Google Summer of Code Projects

[Jim Schaff]

We thank the National Resource for Network Biology (NRNB) for inviting us to submit 3 Google Summer of Code 2013 "ideas" involving VCell and VCell-Cytoscape interoperability. 

 

IDEA 6: One-click transfer/update files between Cytoscape and the Virtual Cell

IDEA 7: Web interface for Querying the Virtual Cell database

IDEA 9: I-phone/Android application for viewing of public/private results in the Virtual Cell

 

see below for initial project descriptions: (see http://nrnb.org/gsoc/ for more details)

 

IDEA 6: One-click transfer/update files between Cytoscape and the Virtual Cell

Goal: Develop a Cytoscape plugin that allows a user to “single-click” transfer pathway data between Cytoscape and the Virtual Cell applications.

The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems providing both client- and server- based modeling and simulation capabilities. The biologically oriented Virtual Cell user interface is primarily focused on physical modeling of cellular processes, but recently incorporated support for biological pathway models compliant with the BioPAX (Biological Pathway Exchange) format and ontology. Cytoscape is an extensible, biologically oriented graph visualization and analysis tool, build using the Java OSGi framework, which provides rich support for BioPAX pathways and connectivity to pathway databases. A Cytoscape plugin (OSGi bundle) is needed which can provide “single-click” client-side transfer/update of pathway data and user selections/actions between Cytoscape and the Virtual Cell applications.

Language and Skills: Java, knowledge of OSGi is a plus
Possible Mentors: Jim Schaff
Contact: vcell-...@googlegroups.com

IDEA 7: Web interface for Querying the Virtual Cell database

Goal: Develop a web application for querying and retrieval SBML models from Virtual Cell database

The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems using Java RMI, providing both client- and server- based modeling and simulation capabilities. The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The models and results are stored on a remote server and presently can be reviewed only in the VCell software. The development of a web application for querying VCell database would provide new resources for biologists by enabling web access to VCell database, searching and retrieving public models in VCML and SBML formats.

Language and Skills: Java, experience with Google Web Toolkit is a plus
Possible Mentors: Michael Blinov, Jim Schaff
Contact: vcell-...@googlegroups.com

IDEA 9: I-phone/Android application for viewing of public/private results in the Virtual Cell

The Virtual Cell modeling and simulation framework is an open source software for modeling and simulations of biological systems providing both client- and server- based modeling and simulation capabilities. The biological simulations run within a batch environment on a centralized computational facility, and the job submission, status and simulation results are controlled and monitored by server side capabilities. Currently, users can only check the status of long running simulation jobs and view simulation results from within the full Virtual Cell client which must be run on a laptop or desktop with sufficient resources and a standard network connection. There is a need for an iOS or android app to view job status, submit or kill jobs, manage user quotas, and provide simple results viewing.

Language and Skills: Java/Android and/or Objective-C/iOS
Possible mentors: Ion Moraru, Jim Schaff
Contact: vcell-...@googlegroups.com

 

 

[Umang Kedia]

Hi Jim,

Thanks for the info. I was out for last three days so couldn't reply you on time. So as far as I understand, you will use RESTful APIs to view, cancel, submit the jobs and other things. All the things will be done by sending request to the server which will reply in either JSON format or the requested type. Please correct me if I am wrong on this.

I have fair amount of experience with REST APIs and I have developed a web-app for PayPal to access data from JIRA(open source bug tracking software) using REST architecture. Since it was a web-app I used PHP, jQuery for accessing the REST APIs. But, I could easily work on android on the REST architecture.

I am also sending you the link to my github repo. I along with a team of three members developed an application for my college fest. My task was to get the data from a XML file (similar to RSS feed) and display the events in a LIstView. The app also notifies users if there is any change in the event. The SQLite part was not used in the app so please ignore the DBHelper part.

Github link: https://github.com/androidify/Pearl

Also, I have thought a little bit about the UI of the app. I plan to develop a sliding menu which will contain the main options such as View Job Status, Manage User Quotas etc. This will require using a third party open source API. The end result will be similar this and the UI can be customized according to our requirement. The two APIs for this purpose are sliding menu and android-undergarments.

Please mail me if you think I my implementation is wrong or if you require any more details. I am really interested fro project and I will apply for it this year.

Thank you.

[Umang Kedia]

Hi,
The application period is going to start and I think the mentors missed by reply. Please reply and post more about the REST interface so that I can apply. I want to work on this project.I have written my introduction in my last post and I have a good amount in working with REST API. Please reply as soon as possible to discuss more about the project.

On Friday, April 12, 2013 3:31:35 AM UTC+5:30, Jim Schaff wrote:

[Jim Schaff]

On Sunday, April 21, 2013 3:40:04 AM UTC-4, Umang Kedia wrote:

Hi,
The application period is going to start and I think the mentors missed by reply. Please reply and post more about the REST interface so that I can apply. I want to work on this project.I have written my introduction in my last post and I have a good amount in working with REST API. Please reply as soon as possible to discuss more about the project.

I look forward to seeing your application, I pledge to be more responsive this week.  

For more information about the mobile app requirements and the VCell Web API, please see my responses on the following threads on this discussion group:  [GSOC 2013] Questions regarding "Android app for Virtual Cell"  and GSOC 2013 (Idea9- Android app for Virtual Cell).

Jim.

[Umang Kedia]

Thanks Jim. Its okay. I just wanted to know more about the REST API and way you are planning to implement the android app. As mentioned above, I have experience with JIRA REST API ( an open source bug tracking software) and I have developed a webapp based on it for PayPal,India. I also have experience with Phonegap and jQuery Mobile. But I wanted to discuss about the architecture and the way you want the app to be implemented like full native or Phonegap. I think these things will give me good overview of the project before applying. Maybe you can point me to the REST API documentation so that I can experiment for a day over it. 

Thank you. 

On Friday, April 12, 2013 3:31:35 AM UTC+5:30, Jim Schaff wrote:

[Jim Schaff]

search the other posts on this google group .. there I've attached some API documentation (a WADL file) of what I have so far ... but it is still incomplete.