Re: R: R: problem with bionetbuilder

[Kevin Drew]

Hi,

Can you give me a little more information about what kind of network you are building including how many genes?   I am noticing very large networks being built which our server has difficulty handling due to the amount of memory required.  If you are building a large network try building one that is smaller and see if that resolves the problem.

Thanks,

Kevin Drew

Bonneau Lab

On Mar 30, 2011, at 6:26 AM, Dario Di Silvestre wrote:

Dear Kevin,

I think that the problem is not solved.

This is the error message that appear when I try to run bionetbuilder.

 

 

 

 

 

<image001.jpg>

 

 

Thanks

dario

 

 

 

 

 

---

Da: Kevin Drew [mailto:kd...@nyu.edu] 
Inviato: Tuesday, March 29, 2011 4:52 PM
A: Dario Di Silvestre
Cc: 'Richard Bonneau'
Oggetto: Re: R: problem with bionetbuilder

 

 

Hi,

 

Thank you for the note.  I have restarted the server and it should be back up and running.  Please let me know if you are experiencing more problems.

 

Thanks,

 

Kevin

 

On Mar 29, 2011, at 4:06 AM, Dario Di Silvestre wrote:

Dear Richard and Kevin,

I wish inform you that Bionetbuilder server is not available.

 

Thanks

Dario

 

---

Da: Richard Bonneau [mailto:bon...@nyu.edu] 
Inviato: Friday, July 30, 2010 3:20 PM
A: Dario Di Silvestre
Cc: Kevin Drew
Oggetto: Re: problem with bionetbuilder

 

Kevin,

 

   I saw that you restarted the server recently, will this fix Dario's problem?

 

Dario,

   Which version of cytoscape and can you show us a log of the failure, or give us a bit more info?

 

,

Rich

 

On Jul 30, 2010, at 3:50 AM, Dario Di Silvestre wrote:

Dear Richard,

my name is Dario Di Silvestre and I work for the ITB-CNR of SEGRATE (Milan-Italy)

I am writing you because I am a user of bionetbuilder server, very useful for our purpose. Our lab perform high-throughput proteomic analysis.

In the last few days when I try to launch cytoscape it is not able to run and it is blocked when it try to charge the bionetbuilder plugin.

Thanks

Dario

 

 

[Kevin Drew]

Hi,

How do you start Cytoscape?  What version of Cytoscape? Do you use the webstarts on the bionetbuilder website?  Also, can you tell me what the server address is under Plugins->Set BioNetBuilder Connection .

Thanks,

Kevin Drew

Bonneau Lab

On Mar 30, 2011, at 11:40 AM, Dario Di Silvestre wrote:

Dear Kevin,

the error appears when I try to run bionetbuilder, so before that I can choose the organism, the genen or other parameters.

dario

---

Da: Kevin Drew [mailto:kd...@nyu.edu] 
Inviato: Wednesday, March 30, 2011 4:16 PM
A: Dario Di Silvestre
Cc: bionet...@googlegroups.com
Oggetto: Re: R: R: problem with bionetbuilder

[Kevin Drew]

Hi,

What version of Java are you running?  Also, are you behind any sort of network firewall or proxy server?  

Thanks,

Kevin Drew

Bonneau Lab

On Mar 30, 2011, at 12:48 PM, Dario Di Silvestre wrote:

Dear Kevin,

cytoscpae 2.6.3 v, Cytoscape is local installed on my pc and the server address is <image002.jpg>

 

If I use the webstarts the error message is the same.

 

 

dario

 

---

Da: Kevin Drew [mailto:kd...@nyu.edu] 
Inviato: Wednesday, March 30, 2011 6:00 PM

A: Dario Di Silvestre
Cc: bionet...@googlegroups.com

Oggetto: Re: R: R: R: problem with bionetbuilder

[Kevin Drew]

Hi,

I noticed a similar problem and it should be fixed now.  Please try it again.

Thanks,

Kevin Drew

Bonneau Lab

On Apr 29, 2011, at 10:27 AM, Dario Di Silvestre wrote:

Hi kevin,

I just tried to use bionetbuilder to create a mus musculus network. But after few second the plugin stop to run and no node and interaction are uploaded.

[Kevin Drew]

Hi,

We had to shutdown that machine due to mechanical failure.  We are working on migrating now but we have not figured out a final solution yet.  I will let you know as soon as we have a plan.  Sorry for the trouble.

Thanks,

Kevin Drew
Bonneau Lab

On Wed, Feb 22, 2012 at 10:16 AM, Dario Di Silvestre <dario.di...@itb.cnr.it> wrote:

Hi, Kevin,

could you check the server?

