# Biological problem addressed 'Model Analysis Type'

Model Analysis Type

Cell Cycle (1) | Enzymology (5) | Gene Expression (5) | Gene Regulatory Network (1) | Genome Scale (1) | Metabolic Network (11) | Metabolic Redesign (0) | Metabolism (2) | Post Translational Modification (0) | Signal Induction (1) | Stress Response (0) | Translation (0) | Stress response/Adaptation (0) | Analysis of HMM hits (0) | Multiple sequence alignment (0)

## Related assays

**97**Assays visible to you, out of a total of

**167**

The main input is the ENA review paper (Function and Regulation of the Saccharomyces cerevisiae ENA Sodium ATPase System, Ruiz&AriĆ±o 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.

**Contributor**: Falko Krause

**Biological problem addressed**: Gene Regulatory Network

**Snapshots: **No snapshots

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.

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

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.

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.

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.

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

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.

**Contributor**: Maksim Zakhartsev

**Biological problem addressed**: Metabolic Network

**Snapshots: **No snapshots

**Contributor**: Sebastian Henkel

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Sebastian Henkel

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

- 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

**Snapshots: **No snapshots

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**: Model Analysis Type

**Snapshots: **No snapshots

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

**Snapshots: **No snapshots

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**: Sebastian Curth

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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

**Contributor**: Sebastian Curth

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Cytoscape based analysis and yED based representation of clostridial Reactomes

**Contributor**: Sebastian Curth

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Sebastian Curth

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Sebastian Curth

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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"

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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

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

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

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

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

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

...

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

**Contributor**: Jurgen Haanstra

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of HK.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1

Kinetic characterisation en mathematical modelling of PGI.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of PFK.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of ALD.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of TPI.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of G3PDH.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of GAPDH.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of PGK.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of PGM.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of ENO.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation en mathematical modelling of PK.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Kinetic characterisation and mathematical modelling of LDH.

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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**: Model Analysis Type

**Snapshots: **No snapshots

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**: Model Analysis Type

**Snapshots: **No snapshots

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**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Inhibition of lactate flux due to glucose transport inhibitor

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Genome scale metabolic model of Sulfolobus solfataricus

specific scenario: modelling of L-fucose degradation pathways

**Contributor**: Jacqueline Wolf

**Biological problem addressed**: Metabolic Network

**Snapshots: **No snapshots

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

**Snapshots: **No snapshots

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

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Growth on D-glucose served as reference scenario

**Contributor**: Matthias KĆ¶nig

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

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**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions

BPG stability analysis

PGK 70C model

PGK - GAPDH models

We have developed a method for comparative analysis of pairs of complex networks based on gene co-expression analysis. We apply this modeling analysis to data set for gene expressions in multiple tissues of mus musculus and homo sapiens.

**Contributor**: Eivind Almaas

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.

**Contributor**: Daniel Seaton

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.

**Contributor**: Daniel Seaton

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

General sandbox

**Contributor**: Andrej Blejec

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Contributor**: Dawie Van Niekerk

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

In future we should split these versions into separate Assays, and link to the four, original component models, when they are imported with the PlaSMo resource into FairdomHub (expected late 2018)

**Contributor**: Andrew Millar

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots