Data files

acetic acid addition 70mM

Basic Graph statistics

RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners

_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes

betw: betweeness of nodes clos: closeness of nodes neigh: neighbours node_degree: number of edges per node path: shortest paths ...

RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners

_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes _upload: entire network before removal of duplicated edges

X_depthY: subgraphs where X is a chosen central component and Y is the Yth of neighbour to ...

Out

Columnwise datamatrix of reactions, gene identifiers, substrates and products. The direction of reactions is not given.

WT (Cy3) vs. trxB (Cy5)_exp. growth phase

WT (Cy5) vs. trxB (Cy3)_stationary growth phase_DyeFlip

WT (Cy3) vs. trxB (Cy5)_stationary growth phase

WT (Cy5) vs. trxB (Cy3)_exp. growth phase_DyeFlip

This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)

An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).

This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory. A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf

This .csv file contains the filtered datset of the aerobic to anaerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This .csv file contains the filtered datset of the anaerobic to aerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.

This .csv file contains the entire transcriptional dataset of the aerobic to anaerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

How to get to the hotel from rail station

The figure contains information necessary to understand the mathematical model of experiments in BSA115. In these experiments sigB response is artificially initiated by the addition of IPTG while sigB is downstream of a Pspac promoter. The figure shows a flow-chart diagram that combines three hypotheses to explain experiments. It contains the ODEs and the fit of the respective models to the data.