update and reservation

2023-03-13T13:48:51Z

New features
- Additional https://bmafreeapp.azurewebsites.net free-tier version of BMA added to run in parallel
- There is a hosting change as part of this to a prepaid reservation.
- Client can now check which server it is connected to from settings
- Team members update
- Publications update
Bugfixes
- Decimals not handled in formulae inputs, added message
- Fixed popup bug caused by stability analysis error
- Standalone console updated to z3 version 4.11.2 (gui-server already on this)

v13 BMA Console Linux

2023-01-16T13:39:49Z

BioModelAnalyzer

BioModelAnalyzer is a user-friendly tool for constructing biological models and verifying them

This version is a prototype for the multi-platform version specially designed for Linux and HPC parallelisation.

Overview

This project can be build as a standalone solution with msbuild on linux or mac.

In Windows

Open the solution BioCheckConsoleMulti.sln

The executable to run will be built in (release or debug):

BioCheckConsoleMulti/bin/Release/netcoreapp3.1/BioCheckConsoleMulti

Mac/Linux

Instructions on installing the dotnet runtime: https://learn.microsoft.com/en-us/dotnet/core/install/linux-ubuntu
Instructions on installing mono: https://www.mono-project.com/docs/getting-started/install/linux/
Run the prepare script
.\PrepareRepositoryNix.sh
Build the project

msbuild BioCheckConsoleMulti.sln /p:Configuration=Release /p:Platform="x64" /t:Rebuild

Simple Example

An example is to call it from the command line like

./BioCheckConsoleMulti -model ToyModelUnstable.json -engine SCM

Further info on WIKI

https://github.com/hallba/BioModelAnalyzer/wiki/LinuxBuild

Linux BMA Console

2023-01-16T13:33:39Z

BioModelAnalyzer

BioModelAnalyzer is a user-friendly tool for constructing biological models and verifying them

This version is a prototype for the multi-platform version specially designed for Linux and HPC parallelisation.

Overview

This project can be build as a standalone solution with msbuild on linux or mac.

L1.13.4

2023-01-16T13:29:01Z

Create Citation.cff

L1.13.3

2023-01-16T09:10:54Z

Updated the readme

version 1.13

2023-01-16T07:23:49Z

BMA 1.13.0002

This is the first release distributed from the UCL ARC team.
New features

ServerVersion added to check server version: call it directly from a browser,e.g. Production ServerVersion
Team members update

Bugfixes

Fixed reported bug: Division by a variable can cause instability that depends on node ID

v1.13.2

2022-09-12T08:16:53Z

Revert the banner change for release to staging plus update release n…

version 1.12

2022-04-08T14:22:22Z

BMA 1.12.0011

This release focuses on bug fixes and minor user interface updates.

New features

Reintroduced the ability to create LTL states from the proof analysis and refined table headers
Allowed users to view proof results through the connections context menu
Changed the constellations rendering to better distinguish cluster links from model edges

Bugfixes

Fixed a minor LTL animation rendering bug

v1.12

2022-04-07T10:19:56Z

package for site updated

version 1.11

2022-03-09T10:25:37Z

BMA 1.11.0035

This release updates multiple components in the user interface to better support the analysis of large models.

New features

Rendering of the stability proof in the analysis tab and extended table has been updated to allow hundreds of components to be viewed. This is achieved through the use of canvas rendering in the tab and an external library in the table view
Results from the proof are now downloadable as a CSV for offline analysis
Proof results persist when models layout is changed (for example, when moving a variable), only being wiped when variable updates are altered

Bugfixes

We have further updated unit tests and build components, and disable the automatic switch for intelligent zoom if the user selects a specific visualisation.