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Supplementary Material

This supplementary material is related to the nutritionAnalyzer interface. It can be accessed on line at http://nutritionanalyzer.genouest.org/SupplementaryMaterial with login:SuppMat and password:tamppuss

../data/synthesefile.png The aim of this tutorial is to explain material and method used to produce all results in the submitted article: ”Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs”. It consists of three parts. In Part I we present the procedure to compute the allocation of Inputs over Output (AIO) for an extremal flux distribution, distribution which maximizing a linear objective function in a simplex (It corresponds to a vertex of the simplex). In Part II we present the procedure for determining all vertices of the simplex so as to determine their AIO and the last part presents the procedure for determining the interval ranges of AIO through the whole simplex. All these three part are illustrated with an example based on a theoretical mammary epithelial cell of a monogastric mammal. The cell taken up AA for protein (peptide) synthesis (9 mmol/h), an excess of leucine (Leucine input = 1 mmol/h) and glucose (input: 80 mmol/h). This cell produced out of the system protein (peptide output = 10 mmol/h), lactose (Lactose ouput= 10 mmol/h), triglycerides (lipid output: 3 mmol/h) composed of 3 C(16:0)-acyl CoA ( C(16:0) output = 9 mmmol/h). In addition, there was a requirement to synthesize serine (Serine output: 1 mmol/h), to do peptide synthesis (since peptide output = 10 mmol/h) and Leucine input was in excess ( and should be catabolized).

Part I: AIO for an extremal flux distribution

A web application dedicated to the computation of allocation for an extremal flux distribution is available at: http://nutritionanalyzer.genouest.org

Here are the main functionnalities of this web application.

Page 1 : Load a metabolic model

In this page, the user has the choice to use a predefined model (simple input mode) are to use its own model either in the propriatary .mdl file format or by providing the stoichiometric matrix of the system in a .csv format (the field separator must be a comma). Notice that these latter files can easily be obtained by using some standard tools (eg. COBRA toolbox). Examples of .mdl and .csv file are provided here: ExampleTutorial_mdlANDcsv_files.zip

../data/page1.png

Page 2 : Define the metabolite types

In this page, the user has to define the type of each metabolites (input/output, co-factor, pivots,...) of the system. More precisely, the type of each columns of the stoichiometric matrix can be defined here. ../data/page2.png

Page 3 : Constraints on fluxes and objective function

Here the user can define some constraints on the reactions fluxes both in a graphical way (by disabling a reaction or imposing a flux value) or by providing a numerical constraint. Examples:

../data/page3.png

Page 4: Extremal flux distribution

Extremal flux distribution corresponds to the vector formed by the values ​​of the flux of each reaction. These values provide the optimal value of the linear objective function. ../data/page4.png

Page 5: Allocation for an extremal flux distribution

It displays four types of relationship, an explicit form of linear equation for calculating allocations; a table, whose columns correspond to the inputs and rows to the outputs, giving the amount of allocation of inputs over each output; a table giving the percentage of allocation of inputs over outputs and a table giving the percentages outputs allocation from inputs ../data/page5.png

Part II: Determination of all vertices of a simplex

To compute all vertices, we generated some random linear objective function to be optimize, on the simplex by using the simplex algorithm. For the model ExampleTutorial.mdl above all vertices can be generated by downloading the .zip below. Notice that to execute the files PHP CLI( Hypertext Preprocesso Command Line Interface) must be properly installed.

The zip is provided here: TutorialExampleVertices.zip

It contains three files

In the php environment run the script as follows
php AllVerticesUsingRandomLinearObjectif.php numberOfRandomObjectiveFunction

numberOfRandomObjectiveFunction is an integer number (it can be 5, 19, 30, 200, 500, ... example of running: php AllVerticesUsingRandomLinearObjectif.php 200)

../data/simplexVertices.png

In addition to this tutorial, Sommets.zip implements a complete parallel method (for both a multicore computer or a cluster of several computers) for computing all the vertices where a well formed .mdl is given. The interest reader should refer to the included README.txt file for details.

Part III: Intervals of AIO

The intervals give the min-max range of AIO through all the simplex. The min-max are obtain by optimizing some no convex functions. An additional problem is to obtain analytical formula for functions to be optimized. Analytical formula are obtain by computing the inverse of a matrix which is always intertible, called M-matrix, using sagemath. We have developed a local search algorithm, which showed that the points corresponding to these minima and maxima are on the edge of the simplex, contrary to libraries that find points near the edge of the simplex. For the model ExampleTutorial.mdl intervals of AIO can be computed by downloading the .zip below. Notice that to execute files matlab and sagemath must be properly installed.

The zip is provided here: IntervalsAIO_ExampleTutorial.zip

It contains three files

Before starting to run the scripts, it is important to have the three files in the same directory.

In the sage environment run the script as follows
load "scriptsageToExample.sage"

../data/sagescript.png

In the matlab environment run the script using fmincon as follows
AllMinMaxUsingFmincon

../data/MinMaxFmincon.png

In the matlab environment run the script using local search algorithm as follows
AllMinMaxUsingLocalSearchAlgo(arg)

../data/MinMaxLocalSearch.png

arg is an input integer parameter for the script. More his value is large more the results obtain close with fmincon results

This web page contains links to the .mdl files used in our study on dairy cows.

The same model under three nutritional conditions with an ATP optimization objective

The three nutritional conditions are synthesized in the following table (Table 2). ../data/Table2.png

The same models with different linear objectives

Here, each file corresponds to a distinct vertex of the flux cone. These files corresponds to results synthesized in the following table (Table 4). ../data/Table4.png

Control

The .mdl files corresponding to the 8 extremal vertices in the CTRL condition: CTRL_condition_allvertices.zip

Casein

The .mdl files corresponding to the 8 extremal vertices in the CN condition: CN_condition_allvertices.zip

Hanigan-Baldwin

The .mdl files corresponding to the 13 extremal vertices in the HB condition: HB_condition_allvertices.zip

Part III: Intervals of AIO

Figure 2 is rendered by CellDesigner v4.2 by using a sbml description of the metabolic network. The sbml file is available here: MammaryGlandModel.sbml.

Picture of a simplified version of the model (pdf version of the picture)

../data/MammarySimplified.png

Picture of the complete model

../data/MammaryGlandModel_picture.png

Slight modifications of the original network

The model can be slightly modified in order to integrate Long Chain Fatty Acids retro control. This gives rise to three new models depending on the quantity of recycled Fatty Acids.

Cover letter for , Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs, article.

CoverLetter.pdf