Running GeneMania in Cytoscape

[Priyadarshini Thirunavukkarasu]

Hi, I am not able to run GeneMania in cytoscape. After I paste the list of genes and click start , it opens a box (Find Related Genes) and shows an error has occured. What should I do to run Genemania in Cytoscape. Thank you

[Barry Demchak]

Can you tell us what error it gives? Also, which version of Cytoscape? Which operating system?? 32 or 64 bit???

Thanks.

Barry Demchak -- from my mobile phone

On May 27, 2015 5:34 AM, "Priyadarshini Thirunavukkarasu" <priy...@gmail.com> wrote:

Hi, I am not able to run GeneMania in cytoscape. After I paste the list of genes and click start , it opens a box (Find Related Genes) and shows an error has occured. What should I do to run Genemania in Cytoscape. Thank you

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[Priyadarshini Thirunavukkarasu]

It just opens up a box, showing "an error has  occurred".I use cytoscape version 3.2. 64 bit.

[Barry Demchak]

Are you using Mac, Windows, or Linux?

Barry Demchak -- from my mobile phone

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[Priyadarshini Thirunavukkarasu]

I am using windows

On Wednesday, May 27, 2015 at 6:04:17 PM UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

[Christian Lopes]

Can you please send us the list of genes you pasted and the selected organism name?

Thanks,
Christian

[Priyadarshini Thirunavukkarasu]

This is my gene list
I selected Homo sapiens

AKAP9

APP  

ATF4

ATF5

BBS4

CCDC141

CCDC88A

CDK5

CTNNB1

DAB1

DISC1

DIXDC1

DRD2

FEZ1

FOXD3

GRB2

GSK3B

IMMT

KALRN

KIF5B

PAFAH1B1

MAP1A

MYH2

NDE1

NDEL1

NRG1

NRG2

OLIG2

PCM1

PCNT

PDE4B

PDE4D

SLC12A2

SOX10

TNIK

TRAF3IP1

TRIO

YWHAE

ZNF365                                                                                                          

RELN

ADCYAP1

DTNBP1

AKT1

ACTB

RHOT1

TRAK1

ITPR1

ZNF385A

[Priyadarshini Thirunavukkarasu]

After clicking start, it shows collecting source networks, then within few minutes "it says an error" has occurred

On Wednesday, May 27, 2015 at 6:04:17 PM UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

[Christian Lopes]

Unfortunately, I can't reproduce the error.
I was able to run the search with 20 and then 200 top related genes without any issues on a virtual machine Windows 8.1 64-bit with 2GB of RAM and Java v1.8.0 (please see attached session files).

Can you please send me your Cytoscape log file?
In order to make it easier for us, you just need to:

1. Shut down Cytoscape
2. Delete the framework-cytoscape.log file in <HOME>\CytoscapeConfiguration\3\
3. Open Cytoscape again and run the GeneMANIA search
   
4. After the problem occurs, send me the new framework-cytoscape.log file

Sorry for all the trouble!

Thanks,
Christian

[Christian Lopes]

You can also try the new version of GeneMANIA (v3.4), released today.

[Priyadarshini Thirunavukkarasu]

As you have suggested I deleted all the framework log files,then did the genemania search in cytoscape.I have attached the framework log file along with this mail.Pls find it.Thank you

Regards
Priya

On Wednesday, May 27, 2015 at 6:04:17 PM UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

[Priyadarshini Thirunavukkarasu]

I tried in Cytoscape version 3.4, still I get an error

Regards
Priya

On Wednesday, May 27, 2015 at 6:04:17 PM UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

[Anvita Gupta]

Hi Priya,

I am facing the same issue. Did you got the solution of your [problem. If yes kindly let me know.

Thanks,

Anvita

[Christian Lopes]

We've had some server issues, but it should be fine now.

Please let me know if you still have any issues.

Thanks,

Christian

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[Elza Rauda]

Hello.

I'm running into the same problem here. Using 64-bit Windows, Cytoscape 3.2.1, GeneMANIA 3.4.0. Attached a screenshot of the error.

On Tuesday, 15 September 2015 17:27:19 UTC+3, Christian Lopes wrote:

We've had some server issues, but it should be fine now.

Please let me know if you still have any issues.

Thanks,

Christian

On Tue, Sep 8, 2015 at 5:21 AM, Anvita Gupta <anvita...@gmail.com> wrote:

Hi Priya,

I am facing the same issue. Did you got the solution of your [problem. If yes kindly let me know.

Thanks,

Anvita

On Monday, 1 June 2015 15:22:44 UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

I tried in Cytoscape version 3.4, still I get an error
Regards
Priya

On Wednesday, May 27, 2015 at 6:04:17 PM UTC+5:30, Priyadarshini Thirunavukkarasu wrote:

Hi, I am not able to run GeneMania in cytoscape. After I paste the list of genes and click start , it opens a box (Find Related Genes) and shows an error has occured. What should I do to run Genemania in Cytoscape. Thank you

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[ilaria palmisano]

Hi
I installed GeneMania from the cytoscape Apps. I am not able to install the mouse dataset (actually any dataset)
The steps I have done are;
Install the Genemania from the Apps of Cytoscape
I have chosen the 2014-08-12 (all) and it is active now
Then "search" and install the mouse dataset
After a while it stops without any error message and the database doesn't seem to be installed
can you please help me?