Assays

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

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.

Metabolomics analysis of liver slices by LC-MS. Samples were analyzed at NTNU by Per Bruheim.

TODO: Information that should be here in SEEK, but currently isn't:
* SOP (standard operating procedure) detailing the sample preparation, machine settings, post-processing pipeline etc. Essentially the same as the Methods section in the paper that we'll eventually write. It should enable a knowledgeable colleague to repeat the analysis. SOPs in SEEK can be free-form files (e.g. Word or PDF) or a URL to
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Record of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater). Young fry arrived at Solbergstranda 2015-02-05 17:20.

Comparison of simulated wild-type and prr7prr9 double mutant under 12L:12D cycles. Simulation with CVODE simulator via SBSI v1.5 framework.

RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL

Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods

Intracellular and extracellular metabolome analysis

This Assay is created to practice on Brussels Workshop. It is not applicable for other purposes.

This Assay is created to practice on Brussels Workshop. It is not applicable for other purposes.

This Assay is created to practice on Brussels Workshop. It is not applicable for other purposes.

Tissue panel for gene expression data in species:
- Danio rerio (Zebrafish, ZF)
- Oryzias latipes (Medaka, Med)
- Oncorhynchus mykiss (Rainbow trout, RT)

Combined sample count tables are provided per species as raw (expected) counts from RSEM (.counts.txt), or as scaled, normalised FPKM (Fragments Per Kilobase per Million reads) counts (.FPKM.txt).

Tissue panel sample information meta file:
/mnt/SeqData3/GenoSysFat/processed_tissue_panel_data/tissue_panel_sample_meta.txt

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

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

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

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

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

Here we will use JERM templates with embedded ontologies to describe and annotate example data