[GSOC 2013] Questions regarding "Android app for Virtual Cell"

[Pruthvi Raj]

Hello

I am Pruthvi, a Computer Science undergraduate student from India. I am an avid mobile app developer. I worked on Phonegap and developed many Windows Phone apps. I am also well versed with native android app development. I have developed an Android app[1] for Exotel Techcom Pvt. Ltd. and it is being used by its clientele of over 2000 firms. 

In my search to find an organization that has challenging problem statements in Mobile application areas, I found NRNB and was very much interested in the this project which requires a mobile app to be built for Virtual cell. While I was trying to come up with a feasible solution and plan to write a good proposal, I got a few questions. 

• Is there any documentation regarding Virtual cell Desktop/Browser Client?
• Are there APIs developed for VCell or should they be developed by student during this project?
• Should this app be developed only as a native app or can a Phonegap option be considered?

I would be very much obliged if I am provided with answers to these questions and whatever questions that may arise in future as they will help me in writing a good proposal and in turn get chosen to NRNB.

List of links:

[1] https://play.google.com/store/apps/details?id=in.exotel.mobile

Regards

Pruthvi Raj

[Pruthvi Raj]

Hello

I hope my mail hasn't missed the attention of mentors. I would be very much obliged if someone coupd answer my questions regarding app.

Thanks

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[Jim Schaff]

Dear Pruthvi,

• Is there any documentation regarding Virtual cell Desktop/Browser Client?

1) Browser Client:  There is no VCell Browser client.  However, I recently prototyped a very limited Browser Client for searching Simulation Tasks which is served up from my prototype RESTful API (see attached image) based on the Restlet framework.  The Web API currently only provides Simulation Task searching and content negotiation (HTML or JSON).  I've attached a WADL file (a RESTful version of a WSDL file) which is downloaded easily by appending ?method=options to the url (see attachment for documentation of the SimulationTask api).  This Web API will be expanded to search for Models, Run Simulations, Retrieve nonspatial simulation results, and other VCell uses.  HTTPS is supported, but authentication has not yet been implemented ... (open for negotiation).

the a JSON representation of a query result is 

[{"simKey":"81599089","simName":"Copy of EBChombo short 1","userName":"anu","userKey":"2302355","htcJobId":"PBS:1253865.master.cm.cluster","status":"completed","startdate":1366312880000,"jobIndex":0,"taskId":48,"message":"completed","site":"TEST","computeHost":"signode09","schedulerStatus":"completed","hasData":true,"modelID":"81599755","modelType":"BioModel"},{"simKey":"81113055","simName":"Simulation1","userName":"anu","userKey":"2302355","status":"completed","startdate":1365784834000,"jobIndex":0,"taskId":0,"message":"completed","site":"ANU_LOCAL_VCELL","computeHost":"\u003c\u003clocal\u003e\u003e","schedulerStatus":"completed","hasData":true,"modelID":"81113057","modelType":"BioModel"},{"simKey":"80993624","simName":"Simulation1","userName":"anu","userKey":"2302355","status":"completed","startdate":1363989414000,"jobIndex":0,"taskId":0,"message":"completed","site":"ANU_LOCAL_VCELL","computeHost":"\u003c\u003clocal\u003e\u003e","schedulerStatus":"completed","hasData":true,"modelID":"80993626","modelType":"BioModel"},{"simKey":"80988255","simName":"Copy of Simulation0","userName":"anu","userKey":"2302355","htcJobId":"PBS:1167744.master.cm.cluster","status":"completed","startdate":1363966214000,"jobIndex":0,"taskId":0,"message":"completed","site":"REL","computeHost":"signode08","schedulerStatus":"completed","hasData":true,"modelID":"81616789","modelType":"BioModel"},{"simKey":"80988255","simName":"Copy of Simulation0","userName":"anu","userKey":"2302355","htcJobId":"PBS:1167744.master.cm.cluster","status":"completed","startdate":1363966214000,"jobIndex":0,"taskId":0,"message":"completed","site":"REL","computeHost":"signode08","schedulerStatus":"completed","hasData":true,"modelID":"80988258","modelType":"BioModel"}]

This is just a first pass, too much information for the mobile client.

2) Android Client: I've also built a very simple Android App which displays a simple list of simulations from the new VCell RESTful API  ... this is only a toy however.  It uses the client-side Restlet framework which conveniently reuses the server's SimulationTask resource definition. (no documentation on this).

3) VCell's Traditional Desktop client is a very large Java application which communicates course-grained transactions with large complicated objects which are either serialized or represented in XML.  VCell's current Server API uses Java RMI and exposes separate Remote Server Objects (via RMI) for Database Access, Simulation Data Retrieval, Simulation Control, and Administration.  There is some description at http://vcell.org about the overall architecture and our VCell Client (please feel free to run the VCell Client for yourself).  There are also You Tube Videos of VCell Tutorials (google "vcell youtube tutorials")

.  Accessbut the production server API is RMI (Java RPC) that is not geared toward the use cases of model/web applications.

I have a prototype RESTful notclient can be launched (Java webstart) from http://vcell.org 

• Are there APIs developed for VCell or should they be developed by student during this project?

The Web APIs for VCell will be developed by the VCell team (with input from the student ... it would be beyond the scope of the project).

• Should this app be developed only as a native app or can a Phonegap option be considered.

We would consider a Phonegap solution, (Adobe Phonegap or Apache Cordova?) but my preference is a native app.  Eventually, we would like the option of expanding the mobile capabilities to include more significant client-side capabilities (visualization/simulation/analysis/client-side database/app-app communication).  On the other hand, a lightweight cross-platform solution has its advantages.

Jim Schaff

VCell Lead Developer.