Visualise Metabolic Networks

Select reactions to visualise

Fill the Cart with reactions

The visualisation is performed on the reactions present in the Cart grid localised in the right-side panel. Select a set of reactions in the reaction grid. There are two ways to fill the cart:

  • Right-click on the grid and select "Copy Selection to Cart" to copy them in the Cart grid."Copy All to Cart" if you want to copy all the reactions in the Cart.
  • Drag and drop the selection in the Cart grid. For this, open the Cart panel, hold down the selection and drag it to the Cart table.




Copy reactions with the right-click menu or by drag&drop from Reaction grid to the Cart.

Handle the Cart data

Remove data from the Cart

Empty cart

To remove all the reactions from the Cart, right-click on the grid and select "Empty Cart".

Delete selected reactions

Select some reactions in the Cart grid (hold Ctrl for selecting several rows), right-click on the grid and select "Delete Selection".

Delete no flux reactions

By clicking on the button "Delete Flux=0", reactions for which the flux lower and upper bounds equal to 0 are removed from the Cart. Note that no flux analysis is done here, only flux bounds indicated for each reaction are taken into account.

Filter from the Cart grid

Propagating filter can be performed from the Cart grid, as for other data grids.

Online visualisation with MetExploreViz

Launch the visualisation with MetExploreViz

There are two ways for drawing the network corresponding to the reactions in the Cart:
  • Right-click on the Cart grid and select "Create network in viz from Cart". Then go to the "Network viz" panel.
  • Go to the "Network Viz" panel and select "Load Network from website"

Visualise and tune the design of the network with MetExploreViz

Consult the documentation of MetExploreViz to learn how to manage the drawing of the network and explore it.

Visualise omics data mappings

if an omics data mapping has been performed in MetExplore, mapping selection appears in the "Network Manager" window of MetExploreViz in the Omics panel. Please consult documentation of MetExploreViz to learn how to visualise mapping data on the network.

Links between MetExplore grids and MetExploreViz nodes

Select rows in grid from network nodes

Right-click on a node in MetExploreViz and click on "Select nodes" and then on "Only this node" for selecting the corresponding row in the Metabolite or Reaction grid. Click on "All the nodes" if you want to select all the rows corresponding to selected nodes in the Metabolite or/and Reaction grids.

See node information

Right-click on a node in MetExploreViz and click on "See more information". A window information will be displayed containing MetExplore data associated to this node.



Network in MetExplore. The contextual menu on a node and an information window are displayed.

Highlight nodes from grids

To highlight nodes from Reaction or Metabolite grid:
  • Select corresponding rows in the grid
  • Right-click on the grid
  • Select "Highlight in visualisation"

Visualisation with Cytoscape

Requirements to use Cytoscape with MetExplore

In MetExplore, Cytoscape is run via Java Web Start. Any browser that supports the Java version 1.5 or higher can launch Cytoscape from MetExplore.

Unblock java security settings (Windows)

You are using JAVA 8
You need to add Met­Ex­plore (http://​met​ex​plore​.toulouse​.inra​.fr/) to the Excep­tion site list by using the fol­low­ing tuto­r­ial: https://​www​.java​.com/​e​n​/​d​o​w​n​l​o​a​d​/​h​e​l​p​/​j​c​p​_​s​e​c​u​r​i​t​y​.​x​m​l
You are using JAVA 7
Since Java ver­sion 7 update 51, default secu­rity con­fig­u­ra­tion is block­ing web start of Cytoscape. To solve this prob­lem, set your “Secu­rity level” to medium fol­low­ing advises on this page: https://​www​.java​.com/​e​n​/​d​o​w​n​l​o​a​d​/​h​e​l​p​/​j​c​p​_​s​e​c​u​r​i​t​y​.​x​m​l

Unblock java security settings (Mac)

You are using JAVA 8
You need to add Met­Ex­plore (http://​met​ex​plore​.toulouse​.inra​.fr/) to the Excep­tion site list by using the fol­low­ing tuto­r­ial: https://​www​.java​.com/​e​n​/​d​o​w​n​l​o​a​d​/​h​e​l​p​/​j​c​p​_​s​e​c​u​r​i​t​y​.​x​m​l
You are using JAVA 7
Since Java ver­sion 7 update 51, default secu­rity con­fig­u­ra­tion is block­ing web start of Cytoscape. First, go to the Java con­trol panel: https://​java​.com/​e​n​/​d​o​w​n​l​o​a​d​/​h​e​l​p​/​m​a​c​_​c​o​n​t​r​o​l​p​a​n​e​l​.​x​m​l Then set your “Secu­rity level” to medium fol­low­ing advises on this page: https://​www​.java​.com/​e​n​/​d​o​w​n​l​o​a​d​/​h​e​l​p​/​j​c​p​_​s​e​c​u​r​i​t​y​.​x​m​l If you are using OS X Mav­er­icks, you may have to set your secu­rity set­tings to allow using appli­ca­tions com­ing from every where.

Unblock java security settings (Ubuntu)

Please check that you the last ver­sion of Ora­cle java is installed. Then, open Applications→Configuration→Oracle Java 8 plu­gin Con­trol Panel. Click on the Secu­rity panel and add http://​met​ex​plore​.toulouse​.inra​.fr in the list of sites with exception. If Cytoscape doesn’t start automatically, go in your down­loads (often a down arrow in the top right cor­ner of the browser), a “.jnlp” file should be there, exe­cute this file

Launch Cytoscape

To start Cytoscape click the but­ton in the cart. The con­tent of the cart will auto­mat­i­cally be loaded in Cytoscape.

Visual style of the MetExplore metabolic networks in Cytoscape


The visual style we use to draw the metabolic networks loaded from MetExplore is an extension of the SBML visual style present in Cytoscape. In particular, the MetExplore visual style allows to represent the reversible reactions.
The legend of the MetExplore visual style is displayed in the table below.

Irreversible reaction

Reversible reaction

Metabolite

Link from a metabolite to a reaction using it

Link from a metabolite to a reaction producing it



Visualise mapping results

More­over, if you mapped data on reac­tions or metabo­lites, they will also be loaded as attributes. The image below represents a MetExplore network displayed in Cytoscape (with the organic layout) with metabolites identified by mapping highlighted.



Visualisation of mapping results in Cytoscape. The mapped metabolites are larger than the others and are colored in dark blue.



All the attributes we described above are directly available in Cytoscape.

Attributes of the network and of the mapping into Cytoscape

Sub-network extraction from nodes identified by mapping

As the representation of the identified nodes in the whole network remains difficult, we developed a Cytoscape plugin to compute the sub-networks linking them. Two ways are available for building a sub-network: by computing the union of the shortest paths or of the lightest paths between the mapped nodes. The second mode often gives more realistic sub-networks as the lightest paths avoid ubiquitous metabolites such as ATP, water, etc...
To launch the plugin, go in the plugins menu and click on "MetExplore: extract sub-networks".



Launch sub-network extraction in Cytoscape

The sub-networks are directly computed and displayed in Cytoscape. Note that the same function exists in the MetExplore online visualisation.



Sub-network extraction in Cytoscape