Thanks

dario

 

---

Da: Kevin Drew [mailto:kd...@nyu.edu]
Inviato: Friday, April 29, 2011 4:51 PM
A: Dario Di Silvestre
Cc: bionet...@googlegroups.com
Oggetto: Re: R: R: problem with bionetbuilder

[Kevin Drew]

Hi,

We are back up and running.  After a few tests things look normal.  Please let us know if you are having problems.

Thanks,

Kevin Drew
Bonneau Lab

[Kevin Drew]

Hi Dario,

We ran into problems with this machine again. I am hoping it will be
back up and running this afternoon.

Thanks for your patience,

Kevin

On Thu, Nov 29, 2012 at 11:20 AM, Dario Di Silvestre
<dario.di...@itb.cnr.it> wrote:
> Hi Kevin,
> how are you? I hope very well. The last time you were solving the problems
> due to the storms. I am writing you for asking if you could check the server
> of Bionetbuilder. Probably it is blocked.
>
> Thanks dario
>
> -----Messaggio originale-----

> Da: Kevin Drew [mailto:kd...@nyu.edu]

> Inviato: Tuesday, October 30, 2012 8:00 PM
> A: Dario Di Silvestre

> Oggetto: Re: R: R: problem with bionetbuilder
>
> Hi,
>

> Because of the storms we have had here, there is a power outage. I am
> guessing we will be able to get it back up and running in a few days.
> Sorry for the inconvenience.
>
> Thanks,
>
> Kevin Drew
> Bonneau Lab, NYU
>
> On Tue, Oct 30, 2012 at 11:09 AM, Dario Di Silvestre
> <dario.di...@itb.cnr.it> wrote:
>> Dear Kevin,
>>
>> could you check the bionetbuilder server?
>>
>> It seems off.

>>
>> Thanks
>>
>>
>>
>> dario
>>
>>
>>
>> ________________________________
>>
>> Da: Kevin Drew [mailto:kd...@nyu.edu]

>> Inviato: Friday, March 30, 2012 6:38 PM
>> A: Dario Di Silvestre
>> Cc: Duncan Penfold-Brown

>>
>>
>> Oggetto: Re: R: R: problem with bionetbuilder
>>
>>
>>
>> Hi,
>>

>> Thanks for letting us know. It should be all running now.
>>
>> Thanks again,
>>
>> Kevin Drew
>> Bonneau Lab
>>
>> On Fri, Mar 30, 2012 at 11:59 AM, Dario Di Silvestre
>> <dario.di...@itb.cnr.it> wrote:
>>
>> Hi kevin,
>>
>> at the moment it seems doesn't work.
>>
>> bye

>>
>>
>>
>> ________________________________
>>
>> Da: Kevin Drew [mailto:kd...@nyu.edu]

>> Inviato: Tuesday, March 06, 2012 11:03 PM
>> A: Dario Di Silvestre
>> Cc: bionet...@googlegroups.com; Duncan Penfold-Brown

[Duncan Penfold-Brown]

Hi all,

The machine hosting bionet builder is back up and running - apologies for the delay. Had a network card burnout, and some difficulty getting the machine back up.

Thanks,

Duncan PB

[Kevin Drew]

Hi Dario,

We have been experiencing problems with the machine where the BioNetBuilder server is hosted.  Unfortunately, we have no plan or resources to fix it so service will be intermittent.  We have restarted the machine and it should be back up and running.  I have been advising other users to try GeneMania as an alternative. 

Thanks and sorry for the trouble,

Kevin Drew

On Mon, Oct 28, 2013 at 12:21 PM, Dario Di Silvestre <dario.di...@itb.cnr.it> wrote:

Hi Kevin,

could you test if Bionetbuilder is running?

 

Thanks

 

dario

 

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Da: Kevin Drew [mailto:kd...@nyu.edu]
Inviato: Friday, March 30, 2012 6:38 PM
A: Dario Di Silvestre
Cc: Duncan Penfold-Brown

Oggetto: Re: R: R: problem with bionetbuilder

 

Hi,

Thanks for letting us know.  It should be all running now.

Thanks again,

Kevin Drew
Bonneau Lab

On Fri, Mar 30, 2012 at 11:59 AM, Dario Di Silvestre <dario.di...@itb.cnr.it> wrote:

Hi kevin,

at the moment it seems doesn’t work.

bye

 

---

Da: Kevin Drew [mailto:kd...@nyu.edu]
Inviato: Tuesday, March 06, 2012 11:03 PM
A: Dario Di Silvestre
Cc: bionet...@googlegroups.com; Duncan Penfold-Brown