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.


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

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

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

Modelling biology -- working through (in-)stabilities and frictions
Taylor, Fisher, Cook, Ishtiaq, Piterman
Computational Culture, Nov 2014

Finding instability in biological models
Cook, Fisher, Hall, Ishtiaq, Juniwal, Piterman
CAV 2014

At the Interface of Biology and Computation
Taylor, Piterman, Ishtiaq, Fisher, Cook, Cockerton, Bourton, Benque
CHI 2013

Model-Checking Signal Transduction Networks through Decreasing Reachability Sets
Claessen, Fisher, Ishtiaq, Piterman, Wang
CAV 2013

BMA: Visual Tool for Modeling and Analyzing Biological Networks
Benque, Bourton, Cockerton, Cook, Fisher, Ishtiaq, Piterman, Taylor, Vardi
CAV 2012

Proving Stabilization of Biological Systems
Cook, Fisher, Krepska, Piterman
VMCAI 2011

Qualitative Networks: A Symbolic Approach to Analyze Biological Signaling Networks.
Schaub, Henzinger, Fisher
BMC Systems Biology. 1:4, 2007