Bio Model Analyzer

Description

Bio Model Analyzer is a new biological modelling tool that illustrates signalling pathways and determines cellular stabilization. The tool represents a merging of perspectives from systems biology, formal methods, human computer interaction and design. At one level, Bio Model Analyzer is a sketching tool that enables users to draw out a biological system of interest (e.g. a genetic regulatory network) by dragging and dropping cells, their contents (DNA, proteins, etc.), extracellular components and relationships onto a simple canvas. At another level, Bio Model Analyzer’s analysis proves stabilization of biological systems, based upon formal methods that were developed for the specification and verification of properties in concurrent software systems.

While Microsoft Research introduced the BMA services, we developed an HTML5 frontend application to visually design and interactively analyze bio models.

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BMA frontend is created using HTML5/TypeScript technologies and uses Model-View-Presenter pattern for Application architecture with passive view approach for effective and maintainable testing of all its components (Martin Fowler, MVP with passive view – http://martinfowler.com/eaaDev/PassiveScreen.html)

bma_scheme

To maintain its stability each component is covered by tests. Test infrastructure uses jasmine framework and chutzpah library as a test runner

BMA tool allows you to create your model using visual designer and build it from specific elements using virtual canvas. It allows you to manipulate with visual elements and their relationships using common things like drag’n’drop, copy/paste and so on. You can also navigate over virtual canvas using pan and zoom and you are not limited to any space. Just use as much as you need with possibility of infinite extending of virtual canvas. There is also a various support of touch devices such as tablets and mobile phones.

You can always export visual representation of you model as a vector graphics in common SVG format to further use in your publications.

People

Sergey Berezin

Nikita Skoblov

Svetlana Kostyukova

Inna Zelenina

Sources

http://biomodelanalyzer.research.microsoft.com/