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Flux balance analysis accounting for metabolite dilution

Tomer Benyamini1*, Ori Folger1, Eytan Ruppin1,2 and Tomer Shlomi3*

1 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

2 The Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

3 Computer Science Department, Technion - Israel Institute of Technology, Haifa 32000, Israel

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Genome Biology 2010, 11:R43 doi:10.1186/gb-2010-11-4-r43

Published: 16 April 2010

Additional files

Additional file 1:

ASAP growth conditions. Excel file including the growth conditions used to model the ASAP experiments used by both FBA and MD-FBA.

Format: XLSX Size: 15KB Download file

Open Data

Additional file 2:

ASAP experimental optical density values. Excel file including the experimentally measured OD values taken from the ASAP database.

Format: XLSX Size: 64KB Download file

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Additional file 3:

Reaction activity difference across subsystems. Figure showing the mean reaction activity difference between FBA and MD-FBA across the different metabolic subsystems available in the model.

Format: XLSX Size: 59KB Download file

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Additional file 4:

Gene essentiality analysis results. Excel file containing the gene essentiality predictions by FBA and MD-FBA as well as the experimental gene essentiality data.

Format: XLSX Size: 198KB Download file

Open Data

Additional file 5:

Cofactor dilution-related demand activity predictions. Excel file containing MD-FBA's predictions for the dilution related growth-demand synthesis of the three cofactors: 10-formyltetrahydrofolate (10fthf), 2-octaprenyl-6-hydroxyphenol (2ohph) and FAD across different gene knockouts.

Format: XLSX Size: 52KB Download file

Open Data