About


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.

Team

Jasmin Fisher
Systems Biology - Microsoft Research
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Nir Piterman
Verification and Automated Reasoning - University of Leicester
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Ben Hall
Systems Biology - University of Cambridge
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Alex Taylor
Socio-Digital Systems - Microsoft Research
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Scarlet Schwiderski-Grosche
Program Management - Microsoft Research
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David Benque
Design - Protoplot
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Sergey Berezin
Architecture and programming - Moscow State University
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Nikita Skoblov
Architecture and programming - Moscow State University
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Svetlana Kostyukova
Programming - Moscow State University
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Alumni

Byron Cook - University College London
Samin Ishtiaq - Microsoft Research
Inna Zelenina - Moscow State University
Publications

Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform
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
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Modelling biology -- working through (in-)stabilities and frictions
Taylor, Fisher, Cook, Ishtiaq, Piterman
Computational Culture, Nov 2014
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Finding instability in biological models
Cook, Fisher, Hall, Ishtiaq, Juniwal, Piterman
CAV 2014
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At the Interface of Biology and Computation
Taylor, Piterman, Ishtiaq, Fisher, Cook, Cockerton, Bourton, Benque
CHI 2013
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Model-Checking Signal Transduction Networks through Decreasing Reachability Sets
Claessen, Fisher, Ishtiaq, Piterman, Wang
CAV 2013
[PDF]

BMA: Visual Tool for Modeling and Analyzing Biological Networks
Benque, Bourton, Cockerton, Cook, Fisher, Ishtiaq, Piterman, Taylor, Vardi
CAV 2012
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Proving Stabilization of Biological Systems
Cook, Fisher, Krepska, Piterman
VMCAI 2011
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Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks.
Schaub, Henzinger, Fisher
BMC Systems Biology. 1:4, 2007
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