Assays
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Kinetic characterisation en mathematical modelling of PFK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of ALD.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of TPI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of G3PDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of GAPDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGM.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of ENO.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation and mathematical modelling of LDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model validation
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
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).
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
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.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
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.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
Submitter: 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.
Submitter: 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.
Submitter: 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.
Submitter: 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.
Submitter: 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.
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Kinetic analysis of metabolic system using tran...
Submitter: Sebastian Henkel
Biological problem addressed: Model Analysis Type
Investigation: Steady state studies for different oxygen avail...
Submitter: Sebastian Henkel
Biological problem addressed: Model Analysis Type
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
Submitter: 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
Submitter: Sebastian Curth
Biological problem addressed: Gene Expression
Investigation: The effect of pH upon the metabolic shift in Cl...