Dummy programme

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:

• maximises the ‘shelf life’ and utility of data generated by SysMO;
• provides an integrated platform for the dissemination ...

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Should be at least public

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The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.

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This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.

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

An investigation into the control mechanisms of glycolytic flux in Lactococcus lactis.

This investigation represents the data and models published by Hoefnagel et al in JWS Online and in M.H.N. Hoefnagel, J. Hugenholtz and J.L. SnoepMol. Biol. Reports 29, 157-161 (2002)

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. This investigation aims to gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae.

This investigation represents the data and models submitted to JWS online by Cronwright et al (http://jjj.biochem.sun.ac.za/cgi-bin/getMoreInfo.py?modeldir=cronwright) and ...

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Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

Pharmacokinetics data set for caffeine

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This study includes the experimental data for model validation and the model predictions of that data set.

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Dear SEEK users, this Assay is just an example Excell sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

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Assay to measure gene expression 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 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)

Glycolysis in Saccharomyces cerevisiae

Assay for transcriptional profiling time course in yeast

Detailed glycolytic model in Lactococcus lactis

A kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally.

An assay to measure exttracellular glycerol using HPLC

Intracellular metabolite concentrations were determined enzymatically by measuring the oxidation or reduction of NADH or NAD+, respectively, at 340 nm in a Beckman Coulter DU640 spectrophotometer

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This is the description

This is the description

This is the description

banana carrot - testing markdown indexing

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

Digitized pharmacokinetics data.

BACKGROUND: The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. RESULTS: Taverna workflows have been developed ...

Glycolytic model for Plasmodium falciparum; closed system

Potato model taken from JWS Online: http://jjj.mib.ac.uk/

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Model for testing

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that ...

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SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.

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An aerobic chemostat culture (above 70% of oxygen saturation) was set up at the specified dilution rate (fraction culture volume per hour; equal to growth rate in steady-state) with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using the specified synthetic defined nutrient-limited medium according to the description of Baganz et al., (1997)

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Biomass samples (20ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7mm-diameter tungsten carbide ball.

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