= SysMO - SUMO - Systems Understanding of Microbial Oxygen Responses =
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[http://www.sysmo.net/ SysMO Web Page]
=== About this wiki ===
The SUMO wiki is the central communication platform for the exchange of information about experimental data, models, ideas and general issues. This subpage is the starting point for publicly available information about the project.
=== About SUMO ===
==== General Information ====
The bacterium ''Escherichia coli'' is a common inhabitant of the human gut but is also of special interest as a laboratory experimental tool; many decades of study have produced an impressive description of processes essential for life.

However we must now consider how the individual components that make up a biological system work together to produce coherent patterns of behaviour. We have chosen to investigate the responses of ''E. coli'' to oxygen availability, because:

   1. The system is composed of relatively simple modules that participate in complex interactions;
   2. There is a detailed parts list of the main regulatory systems (genome sequence, participating proteins, molecular mechanisms);
   3. There are existing published data sets and data from precursor projects that permit the integration of specific and sound mathematical modelling approaches from the very beginning of the project; and
   4. Powerful techniques for highly controlled and reproducible experiments are available (transcriptomics, facile genetics, chemostat culture);
   5. The system is biologically, medically and industrially significant.

This systems approach will reveal new insight into the adaptations that occur in response to changes in oxygen availability and offer opportunities for efficient re-engineering for industrial purposes and target-identification for medical applications. We will collectively obtain and analyse, using commonly agreed protocols, highly reproducible transcriptomic, proteomic, metabolomic and biochemical data sets that describe the dynamics of the response to oxygen. Data sets will be integrated to elaborate predictive mathematical and computer science models in an iterative process of model-based hypothesis generation and experimental design.

Specifically, we will investigate how this bacterium senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an ''E. coli'' population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling approaches using published data sets and data emerging from our own work. We will construct increasingly elaborate models of the system at different levels of detail, which will be used to generate new hypotheses and influence further experimental design.
==== Workpackages ====
|| WP1.1 Molecular Interations & Regulatory Modules (Poole & Green) || WP1.2 Carbon & Electron Fluxes (Teixeira de Mattos) || WP13 WP1.3 Isogenic Mutants (Bettenbrock) || WP14 WP1.4 Single Cells (Bettenbrock & Gilles)||
|| WP21 WP2.1.1 Agent-based Modelling (Holcombe & Maleki-Dizaji) || WP2.1.2 From ''Escherichia coli'' Workflow using Taverna and Web Services (Holcombe & Maleki-Dizaji & Rolfe) ||WP2.2 Reduced-order modelling (Gilles) ||  WP2.3 Detailed Kinetic Modelling (Sauter & Sawodny) ||
==== Personal Pages ====
|| [http://www.shef.ac.uk/mbb Sheffield MBB]          || Robert Poole || Jeff Green || Alison Graham || Matthew Rolfe || ||
|| [http://www.shef.ac.uk/dcs Sheffield DCS]          || Mike Holcombe || Afsaneh Maleki-Dizaji || || || ||
|| [http://www.science.uva.nl/sils Amsterdam SILS]    || Joost Teixeira de Mattos || Alex Ter Beek || || || ||
|| [http://www.isys.uni-stuttgart.de/ Stuttgart ISYS] || Oliver Sawodny || Sebastian Henkel || Thomas Sauter (now [http://wwwen.uni.lu/forschung/fstc/life_sciences_research_unit Université du Luxembourg]) || || ||
|| [http://www.mpi-magdeburg.mpg.de/ Magdeburg MPI]   || Ernst Dieter Gilles || Katja Bettenbrock || Michael Ederer || Sonja Steinsiek || Stefan Stagge||

==== Publications ====
see ***Publications***

=== News ===

=== Upcoming Events ===
|| 2009 May 19th/20th       || SysMO status seminar (including evaluation) in Vienna ||
|| 2009 Autumn || SUMO meeting ||

=== Contact ===
For further information please contact Michael Ederer (concerning this wiki) or Robert Poole (concerning the SUMO project)