Measurements of external metabolites based on growth curve data.
Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate

Contributor: Niels Zondervan

Assay type: Experimental Assay

Technology type: Technology type

Investigation: 1 hidden item

Study: Metabolomics measurements

Organisms:

SOPs: No SOPs

Data files: Master file, metabolite concentration, protein ... and 1 hidden item

Created: 1st May 2017 at 15:06

Combinatorial mutant, perturbation and time series predictions

MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

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

Organisms:

Models: 1 hidden item

SOPs: No SOPs

Data files: 1 hidden item

Created: 1st May 2017 at 12:21

Mathematical models of the Epo-induced AKT, ERK and S6 activation.

Molecular Systems Biology

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Modelling Analysis

Investigation: Adlung et al (2017) Molecular Systems Biology

Study: Figure 2: Model calibration with time-resolved ...

Organisms:

Models: BaF3 model, mCFU-E model

SOPs: No SOPs

Data files: No Data files

Created: 12th Jan 2017 at 09:19, Last updated: 12th Jan 2017 at 09:20

Source data for Figure 2: Experimental time-resolved quantitative immunoblot data

Molecular Systems Biology

No description specified

Contributor: Dawie Van Niekerk

Assay type: Experimental Assay

Technology type: Technology type

Investigation: Adlung et al (2017) Molecular Systems Biology

Study: Figure 2: Model calibration with time-resolved ...

Organisms:

SOPs: No SOPs

Data files: Source data for Figure 2B, Source data for Figure 2C, Source data for Figure 2D, Source data for Figure 2E, Source data for Figure 2F BaF3, Source data for Figure 2F mCFU-E, Source data for Figure 2G BaF3, Source data for Figure 2G mCFU-E

Created: 11th Jan 2017 at 11:38, Last updated: 11th Jan 2017 at 16:02

Cell free extract activity measurements: L-fuc/d-glc

SulfoSys - Biotec

(Show All)

No description specified

Contributor: Jacqueline Wolf

Assay type: Experimental Assay

Technology type: Enzymatic activity measurements

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Study: Comparison of S. solfataricus grown on l-fucose...

Organisms: Sulfolobus solfataricus (batch)

SOPs: No SOPs

Data files: Activity assay L-fuc vs D-glc

Created: 3rd Dec 2015 at 08:24, Last updated: 20th Oct 2016 at 08:23

Metabolic model of Sulfolobus solfataricus

SulfoSys - Biotec

(Show All)

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

Study: Comparison of S. solfataricus grown on l-fucose...

Organisms: Sulfolobus solfataricus

Models: Metabolic model of Sulfolobus solfataricus

SOPs: No SOPs

Data files: No Data files

Created: 3rd Dec 2015 at 08:41, Last updated: 20th Oct 2016 at 08:23

intracellular metabolome analysis: l-fucose vs d-glucose

SulfoSys - Biotec

(Show All)

No description specified

Contributor: Theresa Kouril

Assay type: Metabolite profiling

Technology type: Gas chromatography mass spectrometry

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Study: Comparison of S. solfataricus grown on l-fucose...

Organisms: Sulfolobus solfataricus (batch)

SOPs: No SOPs

Data files: Metabolomics L-fuc vs D-glc

Created: 5th Feb 2015 at 12:51, Last updated: 20th Oct 2016 at 08:23

Proteome analysis: d-fuc / l-glu

SulfoSys - Biotec

(Show All)

No description specified

Contributor: Theresa Kouril

Assay type: Proteomics

Technology type: Tandem mass spectrometry

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Study: Comparison of S. solfataricus grown on l-fucose...

Organisms: Sulfolobus solfataricus (batch)

SOPs: SULFOSYSbiotech_Proteome analysis

Data files: Proteomics L-fuc vs D-glc

Created: 5th Feb 2015 at 13:42, Last updated: 20th Oct 2016 at 08:23

RNA sequencing:l-fuc/d-glu

SulfoSys - Biotec

No description specified

Contributor: Theresa Kouril

Assay type: Rna-seq profiling

Technology type: Next generation sequencing

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Study: Comparison of S. solfataricus grown on l-fucose...

