Formal Methods in Macro-Biology

1. Front Matter

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2. Invited Presentations

   1. Model-Checking in Systems Biology - From Micro to Macro

      • Pieter Collins

      Pages 1-22

   2. Developing Quantitative Methods in Community Ecology: Predicting Species Abundances from Qualitative Web Interaction Data

      • Hugo Fort

      Pages 23-35

   3. Understanding How Biodiversity Is Distributed in Space and Time

      • Hélène Morlon

      Pages 36-39

   4. Computing Longevity: Insights from Controls

      • Pietro Lió

      Pages 40-46

3. Regular Papers

   1. Control of a Bioreactor with Quantized Measurements

      • Francis Mairet, Jean-Luc Gouzé

      Pages 47-62

   2. External Interactions on Hybrid Models of Biological Systems

      • Alberto Casagrande, Carla Piazza

      Pages 63-81

   3. Attractor Equivalence: An Observational Semantics for Reaction Networks

      • Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren

      Pages 82-101

   4. Petri Nets Are a Biologist’s Best Friend

      • Nicola Bonzanni, K. Anton Feenstra, Wan Fokkink, Jaap Heringa

      Pages 102-116

   5. 50 Shades of Rule Composition

      • Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

      Pages 117-135

   6. A Logical Framework for Systems Biology

      • Elisabetta de Maria, Joëlle Despeyroux, Amy P. Felty

      Pages 136-155

   7. Disentangling the Effects of Habitat and Protection on Coral Reef Fish Communities in Long-Established Marine Reserves

      • Dominique Pelletier, Delphine Mallet, Abigail Powel, William Roman

      Pages 156-158

   8. The Challenges of Developing Spatially Explicit Network Models for the Management of Disease Vectors in Ecological Systems

      • Brendan Trewin, Hazel Parry, Myron Zalucki, David Westcott, Nancy Shellhorn

      Pages 159-161

   9. Evaluating Management Scenarios for Fished Resources of the New Caledonian Lagoon Using a Spatially-Explicit Model

      • Bastien Preuss, Dominique Pelletier, Laurent Wantiez

      Pages 162-164

   10. Completing SBGN-AF Networks by Logic-Based Hypothesis Finding

       • Yoshitaka Yamamoto, Adrien Rougny, Hidetomo Nabeshima, Katsumi Inoue, Hisao Moriya, Christine Froidevaux et al.

       Pages 165-179

4. Erratum

   1. Erratum: Disentangling the Effects of Habitat and Protection on Coral Reef Fish Communities in Long-Established Marine Reserves

      • Dominique Pelletier, Delphine Mallet, Abigail Powell, William Roman

      Pages E1-E1

5. Back Matter

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This book constitutes the refereed proceedings of the First International Conference on Formal Methods in Macro-Biology, FMMB 2014, held in Nouméa, New Caledonia, in September 2014.
The 7 revised full and 3 short papers presented together with 7 invited presentations were carefully reviewed and selected from 17 submissions. The scientific program consists of papers on a wide variety of topics, including ecological systems, medical applications, logical frameworks, and discrete continuous and hybrid models for the analysis of biological systems at macroscopic levels.

• applied computing
• bioinformatics
• biological processes
• complex systems
• computational biology
• computational ecology
• formal methods
• health informatics
• life and medical sciences
• logic and verification
• macroevolution
• systems biology

• Inria,, Rocquencourt, France

  François Fages

• Department of Mathematics and Computer Science, University of Udine, Udine, Italy

  Carla Piazza

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