SysMO

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
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Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves

Comparative Systems Biology: Lactic Acid Bacteria

Global metabolic switching in Streptomyces coelicolor

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

Describet here is the ivnestigation

Investigating moths

An investigation in the CCM of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.

Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.

This investigation shows public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Organism: Saccharomyces Cerevisiae

It also is described, but as a study

Studying moths

Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.

It also has a description

Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index.

(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay for transcriptional profiling time course in yeast treated with rapamycin

This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)

Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.

Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.

An exponential decay model was fitted to the experimental data set of GAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for GAP degradation at 70C was estimated to be 0.056 1/min, equivalent to a half life time of 12.4 min.

An exponential decay model was fitted to the experimental data set of DHAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for DHAP degradation at 70C was estimated to be 0.0225 1/min, equivalent to a half life time of 30.8 min.

Mathematical model for FBPAase kinetics

Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.

Cloning and heterologous expression of gluconeogenic enzymes in E. coli

Preparation of cell free extracts of the recombinant E. coli strains expressing the respective S. solfataricus enzymes.

The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.

A stationary-phase culture (10ml) was used to inoculate the fermenter vessel.

Taken from ArrayExpress:
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-115

The procedure describes the preparation of fluorescent DNA probes from human mRNA or total
RNA.

An example of add a presentation hosted from SlideShare.

Hand on for Computer Practical04 Data management in praxis : Day 1 _ ISA in SEEK

This is a working copy, still many changes to come.

Systems Biology is one of the most prominent newly emerging interdisciplinary science areas. By connecting fields such as genomics, proteomics, cell biology, medicine, molecular biology, biochemistry and genetics, with mathematics, bioinformatics, engineering and computation, it enables discovery of yet unknown principles underlying the functioning of living cells. At the same time testable and predictive models of complex cellular pathways and eventually of whole cells are generated, which are
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