Re: [Gmod-ajax] Genome browser

[Ian H. <ih...@be...>]

Hi Gary,

We'd be delighted to follow up with you and help you play with & extend
JBrowse, and would enthusiastically welcome you to the project!

I am CC'ing Mitch Skinner (lead JBrowse developer) and the gmod-ajax
mailing list (the main public forum for JBrowse discussions).

The main JBrowse site is
http://jbrowse.org/

There are links from there to the mailing list, our code repositories,
demos, our bug/feature trackers, etc.

Our imminent plans include opening up the JBrowse API with examples so
people can customize their own features, tracks, images, javascript
behavior etc.

Please do let us know how you get on,
Ian


Gary Churchill wrote:
> Thanks Kevin.  We will follow up on these leads.
> 
> All the best,
> 
> Gary
> 
> 
> On 9/15/09 12:17 AM, "Kevin White" <kp...@uc...> wrote:
> 
> Hi Gary
> 
> Actually we started a project but then realized that a CS group at Berkeley led by Ian Holmes was already working on this kind of a project. For our immediate purposes, implementing their new browser, JBrowse, and making modifications (or suggestions on improvement priorities to Ian's group) has worked pretty well.  If you have not taken a look at it already, I would suggest to do so.  It may have some of the features you are looking for already, or could be modified to do what you need.  I am ccing Ian here, as well as Bob Grossman who is the local faculty in Chicago on our Center grant who implemented Ian's browser.
> 
> Here are references to very recent papers from Ian's group and Bob's & mine.
> 
> JBrowse: A next-generation genome browser. Skinner ME <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Skinner%20ME%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Uzilov AV <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Uzilov%20AV%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Stein LD <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Stein%20LD%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Mungall CJ <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Mungall%20CJ%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Holmes IH <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Holmes%20IH%22%5BAutho
r%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> . Genome Res. <javascript:AL_get(this,%20'jour',%20'Genome%20Res.');> 2009 Sep;19(9):1630-8. Epub 2009 Jul 1.
> Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. <http://www.ncbi.nlm.nih.gov/pubmed/19656951?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum>  Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP, Grossman RL. Bioinformatics. 2009 Aug 5.
> 
> To see our implementation of JBrowse, please check out this site:  https://www.cistrack.org/flynet/
> You can play around with our site to get a feel for at least one instance of it.
> 
> There are definitely improvements/features that we would like to see on JBrowse, but as far as an AJAX enabled genome browser this is the most advanced I know of and might be a good starting point.  What are some of the features you are thinking about?  For us, a parallel window with chromosome "cartoons" with annotation and dynamically selectable for browsing on the main browser would be pretty cool.  Might be useful for rapidly browsing different QTL for you guys.  Adding WIG files or nextgen sequencing peak calling or RNA calling  summaries as tracks (something we just need to do - I think JBrowse will already support this), is one of the high priorities on our local agenda.  Of course we are happy to share any tools, experience, etc... with you.  Obviously Ian's group did the heavy lifting already on the main browser infrastructure, for which we are extremely appreciative!
> 
> Kevin
> 
> 
> From: Gary Churchill [mailto:Gar...@ja...]
> Sent: Monday, September 14, 2009 3:51 PM
> To: kp...@uc...
> Cc: Keith Sheppard; Imogen Hurley; nn...@bs...
> Subject: Genome browser
> 
> Kevin,
> 
> We have been discussing strategies to develop an improved genome browser - inspired by Google Finance.  Keith Sheppard,  SE in my group, has come up with a plan to develop a genome using AJAX technology.  When it came up at group meeting, Imogen pointed out that you may have a similar plan already underway.
> 
> We would be happy to adopt your browser, or to contribute to its development, or to compare plans.  Which depends on how far along your browser development is.   It could be viewed as a cross-center cooperation.  And we'd like to improve on the browser we have.
> 
> Let me know if you are interested in pursuing this.
> 
> Best regards,
> 
> Gary
> 
>