SOS GeneMANIA Error connection Cytoscape 3.4 and 2.8

[Virginia]

Hi, i installed first 2.8 as i wanted to use cPath. Then i figured GeneMania was more up to date so i installed also 3.4 and the GeneMania plugin.

However, when i want to search with geneMania from the App manager it gives me this error:

An error has occurred:

Unable to retrieve data. Please ensure you have a working network connection and a non-restrictive firewall.

Or when i "check for data updates" i get:

An error has occurred:

We experienced an unexpected error while checking for updates:

http://genemania.org/plugin/data/schema-1.1.txt

When i try to instal a plugin on version 2.8, i get similar error. However when i open 2.8 it asks if i allow connection and i click yes.

So i am really stuck. I tried to figure out the proxy settings on Cytoscape 3.4 but no success. I just use DIRECT.

Can anyone help me please?

/Virginia

[Virginia]

I managed to get genemania to work. But is it normale that it takea way longer to import and visualize on cytoscape than it takes on the genemania website? And the final plot of the interactions network originated from just 12 genes has no resolution in cytoscape (not even the gene name, and when I choose Show graphic details my fan wants to take off. On a macbook from 2012), while in genemania it at least shows the interactions among these 12 genes and their names.
Any comment from more experienced users or creators super appreciated.
Cheers
/Virginia

[Virginia]

Since GeneMania Cytoscape App says it works with Cytoscape 3.3 i installed also this version.

No success. When i use Search from the App Manager-> GeneMANIA option i still get the error.

Anyone able to help?

Thanks

/Virginia

[Christian Lopes]

We had some issues with the GeneMANIA server, but it should be working now.

Please try again and let us know if you still have any problems.

Thanks,

Christian Lopes

[Virginia]

Hi Christina,

indeed yesterday and today it's working. Thanks!

I have noticed that the loading time (and a bit the result) is extremely different when i used the app->search and when i use import->from public database->genemania.

The latter being very very heavy and slow and giving a much greater number of hits, probably many redundant ones.

Could you comment on that?

I have also noticed that some proteins i cannot find through gene mania, but i find on IntAct or Mentha for instance.

Any comments on that too?

And one more question, just in case you happen to know, can you advice a database for search of lipid-protein interactions that can be used with Cytoscape?

Thanks for support

Kind regards

/Virginia

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[Virginia]

of cours Christian, sorry for misspelling... :-/

[Gary Bader]

Hi Virginia,

On 2016-07-05, at 8:25 AM, Virginia <virginia...@gmail.com> wrote:

> Hi Christina,
> indeed yesterday and today it's working. Thanks!
> I have noticed that the loading time (and a bit the result) is extremely different when i used the app->search and when i use import->from public database->genemania.

GeneMANIA search uses the GeneMANIA algorithm to find the most closely related nodes to your input gene list. If you import from public database, it queries all of the interactions in GeneMANIA. For most cases, we recommend using the GeneMANIA search and setting the number of genes you would like returned.

> The latter being very very heavy and slow and giving a much greater number of hits, probably many redundant ones.
> Could you comment on that?
> I have also noticed that some proteins i cannot find through gene mania, but i find on IntAct or Mentha for instance.

We are planning a data update for GeneMANIA that will use the latest versions of these databases and this will hopefully fix this problem.

> Any comments on that too?
> And one more question, just in case you happen to know, can you advice a database for search of lipid-protein interactions that can be used with Cytoscape?

Not really, but you can search http://pathguide.org/ for lipid related resources. e.g. http://www.lipidmaps.org/pathways/index.html

Best,
Gary

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