Met­Ex­plore

Find­ing your path through net­work complexity

Prob­lems with Cytoscape
Browser issues
Cit­ing MetExplore
SBML files
KEGG import

  • jnlp file is down­loaded but doesn’t start [Mac, Win­dows, Linux]

If the jnlp file is dis­played and Cytoscape is not start­ing, please check that you have the lat­est ver­sion of Java installed.

For linux users, it can occur that it does not work with open­Jdk: please install the lat­est ver­sion of ora­cle Java.


  • Cytoscape is blocked by java secu­rity set­tings, how can I unblock it? [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


  • Cytoscape is blocked by java secu­rity set­tings, how can I unblock it? [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.


  • Cytoscape is blocked by java secu­rity set­tings, how can I unblock it? [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.


  • Cytoscape is not start­ing automatically[Mac, PC, Linux]

If Cytoscape doesn’t start

  1. go in your down­loads (often a down arrow in the top right cor­ner of the browser)
  2. a “.jnlp” file should be there, exe­cute this file

  • How can I use Met­Ex­plore plu­gin on the Cytoscape ver­sion installed on my computer?

Pre­lim­i­nary remark: Met­Ex­plore plu­gin is not work­ing with Cytoscape ver­sion 3 and above. Use ver­sion 2.8.
Met­Ex­plore plu­gin comes as a .jar file called MetExplorePlugin.jar

  1. Go to this page: http://​met​ex​plore​.toulouse​.inra​.fr/​r​e​s​o​u​r​c​e​s​/
  2. Down­load the file MetExplorePlugin.jar
  3. Go in the direc­tory Cytoscape is installed (e.g. C:\Program Files\Cytoscape_v2.8.2)
  4. Go in the plu­g­ins direc­tory and put the MetExplorePlugin.jar file (sorry, it doesn’t work with Plugins→Install Plu­gin From File)
  5. Restart Cytoscape


  • Does Met­Ex­plore work with any browser?

Met­Ex­plore is using up to date web tech­nolo­gies (javascript and HTML5). These tech­nolo­gies are stan­dard but may nev­er­the­less have been imple­mented in dif­fer­ent ways in each browsers.

We strongly sug­gest using Chrome. Fire­fox is also a good option even if dis­play maybe slower and of lower quality.

We rec­om­mend not using Inter­net Explorer since some func­tions may not work properly.


  • How can I cite MetExplore?

If Met­Ex­plore helped you in deal­ing with meta­bolic net­works, please cite:

Cottret,L., Wildridge,D., Vinson,F., Barrett,M.P., Charles,H., Sagot,M.-F. and Jourdan,F. (2010) MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic acids research, 38, W132–7.

  • What is SBML?

SBML is a stan­dard file for­mat allow­ing to describe bio­log­i­cal net­works. It is based on XML for­mat­ing which allows spec­i­fy­ing the struc­ture of the file. This kind of for­mat can be read by sev­eral soft­ware tools and is often attached to publications.

If you want more infor­ma­tion on this file for­mat, please visit: http://​sbml​.org/​M​a​i​n​_​P​a​g​e


  • How can I check SBML file valid­ity before upload­ing in MetExplore?

SBML files have to fol­low con­straints defined by SBML con­sor­tium. Met­Ex­plore import func­tion is based on lat­est ver­sion of SBML. Before upload­ing your file, you may check its valid­ity using online SBML val­ida­tor.


  • Why KEGG data­base con­tains more genes than the cor­re­spond­ing net­work in MetExplore?

KEGG is a data­base con­tain­ing whole anno­tated genomes. Thus, for a given organ­ism, it stores genes that are not involved in metab­o­lism. In Met­Ex­plore, we extract only genes related to meta­bolic functions.

For instance, Rat­tus Norvegi­cus genome con­tains 23640 genes while the net­work involves 1465 genes.