BMA 1.9.0075

This release introduces several major new features to enable the visualisation of large-scale models.

New rendering engine and model views

- Novel visualisation options; at far zoom, models are replaced by a simplified “bubble” representation based on the results of a k-means clustering. This allows hubs and subnetworks of genes to be clearly viewed in large models. Bubble visualisations can be annotated with stability analysis results, allowing for rapid analysis, visualisation, and refinement.
- A new rendering engine increases canvas performance
- New mechanism for changing protein interactions through a contextual menu

Bugfixes

- Fixed issue with positioning of settings popup on small screens
- Fixed issue with color displaying in popup for variable in top panel
- Added display of current selected relationship type in context menu
- Fixed issue with loading of huge tables for proof results

BMA 1.8.0053

This major update brings a plethora of changes to BioModelAnalzyer focused on model storage and motif use!

New combined model and motif library

Motif libraries support the construction of large models from the reuse of small networks that capturing fundamental biological phenomena. Our previous releases allowed users to interact through a dedicated carousel, allowing users to preview the motifs but gave limited options for sorting and storage. Similarly, users with large model libraries may struggle to sort and find single models. In this release we have developed a new interface to the model repository that combines the unique interface of the model carousel with new sorting and searching functions. In addition to providing a library of developer created models and motifs, users can build and store models and motifs. Models can be opened directly to the canvas, or treated as a motif and dragged into an already open model for reuse and mixing models. Large libraries are made more manageable through search and sorting functions, and models can be annotated with short descriptions.

- Motif library was removed from interface.
- Model repository interface completely reworked. Now it has new layout and structure.
- All motifs are displayed together with models in repository menu.
- Added possibility to create user motifs and save them to storage.
- Preloaded models from launch page added to model repository.
- Added possibility to filter and search the repository.
- Added possibility to preview model and motif berfore its loading to model designer.
- Added possibility to add model contents to existing model rather that just replace it.
- Added possibility to load motif by replacing current model designer content with motif contents.
- Added possibility to edit model/motif name and description for user created models and motifs.

Design updates and bug fixes

- Fixed issue with model fitting to screen for some models with 2x2 and 3x3 cells.
- Color options in palette popup for variables now show last selected result and highlight options on hover.
- BMA styles updated which includes loading animation, shadows spec, design of popups and some other elements.
- Save button now displays animation when using it.

BMA 1.7.0019

This release brings some new features and refinements to existing tools!

Variable colour choice

Building large, complex models can get confusing quickly. Lots of variables in a small space can make individual pathways hard to view. In this new update we have enabled a choice of different colours for variables! Create a selection of variables with shift-left click and drag, and change their colour using the colour palette tool, or change the colour of the variables you drop onto the canvas by hovering over the tool panel and selecting a new colour. Colours automatically update depending on their location in the cell, with pale extracellular genes and bright intracellular genes.

Bugfixes

- Cut/copy/paste now works when selecting text from the variable target function editor.
- Variable names in LTL states tooltip are extended to increase readability.
- All user modes (pan, variable drop, cell drop, and edge drop) can now be used to create selections.

BMA 1.6.0132

This release brings a major new features in the tool, and with it a substantial redesign of the canvas. Several new tools are available to users:

Select, cut, copy, and paste

Users can create selections complex through right-click and drag when navigating the canvas, or right clicking variables. Selections can later be cleared by clicking the navigate icon or through the right-clickable context menu. Selected variables and edges can be copied and pasted within the canvas, or sent through the right click menu to the motif carousel. Moreover, selected regions can be copied to text files and analysed outside of the main tool, and externally created model-text can be pasted into the UI.

Design rethink

To enable more complex user interaction with the canvas and improve accessibility variable icons and colours have been extensively redesigned. This includes new hover and selection highlights for variables, interactions, and grid cells, alongside a reordering of the top menu and introduction of a “fit to view” button. For users who need the old colour scheme for ongoing work, this is available as an option in the settings menu. Finally, variables with broken target functions are now highlighted in the canvas simplifying model refinement.

BMA fundamentals

The backend service has been updated, and initial support for GINML import added to the user interface.