Biological problem addressed 'Modelling Analysis'

Related assays

The main input is the ENA review paper (Function and Regulation of the Saccharomyces cerevisiae ENA Sodium ATPase System, Ruiz&Ariño 2007) and the papers referenced.
Another source are the papers linked from the ENA page of SGD http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=ENA1

A boolean network was created using booleannet (after experimenting with Squad and CellNetAnalyzer). This network can be simulated and visualized using additional software components that will be part of the pyMantis CMS that is developed by the Translucent project.

A interaction network analysis tool (currently based on the BioGrid - PSICQUIC web services) was created that helps to discover interactions of Yeast proteins. The tool will at some point be freely available on the www as part of the pyMantis CMS created within the Translucent project.

No description specified

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Promotor Anaysis

Elucidation of protein networks involved in the regulation of cation homeostasis using protein interaction datasets.

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Bioinformatic studies

Development of bioinformatic tools to investigate the role of transcription factors and 14-3-3 proteins in the regulation of genes involved in cation homeostasis.

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Bioinformatic studies

Based on a kinetic model a description of the potassium current is achieved. Its properties with respect to changes in membrane potential and potassium concentrations are derived.

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Kinetic properties of Trk

Proton fluxes ensue a change in the membrane potential to which the potassium uptake responds. The membrane potential changes depend on the extrusion of protons, buffering capacities of the media and experimental parametes.

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Kinetic properties of Trk

Analytical methods and computational analyses (regression, fitting) will be employed to find properties of the Trk system under different external conditions.

Contributor: Falko Krause

Biological problem addressed: Modelling Analysis

Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...

Study: Kinetic properties of Trk

No description specified

Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.

Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.

Theoretical analysis of hypothetical sigma factor competition.
Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.

We use BSA115 strain which lacks RsbU and RsbW proteins. Therefore, there is limited post-transcriptional regulation of sigmaB activity.

There occurs an unexpected drop in the beta-Gal activity after sigB induction. This modelling effort aims to clarify the reasons.

The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.

No description specified

- Comparison of metabolic flux distribution in carbon core metabolism (EMP, PPP, TCA) of Bacillus subtilis under 3 different conditions: "salt-free" reference, "stress" chemostat, "osmoprotected" chemostat.
- Model created using OpenFLUX and Microsoft Excel
- Model computed using MatLAB

Using PCA, three components, beam size 8.
Clustering via MCL from Biolayout Express 3D

Data is taken from "Genome-Wide Gene Expression Analysis of the Switch between Acidogenesis and Solventogenesis in Continuous Cultures of Clostridium acetobutylicum." Grimmler et al. 2011
DOI: 10.1159/000320973

Pyruvate formate-lyase (PFL) is an important enzyme in the metabolic pathway of lactic acid bacteria (LAB) and is held responsible for the regulation of the shift between homolactic acid to mixed acid fermentation. PFL catalysis the reversible reaction of acetyl-CoA and formate into pyruvate and CoA. A glycyl radical, who is regenerated within the reaction, is involved; therefore, PFL works only under strictly anaerobic conditions. For its activation, the C-terminal domain has to bind to the
...

Contributor: Stefan Henrich

Biological problem addressed: Modelling Analysis

Investigation: The Attic

Study: Pyruvate formate-lyase (PFL)

Metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors

Metabolic network of Enterococcus faecalis including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors

Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)

Cytoscape based analysis and yED based representation of clostridial Reactomes

No description specified

Contributor: Sebastian Curth

Biological problem addressed: Modelling Analysis

Investigation: Modular Model Building

Study: Automated Model Building

The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.

Using TFinfer2 to analyse data from "Characterization of MG1655 and mutant strains under conditions of glucose excess and limitation"

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

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

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Study: Model Gluconeogenesis

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Modelling the degradation of BPG, GAP and DHAP at high temperature

The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place.
To answer these questions a computational modelling approach was developed. This
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Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact)
...

We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments

The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length

Kinetic characterisation en mathematical modelling of HK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of PGI.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of PFK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of ALD.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of TPI.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of G3PDH.

Kinetic characterisation en mathematical modelling of GAPDH.

Kinetic characterisation en mathematical modelling of PGK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of PGM.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of ENO.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation en mathematical modelling of PK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

Kinetic characterisation and mathematical modelling of LDH.

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model construction

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Glucose metabolism in Plasmodium falciparum tro...

Study: Model validation

RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).

OptKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

RobustKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

No description specified
No description specified

Genome scale metabolic model of Sulfolobus solfataricus
specific scenario: modelling of L-fucose degradation pathways

The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
...

No description specified

Contributor: Ron Henkel

Biological problem addressed: Cell cycle

Investigation: Hands-on: Model Management in SEEK

Study: Hands-On: Tyson1991 - Cell Cycle 6 var

No description specified
No description specified

Simulation of double mutants and perturbations and time series samples using for Sample 1 only OE mutants of which we update the enzyme concentrations. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model.
Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

Contributor: Niels Zondervan

Biological problem addressed: Modelling Analysis

Investigation: 1 hidden item

Study: Core model combinatorial predictions

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