What is the BMA?

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. We hope you enjoy using Bio Model Analyzer and welcome your feedback.

Tutorial PDF Example Library F.A.Q. Privacy Policy
Bio Model Analyzer Demonstration
Introduction to Bio Model Analyzer
Live Bio Model Analyzer demonstration
Modelling biological networks with the Bio Model Analyzer
Launch Tool
Example Library and References
Toy Example 1 (stabilising)
[Download JSON]
Load model in tool
Toy Example 2 (non stabilising)
[Download JSON]
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Cancer Signalling Tutorial
[Download JSON]
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Metabolism Network Tutorial
[Download JSON]
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Cell fate determination during C. elegans vulval development
[Download JSON] Reference paper [Go to pubication]
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Mammalian Epidermis
[Download JSON] Reference paper [Go to pubication]
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Understanding leukaemia
[Download JSON] Reference paper [Go to pubication]
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Publications
Dana Silverbush, Shaun Grosskurth, Dennis Wang, Francoise Powell, Berthold Gottgens, Jonathan Dry, Jasmin Fisher
Cancer Research 2/2017: pages 827-838; DOI:10.1158/0008-5472.can-16-1578
David Shorthouse, Angela Riedel, Jacqueline Shields, Benjamin A. Hall
CMSB 2016, DOI:10.17863/CAM.4585 IEEE TCSIM best poster award
Zara Ahmed, David Benque, Sergey Berezin, Anna Caroline E. Dahl, Jasmin Fisher, Benjamin A. Hall, Samin Ishtiaq, Jay Nanavati, Nir Piterman, Maik Riechert, Nikita Skoblov
Verification, Model Checking, and Abstract Interpretation, 01/2017: pages 1-13; ISBN: 978-3-319-52233-3, DOI:10.1007/978-3-319-52234-0_1
Benjamin A Hall, Nir Piterman, Alex Hajnal, Jasmin Fisher
Biophysical Journal 07/2015; 109(2):428-38., DOI:10.1016/j.bpj.2015.06.007
Chuang R., Hall B.A., Benque D., Cook B., Ishtiaq S., Piterman N., Taylor A., Vardi M., Koschmieder S., Gottgens B., and Fisher J.
Scientific Reports, 5:8190, Nature Publishing Group, February 2015
Taylor, Fisher, Cook, Ishtiaq, Piterman
Computational Culture, Nov 2014
Cook, Fisher, Hall, Ishtiaq, Juniwal, Piterman
CAV 2014
Taylor, Piterman, Ishtiaq, Fisher, Cook, Cockerton, Bourton, Benque
CHI 2013
Claessen, Fisher, Ishtiaq, Piterman, Wang
CAV 2013
Benque, Bourton, Cockerton, Cook, Fisher, Ishtiaq, Piterman, Taylor, Vardi
CAV 2012
Cook, Fisher, Krepska, Piterman
VMCAI 2011
Schaub, Henzinger, Fisher
BMC Systems Biology. 1:4, 2007
Team

Jasmin Fisher
Systems Biology Microsoft Research & University of Cambridge
Nir Piterman
Verification and Automated Reasoning University of Leicester
Ben Hall
Systems Biology University of Cambridge
Alex Taylor
Socio-Digital Systems University of London
Sergey Berezin
Architecture and programming Moscow State University
Nikita Skoblov
Architecture and programming Moscow State University
Nicole Kapitza
Design Kapitza Studio
Frequently Asked Questions
How do I open Bio Model Analyzer?
How do I drag and drop elements onto the canvas?
How do I zoom and scroll around the canvas?
How do I name and give ranges to variables?
What are some basic target functions?
How do I use advanced target functions?
What happens with variables with different ranges?
How do I save my work to the model library?
How do I export and import XML files?
How do I move between models in my library?
Bio Model Analyzer freezes while I’m working;
how do I stop this?
Is this just a nice drawing tool?
What kind of analysis does Bio Model Analyzer do?
Why are there only one variable and one constant icon?
How am I to represent the many different kinds of biological elements?
Contact Us
Open Source

The BioModelAnalyzer is an open source project, available under the MIT license. In addition to the web interface, command line tools are available that offer new analyses not currently available through the GUI.

View Source
Alumni
Byron Cook - University College London
Samin Ishtiaq - Microsoft Research
Scarlet Schwiderski-Grosche - Microsoft Research
David Benque - Protoplot
Inna Zelenina - Moscow State University
Svetlana Kostyukova - Moscow State University
Dmitry Kats - Moscow State University
Dmitry Voytsekhovskiy - Moscow State University