Statecharts: A visual formalism for complex systems
Science of Computer Programming
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
Formalization of the Protein Production by Means of Petri Nets
ICIIS '99 Proceedings of the 1999 International Conference on Information Intelligence and Systems
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
Generic Reactive Animation: Realistic Modeling of Complex Natural Systems
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
Modeling Biology using Generic Reactive Animation
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Communications of the ACM
BMA: visual tool for modeling and analyzing biological networks
CAV'12 Proceedings of the 24th international conference on Computer Aided Verification
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The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic and proteomic data have not yet led to a satisfactory model of working cell in silico. We have set out to devise a user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells. Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication, death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that depend on the cell's history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable platform for biological modeling and analysis, supporting user-friendly in silico experimentation, animation, discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems.