Task 6: Biological applications: cooper bacteria, urchin translation and TGF-beta signaling network.
This task aims at applying the methods to three real applications.
Control of biomining bacteria in bioleaching process of cooper minerals. (Coordinator: D. Eveillard / A. Maass)
This question is actually handled with integrative biology approaches, new developments are needed to integrate dynamical consideration in these approaches. Thus it appears to be a very good concrete example of applications of our goal to integration time consideration in meta-analysis, in order to switch from static model to chronological models.
- Studied within Task 2 (static models).
- Meetings: 11/2011(Chili), 07/07/12 (Nantes), 14/09/2012(Rennes)
- Andres Aravena, Carito Guziolowski, Anne Siegel and Alejandro Maass. Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network . Preliminary results. JOBIM Conference. 2012.
Crossover in TGFbeta signaling network (Coordinator: M. Le Borgne / N. Théret)
Some partners of the program have had a strong collaboration to propose an integrative view of events related to the regulation of the protein TGF-beta. Presently TGF-beta signaling is modeled as an interaction graph. The challenge is to transform this graph into a discrete event model including temporal constraints on events.
- Studied within Task 3 (hybrid models) and 5 (reduction methods).
- 29/06/2011 (Nantes), 6/02/2012 (Roscoff), 10/02/2012 (Rennes), 25/05/2012 (Nantes), Paris (9/11/2012)
Initiation of translation in sea urchin (Coordinator: A. Richard / R. Bellé)
For this biological question, a chronological model is available, together with very precise temporal observations. Therefore this example is a typical application for the switch from a chronological model to a chronometric model.
- Studied within Task 4 (population scale models).
- Meetings: Roscoff (9&10/05/2011), Rennes (10/10/2011), Roscoff (6,7/02/2012), Paris (9/11/2012)