# Biological problem addressed 'Modelling Analysis'

Modelling Analysis

Cell cycle (1) | Enzymology (5) | Gene expression (5) | Gene regulatory network (1) | Genome scale (0) | Metabolic network (11) | Metabolism (2) | Signal transduction (1) | Translation (0) | Metabolic Redesign (3) | Stress response/Adaptation (0) | Post translational modification (0)

## 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

**Contributor**: Falko Krause

**Biological problem addressed**: Gene expression

**Investigation:** ENA1 Transcription in Saccharomyces cerevisiae

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.

**Contributor**: Falko Krause

**Biological problem addressed**: Gene regulatory network

**Investigation:** ENA1 Transcription in Saccharomyces cerevisiae

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.

**Contributor**: Falko Krause

**Biological problem addressed**: Modelling Analysis

**Investigation:** ENA1 Transcription in Saccharomyces cerevisiae

**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

**Contributor**: Jay Moore

**Biological problem addressed**: Metabolic network

**Investigation:** Metabolism of Streptomyces coelicolor (SysMO ST...

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

**Contributor**: Sara Jabbari

**Biological problem addressed**: Metabolic network

**Investigation:** The effect of pH upon the metabolic shift in Cl...

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

**Contributor**: Sara Jabbari

**Biological problem addressed**: Gene expression

**Investigation:** The effect of pH upon the metabolic shift in Cl...

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.

**Contributor**: Ulf Liebal

**Biological problem addressed**: Gene expression

**Investigation:** The transition from growing to non-growing Baci...

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.

**Contributor**: Ulf Liebal

**Biological problem addressed**: Gene expression

**Investigation:** The transition from growing to non-growing Baci...

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.

**Contributor**: Maksim Zakhartsev

**Biological problem addressed**: Metabolic network

**Investigation:** Kinetic analysis of metabolic system using tran...

**Contributor**: Sebastian Henkel

**Biological problem addressed**: Modelling Analysis

**Investigation:** Steady state studies for different oxygen avail...

**Contributor**: Sebastian Henkel

**Biological problem addressed**: Modelling Analysis

**Investigation:** Steady state studies for different oxygen avail...

- 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

**Contributor**: Michael Kohlstedt

**Biological problem addressed**: Metabolic network

**Investigation:** Multiomics study of Bacillus subtilis under osm...

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

**Contributor**: Sebastian Curth

**Biological problem addressed**: Gene expression

**Investigation:** The effect of pH upon the metabolic shift in Cl...

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

**Contributor**: Jennifer Levering

**Biological problem addressed**: Metabolic network

**Investigation:** Investigation of glycolysis and pyruvate branch...

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

**Contributor**: Nadine Veith

**Biological problem addressed**: Metabolic network

**Investigation:** Investigation of glycolysis and pyruvate branch...

**Contributor**: Sebastian Curth

**Biological problem addressed**: Modelling Analysis

**Investigation:** General Method Development

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

**Contributor**: Sebastian Curth

**Biological problem addressed**: Modelling Analysis

**Investigation:** Modular Model Building

**Study:** Reactome Analysis

Cytoscape based analysis and yED based representation of clostridial Reactomes

**Contributor**: Sebastian Curth

**Biological problem addressed**: Modelling Analysis

**Investigation:** Modular Model Building

**Study:** Reactome Analysis

**Contributor**: Sebastian Curth

**Biological problem addressed**: Modelling Analysis

**Investigation:** Modular Model Building

**Study:** Automated Model Building

**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.

**Contributor**: Michael Ederer

**Biological problem addressed**: Metabolic network

**Investigation:** Steady state studies for different oxygen avail...

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

**Contributor**: Botond Cseke

**Biological problem addressed**: Modelling Analysis

**Investigation:** Analysis of the glucose transport in Escherichi...

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Modelling Analysis

**Investigation:** Yeast Glycolytic Oscillations

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Modelling Analysis

**Investigation:** Yeast Glycolytic Oscillations

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

**Contributor**: Jacky Snoep

**Biological problem addressed**: Metabolic network

**Investigation:** Central Carbon Metabolism of Sulfolobus solfata...

**Study:** Model Gluconeogenesis

Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates.

https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Metabolic network

**Investigation:** Central Carbon Metabolism of Sulfolobus solfata...

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

**Contributor**: Jacky Snoep

**Biological problem addressed**: Enzymology

**Investigation:** Central Carbon Metabolism of Sulfolobus solfata...

**Study:** Model Gluconeogenesis

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

**Contributor**: Jacky Snoep

**Biological problem addressed**: Metabolism

**Investigation:** Central Carbon Metabolism of Sulfolobus solfata...

**Study:** Model Gluconeogenesis

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

...

**Contributor**: Ulf Liebal

**Biological problem addressed**: Signal transduction

**Investigation:** The transition from growing to non-growing Baci...

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)

...

**Contributor**: Anna Feldman-Salit

**Biological problem addressed**: Metabolism

**Investigation:** Investigation of glycolysis and pyruvate branch...

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

**Contributor**: Jurgen Haanstra

**Biological problem addressed**: Enzymology

**Investigation:** Kinetic understanding of the T. brucei trypanot...

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

**Contributor**: Jurgen Haanstra

**Biological problem addressed**: Modelling Analysis

**Investigation:** Gene expression in Trypanosoma brucei

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.

**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 GAPDH.

**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 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

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model validation

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model construction

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model construction

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model construction

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model construction

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model construction

**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).

**Contributor**: Natalie Stanford

**Biological problem addressed**: Metabolic Redesign

**Investigation:** Designing a new way to predict engineering stra...

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.

**Contributor**: Natalie Stanford

**Biological problem addressed**: Metabolic Redesign

**Investigation:** Designing a new way to predict engineering stra...

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.

**Contributor**: Natalie Stanford

**Biological problem addressed**: Metabolic Redesign

**Investigation:** Designing a new way to predict engineering stra...

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model analysis

Inhibition of lactate flux due to glucose transport inhibitor

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model analysis

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Glucose metabolism in Plasmodium falciparum tro...

**Study:** Model analysis

Genome scale metabolic model of Sulfolobus solfataricus

specific scenario: modelling of L-fucose degradation pathways

**Contributor**: Jacqueline Wolf

**Biological problem addressed**: Metabolic network

**Investigation:** L-fucose degradation in Sulfolobus solfataricus P2

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

...

**Contributor**: Maksim Zakhartsev

**Biological problem addressed**: Metabolic network

**Investigation:** Metabolic analysis of effects of sucrose transl...

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Bachmann et al (2011) Molecular Systems Biology...

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Kolodkin et al (2010) Molecular Systems Biology...

**Contributor**: Ron Henkel

**Biological problem addressed**: Cell cycle

**Investigation:** Hands-on: Model Management in SEEK

**Contributor**: Matthias König

**Biological problem addressed**: Modelling Analysis

**Investigation:** MM-PLF: Multiscale modeling for personalized li...

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Modelling Analysis

**Investigation:** Adlung et al (2017) Molecular Systems Biology

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