[MOBY-l] New MOBY application: "BioGraphNet: a distributed fo rum for heterogeneous biological networks"

Fri May 21 16:58:18 UTC 2004

Hi Frank,

If you are interested in Java Graphlayout Applet look at the following links
http://java.sun.com/applets/jdk/1.0/demo/GraphLayout/

Several groups have modified this program to suit their needs.

A modified version for my application TransMiner
(http://www.bisti.nih.gov/2003meeting/Abstracts/III45.pdf) can be found at

http://sifter.cs.iupui.edu/~sifter/transMiner/BCTrans1.html 

Let me know if you are interested in this Graphlayout applet.

Cheers,

Vijay

-----Original Message-----
From: Simon Twigger [mailto:simont at mcw.edu] 
Sent: Thursday, May 20, 2004 11:01 AM
To: Frank Gibbons
Cc: 'moby-l at biomoby.org'; vnarayan at mcw.edu
Subject: Re: [MOBY-l] New MOBY application: "BioGraphNet: a distributed
forum for heterogeneous biological networks"

Hi Frank,

This looks very nice - is it possible to view the graph data into 
something like a java graph-viewing applet so people could zoom in and 
select things, etc? The image that comes back is nice but too small to 
see anything. Im cc'ing this to Vijay Narayanasamy in my group as he 
has built tools like this that display interaction data using this type 
of applet and he might be able to offer some suggestions and show you 
what he has done previously so you can see if it would be of use.

I wonder if it would be worth coloring the genes (grey elipses) as well 
as the lines connecting the genes? It might give a better overview of 
the types of interacting partners if they were colored light green, 
light pink, etc. rather than all being grey.

I'd be interested in getting you some rat data, we're working on some 
rat services here so perhaps we can chat more about that and see what 
makes sense. I'd love to see the tools you have for making text files 
available - I've done similar stuff myself but its not very generic, if 
you have something like that we can certainly make use of it.

I have to run to a meeting but will probably write some more later on.

Cheers,

	Simon.

On May 20, 2004, at 10:23 AM, Frank Gibbons wrote:

> Hey fellow MOBYers,
>
> Below is an abstract I've submitted for BOSC (Bioinformatics Open 
> Source Conference) and BioPathways, satellite conferences of ISMC/ECCB 
> in Glasgow, Scotland this year. BioGraphNet is our 'sandbox' within 
> the BioMOBY 'playground', in which we're looking at ways to share and 
> view biological networks.
>
> At this point, Gabriel Berriz and I have a working prototype: a 
> registered object for describing fairly generic pairwise interactions, 
> half a dozen working services, and an application that runs in a 
> web-browser to allow end-users to play with the interaction data. A 
> key element of this is that anyone can make their data available at 
> any time, and it will be discovered and included in the webpage 
> displayed to users (bench biologists). There's no installation, no 
> updating of databases. I'd appreciate your giving it a try 
> (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what 
> you think. We're looking for feedback on a number of levels:
>
> * Does the overall idea, (being able to view an interactive graphical 
> display of your chosen data sources for your favorite genes), seem 
> useful to you? What pitfalls do you see in the near or distant future?
> * So far we've got correlated expression, synthetic lethality, 
> homology, transcription-factor/target (known and predicted), as well 
> as experimental protein-protein interaction results. What kinds of 
> data would make it more useful?
> * Do you have some data you'd like to share? We've developed tools to 
> facilitate making data available as a MOBY service: drop a text file 
> in the right place, enter the textual description of your service - 
> BOOM, it's registered and available to the world. One goal of this 
> project is to make it easy for people with data to put it out there.
> * Anything else that strikes you....
>
> We're really keen to get input on this, just reply to me: 
> mailto:fgibbons at hms.harvard.edu
>
> I'm looking forward to seeing some of you again in Glasgow!
>
> -Frank Gibbons
>
> --------------------------------------- ABSTRACT 
> ---------------------------------------
>
> TITLE: BioGraphNet, a distributed forum for heterogeneous biological 
> networks.
> AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
> Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood 
> Ave., Harvard Medical School, Boston MA 02115, USA
>
> ABSTRACT:
> Biological network information is increasingly abundant.  The 
> combination of biological networks may be viewed as a multicolor 
> graph, with each color representing a different gene-gene or 
> protein-protein relationship, e.g., protein interaction, sequence 
> homology, correlated expression, transcriptional regulation, genetic 
> interaction (sensu synthetic lethality), or metabolic relationship.  
> Relationship types may be further stratified by type of evidence 
> supporting the relationship, by directionality or by confidence 
> measure.  Furthermore, each organism has its own collection of 
> networks.  Although this information's complexity argues for its 
> maintenance by distributed groups, much of its value is derived 
> through network integration.
>
> BioMOBY has established a 'playground' for distributed services.  We 
> have developed a 'sandbox' within BioMOBY called BioGraphNet.  
> BioGraphNet is a common standard and collection of services for 
> sharing distributed network information.  We now serve several network 
> data types, and encourage others to participate, using the common 
> standard objects we have registered in BioMOBY's ontology.
>
> As an example application illustrating the use of BioGraphNet, we 
> provide BioTrawler, a web-based biological network browser that 
> dynamically discovers suitable distributed data sources within 
> BioGraphNet, integrates those selected by the end-user 'just in time', 
> and visualizes the graph neighboring a user-defined set of genes. 
> Graph layout is handled by the open-source GraphViz package (modified 
> to handle multiple edges between a pair of nodes). BioTrawler also 
> exports graph representations in several commonly used formats (GIF by 
> default, but also Pajek, Cytoscape, and PDF).
>
> The combination of BioMOBY and BioGraphNet represents a distributed 
> network annotation system analogous to the Distributed Annotation 
> System (DAS) for sharing genome annotation.
>
> LICENSING:
> The object descriptions and service interfaces are already available 
> to all BioMOBY users. We plan to release BioTrawler under the Artistic 
> License.
>
> URL: http://llama.med.harvard.edu/cgi/BioTrawler
>
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 
> 02115, USA.
> Tel: 617-432-3555       Fax: 617-432-3557       
> http://llama.med.harvard.edu/~fgibbons
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw