Computational modeling of cyanobacterial cells in natural and controlled environments

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Overview

The primary goal of the project “Local team and international consortium for computational modeling of a cyanobacterial cell” is to build a computational model of cyanobacteria at the molecular, cellular, and environmental level.  The approach depends on an international team of scientists working at the interface between the biological and computational sciences to create bottom-up models of cellular processes and top-down models of cell dynamics in environmentally controlled state-of-the-art photobioreactors.

The aim is to build validated models that accurately simulate the behavior of cyanobacteria under a broad range of biological and environmental parameters that will drive experimental research and accelerate discovery.  Another goal of the project is to advance education in biology, complex systems, modeling, and the computer sciences by developing university-level courses and by training of students and early career scientists.  A key element in achieving these goals is to outreach to all scientists interested in cyanobacteria research. 

The ultimate goal is to provide computer models that can be used by the entire research community to model and simulate the behavior of cyanobacteria under environmentally diverse conditions. 

The primary goal of the project “Local team and international consortium for computational modeling of a cyanobacterial cell” is to build a computational model of cyanobacteria at the molecular, cellular, and environmental level ...more

Impact

Cyanobacteria are photoautotrophic organisms that play an important role in the stability and continuity of life on Earth.  This is demonstrated by the fact that marine cyanobacteria contribute by tens of percents to the molecular oxygen released into the atmosphere by photosynthesis.  Cyanobacteria are being developed and employed to produce ce biofuels, in water treatment facilities, and in the production of commercially valuable compounds.  Understanding the molecular processes and growth behavior of cyanobacteria in nature and growth facilities provides knowledge that will advance biotechnology applications, contribute to a deeper understanding of the factors underlying ocean dynamics and global climate change.

Cyanobacteria are photoautotrophic organisms that play an important role in the stability and continuity of life on Earth ...more

Approach

A core group of researchers, the local workgroups, are responsible for building the primary models, model validation, and providing experimental parameters.  Although the research is centered in the Czech Republic, the success of the project depends on the participation of a broad international range of scientists and modelers.  To this end, the research project and the models are open to international research community.  Collaborators are invited to participate by joining CyanoNetwork

Future events

ISBE/C4Sys RoadShow - CyanoTeam follow up project, June 8th, Prague

An introduction of the European and Czech systems biology infrastructures C4Sys and ISBE

Flyer download

 

 

Past events

November 27, 2015. Colloquium talk by Dr. Vashti Galpin, Ph.D: "Boolean Network Identification from Multiplex Time Series Data"

February 12-13, 2015. Invited block lecture by Dr. Andrzej Mizera, Ph.D.: "Probabilistic Boolean networks as models of real-size biological regulatory networks: challenges & future perspectives"

January 28-30, 2015. CyanoNetwork workshop "Cyanobacterium in silico" in Brno.

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January 21-22, 2015. Invited block lecture by Dr. Nicola Paoletti, Ph.D: "Synthesising robust and optimal parameters for cardiac pacemakers using symbolic and evolutionary computation techniques"

July 26-29, 2014. Systems Biology Summer School 2014 "Photosynthesis in Cyanobacteria" in Nové Hrady

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July 7, 2014. Open CzechGlobe Disputation with Dr. Alexandra Jammer: "A System Biology Analyses of the Methabolic Regulation of Development and Carbohydrate Accumulation in Photosynthetic Organisms"

May 16, 2014. Colloquium talk by Michaela Sikulova: "Evolutionary Optimization Techniques"

April 4, 2014. Colloquium talk by Tomas Stanek: "A case study of a bioreactor control system"

July 27-30, 2013. Systems Biology Summer School 2013 in Nové Hrady

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March 5, 2013. Colloquium talk by Dr. Vashti Galpin, Ph.D: "Formal modelling of biological systems"

November 14, 2012. Colloquium talk by Dr. Christoph Flamm: "Exploring Chemical Transformation Space"

October 31, 2012. Colloquium talk by Dr. Ralf Steuer: "Computational Models of Cyanobacterial Metabolism: Systemic properties of phototrophic growth"

October 17, 2012. Colloquium talk by Prof. Jan Van Schuppen: "Photosynthesis of a cyanobacterium - Modeling and system identification"

May 8-11, 2012. Cyanonetwork workshop "Cyanobacterium in silico" in Mikulov

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Quick links

Our twin web site with working models
http://www.e-cyanobacteria.org

CyanoBase
http://genome.kazusa.or.jp/cyanobase/

CyanoSite
http:// www-cyanosite.bio.purdue.edu/index.html

ASU site on Synechocystis sp. 6803
http://synechocystis.asu.edu/

 

Funding support:
Partners:
This website is an output of EC OP project financed from EU with the support of MEYS CR: Local Team and International Consortium for Computational Modelling of a Cyanobacterial Cell, Reg. No. CZ.1.07/2.3.00/20.0256 and CzechGlobe – Centre for Global Climate Change Impacts Studies (project Reg. No. CZ.1.05/ 1.1.00/02.0073).
Copyright CyanoTeam.org, 2012