Organisms: Sulfolobus solfataricus (batch)

SOPs: SulfoSYS_BIOTECH: RNA isolation and sequencing

Data files: Transcriptomics L-fuc vs D-glc

Created: 17th Dec 2014 at 14:08, Last updated: 20th Oct 2016 at 08:23

Model for JAK2/STAT5 signaling

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

Study: Figure 3A: Model calibration with experimental ...

Organisms:

Models: JAK2/STAT5 model

SOPs: No SOPs

Data files: No Data files

Created: 3rd Mar 2016 at 11:04, Last updated: 17th Oct 2016 at 16:08

Model nuclear receptor (NR) signaling

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...

Study: Figure 2B: Transcriptional response to a sudde...

Organisms:

Models: NR model 1, NR model 2, NR model 3, NR model 4, NR model 5, NR model 6

SOPs: No SOPs

Data files: No Data files

Created: 17th May 2016 at 14:18, Last updated: 13th Sep 2016 at 21:11

Model Validation Gluconeogenesis in S. solfataricus

SulfoSys

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...

Study: Carbon Loss at High Temperature

Organisms: Sulfolobus solfataricus

Models: Model of reconstituted gluconeogenesis system i...

SOPs: No SOPs

Data files: Experimental Data for Reconstituted Gluconeogen..., Simulation for Reconstituted Gluconeogenic System

Created: 1st Aug 2013 at 14:59, Last updated: 13th Sep 2016 at 18:27

GLC incubation

Whole body modelling of glucose metabolism in malaria patients

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

Organisms:

Models: Kinetic model for incubation (penkler2)

SOPs: Validation experiments

Data files: 5mM GLC runout data.

Created: 11th Aug 2014 at 09:52, Last updated: 13th Sep 2016 at 18:18

BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

Kinetics on the move - Workshop 2016

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

Organisms:

Models: BIOMD0000000005 from BioModels Database

SOPs: No SOPs

Data files: SEDML for BIOMD0000000005

Created: 26th May 2016 at 13:04, Last updated: 23rd Aug 2016 at 03:05

Galactose Modelling

Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)

No description specified

Contributor: Matthias König

Biological problem addressed: Modelling Analysis

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

Study: A Multiscale Computational Model of Human Galac...

Organisms:

Models: Hepatic galactose model

SOPs: No SOPs

Data files: No Data files

Created: 16th Aug 2016 at 16:19

Whole genome sequencing (Illumina)

Noisy-Strep

No description specified

Contributor: Jan-Willem Veening

Assay type: Experimental Assay

Technology type: Next generation sequencing

Investigation: Chromosome segregation and cell division in Str...

Study: Genome wide marker frequency analysis on new st...

Organisms:

SOPs: No SOPs

Data files: DCI15, MK453, MK454, Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai..., Whole genome marker frequency analysis on strai...

Created: 19th Jul 2016 at 10:33

Characterization of flux distribution of S. pyogenes M9 wild type and the arcA- and glnA-knockout mutant in continuous cultures

SysMO-LAB

S. pyogenes wildetype, an arcA- and a glnA-deletion mutants were grown in CDM-LAB cultures at pH 6.5 and 7.5 and at a growth rate of 0.05

Contributor: Antje Sieg

Assay type: Experimental Assay

Technology type: Hplc

Investigation: Amino acid metabolism of four LAB species: Stre...

Study: Arginine and Glutamine metabolism in S. pyogenes

Organisms: Streptococcus pyogenes : M49 (591) (wild-type / wild-type) (chemostat)

SOPs: Analysis of organic acid by HPLC, SOP 2.1 Method for synthesis of LAB-medium used...

Data files: Characterization of chemostats from S. pyogenes...

Created: 3rd Apr 2012 at 11:20, Last updated: 12th May 2016 at 17:55

Construction of in vivo-like buffer for S. pyogenes

SysMO-LAB

In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.

Contributor: Araz Zeyniyev

Assay type: Metabolite profiling

Technology type: Inductively coupled plasma mass spectrometry

Investigation: Amino acid metabolism of four LAB species: Stre...

Study: Determination of essential amino acids for Stre...

Organisms: Streptococcus pyogenes : M49 (591) (wild-type / wild-type) (chemostat)

SOPs: No SOPs

Data files: No Data files

Created: 5th Apr 2012 at 16:59, Last updated: 12th May 2016 at 17:55

Determination of essential amino acids for Streptococcus pyogenes

SysMO-LAB