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jamiewaese / ePlant

ePlant is a data visualization tool for integrating and exploring multiple levels of biological data.
MIT License
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Try to query genes within an interval of chromosome position via REST #32

Closed yuzhenmi closed 10 years ago

yuzhenmi commented 10 years ago

Instead of loading all genes at the start, and then figuring out which genes are within a chromosome position interval, query with REST so that genes don't have to be all loaded at start. This is because there will be data for more genetic elements that will be incorporated into the chromosome view, and it is best to avoid loading all the data at start.

yuzhenmi commented 10 years ago

I could not find any database table on BAR that contains gene position information. For now, I will attempt to store the genes data in a file and write a CGI script that accesses the data from the file. I will store the data in JSON format since it is effortless to parse.

jamiewaese commented 10 years ago

So you're writing your own web service? Nice solution.

Maybe check with Asher or Nick if that's necessary?

On Oct 20, 2013, at 8:12 PM, Hans Yu notifications@github.com wrote:

I could not find any database table on BAR that contains gene position information. For now, I will attempt to store the genes data in a file and write a CGI script that accesses the data from the file. I will store the data in JSON format since it is effortless to parse.

— Reply to this email directly or view it on GitHub.

yuzhenmi commented 10 years ago

I wrote a very simple CGI script for this. For now, it only retrieves the gene identifiers from the BAR server. I should probably add aliases, annotations, strand, etc. in there too.

http://bar.utoronto.ca/~eplant/cgi-bin/querygenesbyposition.cgi?chromosome=1&start=1&end=30000

nprovart commented 10 years ago

Cool, Hans! Yes, definitely strand needs to be in there... N.

......................................... Nicholas Provart, PhD Associate Professor, Plant Cyberinfrastructure & Systems Biology Chair, Bioinformatics SC, Multinational Arabidopsis Steering Committee Member, North American Arabidopsis Steering Committee and IAIC Member, Centre for the Analysis of Genome Evolution and Function

Currently on sabbatical in the Brady Lab at UC Davis

Phone. +1-530-752-2728 Skype. nicholas.provart, Fax. +1-425-675-7036 URL. http://www.csb.utoronto.ca/faculty/provart-nicholas The Bio-Analytic Resource. http://www.BAR.utoronto.ca email. nicholas.provart@utoronto.ca

On Tue, Oct 22, 2013 at 5:57 PM, Hans Yu notifications@github.com wrote:

I wrote a very simple CGI script for this. For now, it only retrieves the gene identifiers from the BAR server. I should probably add aliases, annotations, strand, etc. in there too.

http://bar.utoronto.ca/~eplant/cgi-bin/querygenesbyposition.cgi?chromosome=1&start=1&end=30000

— Reply to this email directly or view it on GitHubhttps://github.com/jamiewaese/ePlant/issues/32#issuecomment-26871348 .

yuzhenmi commented 10 years ago

Gene list popup now appears either when the user mouses over a chromosome for 20 frames (1/3 second on max FPS) or when the user clicks on a chromosome. Clicking before or after the popup appears will pin the popup. Clicking elsewhere will unpin the popup and remove it (it used to just unpin and not remove until you move the mouse).

On my computer, the gene list gets populated after more than a second. I hope the new database will solve this issue.

Please let me know if this feels right!

yuzhenmi commented 10 years ago

Much faster with the new database.