Computational Methods in Systems Biology

1. Front Matter

   PDF

2. Formalisms for Modelling Biological Processes

   1. On Defining and Computing “Good” Conservation Laws

      • François Lemaire, Alexandre Temperville

      Pages 1-19

   2. SAT-Based Metabolics Pathways Analysis without Compilation

      • Sabine Peres, Martin Morterol, Laurent Simon

      Pages 20-31

   3. Model Integration and Crosstalk Analysis of Logical Regulatory Networks

      • Kirsten Thobe, Adam Streck, Hannes Klarner, Heike Siebert

      Pages 32-44

3. Model Inference from Experimental Data

   1. Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods

      • Attila Gábor, Julio R. Banga

      Pages 45-60

   2. Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More

      • Fabian Fröhlich, Fabian J. Theis, Jan Hasenauer

      Pages 61-72

   3. Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis

      • Fabian Fröhlich, Sabrina Hross, Fabian J. Theis, Jan Hasenauer

      Pages 73-85

4. Frameworks for Model Verification, Validation, and Analysis of Biological Systems

   1. Precise Parameter Synthesis for Stochastic Biochemical Systems

      • Milan Češka, Frits Dannenberg, Marta Kwiatkowska, Nicola Paoletti

      Pages 86-98

   2. Parameter Synthesis for Cardiac Cell Hybrid Models Using δ-Decisions

      • Bing Liu, Soonho Kong, Sicun Gao, Paolo Zuliani, Edmund M. Clarke

      Pages 99-113

   3. Trace Simplifications Preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock

      • Pauline Traynard, François Fages, Sylvain Soliman

      Pages 114-128

   4. Characterization of Reachable Attractors Using Petri Net Unfoldings

      • Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé, Stefan Schwoon

      Pages 129-142

   5. Dynamic Modeling and Simulation of Leukocyte Integrin Activation through an Electronic Design Automation Framework

      • Nicola Bombieri, Rosario Distefano, Giovanni Scardoni, Franco Fummi, Carlo Laudanna, Rosalba Giugno

      Pages 143-154

5. Models and Their Biological Applications

   1. Towards Real-Time Control of Gene Expression at the Single Cell Level: A Stochastic Control Approach

      • Lakshmeesh R. M. Maruthi, Ilya Tkachev, Alfonso Carta, Eugenio Cinquemani, Pascal Hersen, Gregory Batt et al.

      Pages 155-172

   2. A Rule-Based Model of Base Excision Repair

      • Agnes Köhler, Jean Krivine, Jakob Vidmar

      Pages 173-195

   3. Using Process Algebra to Model Radiation Induced Bystander Effects

      • Rachel Lintott, Stephen McMahon, Kevin Prise, Celine Addie-Lagorio, Carron Shankland

      Pages 196-210

   4. Exploring the Cellular Objective in Flux Balance Constraint-Based Models

      • Rafael S. Costa, Son Nguyen, Andras Hartmann, Susana Vinga

      Pages 211-224

6. Computational Approaches for Synthetic Biology

   1. Optimization Based Design of Synthetic Oscillators from Standard Biological Parts

      • Irene Otero-Muras, Julio R. Banga

      Pages 225-238

7. Flash Posters

   1. Modelling Polar Retention of Complexes in Escherichia coli

      • Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro

      Pages 239-243

   2. Extensible and Executable Stochastic Models of Fatty Acid and Lipid Metabolism

      • Argyris Zardilis, João Dias, Animesh Acharjee, James Smith

      Pages 244-247

   3. FM-Sim: Protocol Definition, Simulation and Rate Inference for Neuroscience Assays

      • Donal Stewart, Stephen Gilmore, Michael A. Cousin

      Pages 248-251

This book constitutes the proceedings of the 12th International Conference on Computational Methods in Systems Biology, CMSB 2014, held in Manchester, UK, in November 2014.
The 16 regular papers presented together with 6 poster papers were carefully reviewed and selected from 31 regular and 18 poster submissions. The papers are organized in topical sections on formalisms for modeling biological processes, model inference from experimental data, frameworks for model verification, validation, and analysis of biological systems, models and their biological applications, computational approaches for synthetic biology, and flash posters.

• agent models
• biological networks
• computational biology
• computational transcriptomics
• constraints
• continuous simulation
• discrete models
• estimation
• formalisms
• gene regulatory network
• multiobjective optimization
• multiscale systems
• probabilistic inference problems
• rule-based modeling
• simulation and modeling
• systems biology
• validation
• verification

• Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK

  Pedro Mendes, Joseph O. Dada, Kieran Smallbone

Policies and ethics