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Team:KU Leuven/Project/Glucosemodel/MeS/Modelling-FBA
From 2013.igem.org
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<p align = "justify"> <b>COBRA</b> stands for <b>Constraint-Based Reconstruction and Analysis</b> (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells. Probably the most used analysis in COBRA is the <b>Flux Balance Analysis (FBA)</b> which will be discussed in more detail below. <br/> <br/> | <p align = "justify"> <b>COBRA</b> stands for <b>Constraint-Based Reconstruction and Analysis</b> (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells. Probably the most used analysis in COBRA is the <b>Flux Balance Analysis (FBA)</b> which will be discussed in more detail below. <br/> <br/> | ||
<b>COBRA has been successfully applied to study the possible phenotypes that arise from a genome </b>(Covert, Schilling <i>et al.</i> 2001). COBRA consists of two fundamental steps. First, a GENRE (=GEnome-scale Network REconstruction) is formed, and second, the appropriate constraints are applied to form the corresponding GEMS (GEnome-scale Model <i>in Silico</i>). Cellular functions can be limited by different types of constraints in a biological system: e.g. physico-chemical constraints, topo-biological, environmental and regulatory constraints. | <b>COBRA has been successfully applied to study the possible phenotypes that arise from a genome </b>(Covert, Schilling <i>et al.</i> 2001). COBRA consists of two fundamental steps. First, a GENRE (=GEnome-scale Network REconstruction) is formed, and second, the appropriate constraints are applied to form the corresponding GEMS (GEnome-scale Model <i>in Silico</i>). Cellular functions can be limited by different types of constraints in a biological system: e.g. physico-chemical constraints, topo-biological, environmental and regulatory constraints. | ||
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| + | <ol><li><b>Physico-chemical constraints</b> refer to reaction rates, enzyme turnover rates, diffusion rates etc. Moreover mass, energy and momentum must be conserved and biochemical reactions must result in a negative free-energy change to proceed in the forward direction.</li> | ||
| + | <li><b>Topo-biological constraints</b> refer to the crowding of molecules in the cell. An example is the organisation of DNA in <i>Escherichia coli</i> by spatio-temporal patterns (Huang, Zhang <i>et al.</i> 2003). Therefore there are two competing needs that constrain the physical arrangement of DNA in the cell.</li> | ||
| + | <li><b>Environmental constraints</b> are nutrient availability, pH, temperature, osmolarity and the availability of electron acceptors. They are time and condition dependent. Environmental constraints are of fundamental importance for the quantitative analysis of microorganisms. Defined media and environmental conditions are needed to integrate data into quantitative models that are both accurately descriptive and predictive.</li> | ||
| + | <li><b>Regulatory constraints</b> differ from the others because they are self-imposed and are subject to evolutionary change. For this reason, these constraints may be referred to as regulatory restraints, in contrast to 'hard' physico-chemical constraints and time-dependent environmental constraints. On the basis of environmental conditions, regulatory constraints allow the cell to eliminate suboptimal phenotypic states and to confine itself to behaviours of increased fitness. Regulatory constraints are implemented by the cell in various ways, including the amount of gene products made (transcriptional and translational regulation) and their activity (enzyme regulation).</li> | ||
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Revision as of 17:45, 4 October 2013
Secret garden
Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!
- A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
- For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
- We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?
Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!
Methylsalicylate Modelling - Flux Balance Analysis
INLEIDING DIE NOG GESCHREVEN MOET WORDEN
Matlab: Cobra Toolbox
COBRA stands for Constraint-Based Reconstruction and Analysis (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells. Probably the most used analysis in COBRA is the Flux Balance Analysis (FBA) which will be discussed in more detail below.
COBRA has been successfully applied to study the possible phenotypes that arise from a genome (Covert, Schilling et al. 2001). COBRA consists of two fundamental steps. First, a GENRE (=GEnome-scale Network REconstruction) is formed, and second, the appropriate constraints are applied to form the corresponding GEMS (GEnome-scale Model in Silico). Cellular functions can be limited by different types of constraints in a biological system: e.g. physico-chemical constraints, topo-biological, environmental and regulatory constraints.
- Physico-chemical constraints refer to reaction rates, enzyme turnover rates, diffusion rates etc. Moreover mass, energy and momentum must be conserved and biochemical reactions must result in a negative free-energy change to proceed in the forward direction.
- Topo-biological constraints refer to the crowding of molecules in the cell. An example is the organisation of DNA in Escherichia coli by spatio-temporal patterns (Huang, Zhang et al. 2003). Therefore there are two competing needs that constrain the physical arrangement of DNA in the cell.
- Environmental constraints are nutrient availability, pH, temperature, osmolarity and the availability of electron acceptors. They are time and condition dependent. Environmental constraints are of fundamental importance for the quantitative analysis of microorganisms. Defined media and environmental conditions are needed to integrate data into quantitative models that are both accurately descriptive and predictive.
- Regulatory constraints differ from the others because they are self-imposed and are subject to evolutionary change. For this reason, these constraints may be referred to as regulatory restraints, in contrast to 'hard' physico-chemical constraints and time-dependent environmental constraints. On the basis of environmental conditions, regulatory constraints allow the cell to eliminate suboptimal phenotypic states and to confine itself to behaviours of increased fitness. Regulatory constraints are implemented by the cell in various ways, including the amount of gene products made (transcriptional and translational regulation) and their activity (enzyme regulation).
