Data files

qATP values were calculated based on fermentation product formation and expected used biochemical pathways. These were averaged and used for calculation of the ATP required for maintenance and for growth. These data were subsequently used to calculate the qATP at the maximal growth rate by extrapolation

Table describing the catabolite repression of β-xylosidase by different carbon sources(glucose, sorbitol, fructose, maltose, glycerol. mannitol) in various mutants of CcpA cofactors (HprK, crh)

Cell volume_trk_

Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

S. pyogenes was grown in C-limited cultures at pH 6.5 and 7.5 and at a growth rate of 0.05 The glnA mutant strain shows decreased growth in low glutamine and excess glutamate conditions and no growth at all in low glutamine and low glutamate conditions. Preliminary results of glucose-limited chemostat cultures indicate a reversion of the pH dependency of the shift from homolactic to more mixed acid fermentation: wild type - lactate/formate ratio at pH 6.5 = 11.8, at pH 7.5 = 2.8 glnA mutant - ...

E. faecalis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

L. lactis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05, 0.15 and 0.40

S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase

acetic acid puls during acidogenesis shift to solventogensis back-shift to acidogenesis butyric acid puls during acidogenesis

butyric acid pulse during acidogenesis acetic acid pulse during acidogenesis butyric acid pulse during solventogenesis

This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

GEO format data

Photos of drop test conpresed in .zip file

nha1, ena1-5, double deletion

The output includes the similarity matrix of LDH enzymes based on comparison of the electrostatic potentials at allosteric and catalytic binding sites, separately. The similarity indices were generated by the PIPSA program (http://projects.villa-bosch.de/mcmsoft/pipsa/3.0/).

L. lactis was grown in rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

Concentrations of 22 extracellular metabolites (major medium components) from T. b. brucei 427

Arginine kinase has been thought of as a potential stress marker (see 'Metabolic changes by oxidative stress in T. b. brucei 427'), the gene knockout cells have been constructed.

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.

Data for three biological replicates of control culture and 37°C and 57°C in the file.

B. subtilis was grown in M9 media with glucose as carbon source and the samples for RNA were harvested at OD600nm- 0.4 , 1.3 and 1.0 ). Culture was done at 37°C and samples at OD600nm- 0.4(Exponential), OD600nm- 1.3 (Early stationary), OD600nm-1.0(Late Stationary). All the samples were analysed for transcriptome as biological triplicates.

• automated integration of transcriptomic and reactome data to differential equations
• structure of the paths is maintained
• continuous fermentation model in standard format for data integration, two component model (cell and fermenter)

call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example

where model_map is the desired mapping of species, reaction_compounds_final.csv is the entire network, extracellular.txt is a manual ...

TRK1, TRK2