Re: Questions about BioNetBuilder
Kevin Drew
Hi,
I have just restarted the server. We sometimes experience memory issues on the server when there are large networks being built and I think that was the case here. Please let me know if this does not clear up your problems.
Thanks,
Kevin Drew
Bonneau Lab
On Feb 8, 2011, at 5:05 AM, Jia-Hong Wu wrote:
> Dear Kevin,
>
> I was using BioNetBuilder, and found that if I tried to use the wizard to build a network
> surrounding some seed protein (i.e. finding the proteins that directly interact with the seed),
> sometimes only a single node appears after I pressed finish (when I selected only BIND and IntAct)
> and sometimes a set of nodes but with no edges (when all databases were selected). The
> plugin worked fine about a week ago. Maybe there is a server issue?
>
> Also, I am wondering if the BioGrid database is not usable now in BioNetBuilder, as the number
> of edges is zero when I tried using some seed protein and chose to add first neighbors of nodes
> (and pressed "Calculate number of edges")?
>
> A third question: last week I tried to union the direct PPI partners of some seed protein in some
> of the databases (by selecting multiple databases and choosing "add first neighbors"). I found
> that the final output contains interactions that do not involve the seed protein. Could you tell
> me if I can conduct an exact union of results from multiple databases in BioNetBuilder?
>
> Thank you.
>
> Sincerely,
> Jia-Hong
>
>
Jia-Hong Wu
Kevin Drew
Hi,
Often times when you can find an interaction in the online database but not through BioNetBuilder is because our databases are a little out of date. We try to do a global update of all the databases at least once a year but since we do not have a full time programmer dedicated to this we might be a little late. One thing you can do if you are interested is set up your own server with instructions from us and you can update it when needed. I think it would be very beneficial to the community have additional servers available. Please let me know if you are interested.
Thanks,
Kevin Drew
Bonneau Lab
On Feb 10, 2011, at 1:50 AM, Jia-Hong Wu wrote:
> Dear Kevin,
>
> Thank you for resolving the server issue.
>
> I wonder if you could answer the question on why I am not able to find any PPI partner of some proteins from
> BioGrid using BioNetBuilder, while such partners exist on the database I downloaded from BioGrid? It would
> be great if I could use this convenient tool to query PPI partners directly on cytoscape.
>
> Thank you for your help.
>
> Jia-Hong