Visualization tools for genomic data and What's is more important?

Mar 18, 2013 at 7:06 PM
Dear all

I want to know, what's is the apllicatión that appears in this video http://www.microsoft.com/silverlight/pivotviewer/# in the Scenarios video section, at time1:30.

so i want to take advantage to this discussion to make a question to all, but specifically to the coordinators and the developers of this project:
What do you consider more important in the .NET Bio project?
a- The visualization for genomic and biological data using office add-ins like pivot and silverlight in general.
b- improve the algorithms for assembly and annotations process, like padena algorithm, Needleman-Wunsch, Smith-Waterman, etc.

if your response is the a option, what do you have in mind?

Best regards,


Leonardo
Coordinator
Mar 20, 2013 at 6:40 PM
Leonardo, I am not sure about your question regarding the video. I think it's just Pivot you are seeing...

As to what's more important to .NET Bio - well both A and B :)

As for A I know that has been brought up over time. We have invested in some apps that do visualization but for a variety of reasons those are not part of this project. There is a sample app - Sequence Assembler that is part of .NET Bio BTW. Look under the sample applications menu for that. I think all the coordinators would like to see the project move forward in this area. If you have specific ideas please post for all to see.

As for B - we do expect to have new reference algorithms for Needleman-Wunsch and Smith Waterman available in .NET Bio 1.02. When that comes out I'll include some details in the release notes regarding these changes.

Rick
Mar 20, 2013 at 11:30 PM
Rick, i want to explore the both areas, but per now my priority is make new applications for visualization biological data, using pivot, something similar to tablet assembly viewer, our implementation over pivot, is tool for visualising assembly data and spread BLIP in the scientifi community i'm planning in visualize the xml results of BLAST and execute BLIP with my own BLAST. without NCBI-BLAST

I want to take advantage of the discussion, to make a another questions:

first, i presume silverlight, like the implementation of flash powered by microsoft, if flash now is a "sunset" technology, is silverlight too? what do you think about begin to make new visualizations tools using HTML5?

PD: i'm open to more proposals and ideas to develop for visualizing biological data.

about the video, this is the aplication that i asked, and appears in the video,

http://www.freeimagehosting.net/yyqma
Coordinator
Mar 21, 2013 at 4:09 AM
I woudl say that algorithms and visualization tools are important - the former would be a better fit wtht eh core library, whereas the latter tend to be implemented as standalone applcations, - so in terms of extending .NEt Bio, I would thing algorithms (or persers for new file formats, or connectors to different web services) would be the better fit.

Really though, I think a better approach would be to add something that biological scientists you know have a need for, and would use. If you know of anyone doing genomics, you could ask them what tasks they need help with, and produce an application that would help them in their work - and if that application needed functionality not currently in .NET Bio, then you could add that as part of the project.
Coordinator
Mar 21, 2013 at 5:16 AM
One other thing - the application you mention on the Silverlight PivotViewer page is a demonstration collection of human genes created by one of the Pivit team - it is no longer available, but was in fact a set of interlinked Pivot data collections, one per chromosome. It illustrates what can be done with Pivot and the deepzoom technology.

With regard to whether to use Silverlight; that is really for you to decide, PivotViewer is a freely-available component and is certainly useful for some applications; at the same time, HTML5 is rapidly becoming the de facto standard for web-based visualization and simplifies cross-platform browser support. There's a lot to be said for adopting common standards - but of course programming a deep zoom-like application using HTML5 would be a lot of work (we did this in our team for the Chronozoom project). I would say that if you want to build an application easily, Silverlight works for your intended user base, and you are not planning to release updates to your application over the coming years, use PivotViewer - and if you want something that is more standard and probably more 'future-proof', HTML5 is the better route - but you will have to do much more programming.