LIFEWARE - 2016 - Annual activity report

LIFEWARE

LIFEWARE - 2016

Project-Team Lifeware

Members

Overall Objectives

Research Program

Application Domains

Highlights of the Year

New Software and Platforms

New Results

Analog computation in the cell: specifications, compilation into biochemical reactions and computational complexity
Influence systems vs reaction systems
What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast
The cost of cellular adaptation to stress: tradeoff between short-term and long-term adaptation to osmotic stress in yeast
Balancing a genetic inverted pendulum
A look-ahead simulation algorithm for DBN models of biochemical pathways
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation
Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: prediction of RevErb–α up-regulation during mitosis
Stochastic continuous optimization backend for the constraint modelling language MiniZinc with applications to geometrical placement problems
Mixture model CMA-ES
Metro energy optimization through rescheduling

Partnerships and Cooperations

Dissemination

Bibliography

Publications of the year

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Section: New Software and Platforms

BIOCHAM

The Biochemical Abstract Machine

Keywords: Systems Biology - Bioinformatics

Functional Description

The Biochemical Abstract Machine (BIOCHAM) is a software environment for modeling and analyzing biochemical reaction systems, performing static analyses, making simulations, specifying behaviors in temporal logic and searching parameter values in high dimension.

This year BIOCHAM has been completely rewritten with a modular architecture. The new version v4.0 will be released soon with new features for synthesizing biochemical reaction systems from input/output function specifications.

Participants: François Fages, Guillaume Le Guludec, Thierry Martinez Sylvain Soliman
Contact: François Fages
URL: http://lifeware.inria.fr/biocham/

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