Develop and deploy cyTRON: an application to show and explore cancer progression models

[marcoxa]

Background

The BIMIB group has constructed a series of algorithms that reconstruct cancer progression models starting from cross-sectional data. See https://www.bioconductor.org/packages/release/bioc/html/TRONCO.html. The progression models are reconstructed using a theory of "probabilistic causation" rooted in Suppes' work. At the time of this writing, the R TRONCO library produces a DAG data-structure encoded in an adjacency matrix that is statically visualized using the R graphviz interface. A TRONCO to Cytoscape bridge is already available, based on RServe.

Goals

In order to improve the visualization of the progression models, we have started to develop cyTRON, a Cytoscape app to visualize them. We would like to propose cyTRON further development as a GSoC project for a motivated programmer. The main goal will be to read in the progression model DAG data-structure with all its annotations over the RServe bridge (or, possibly, over a new cyREST bridge) and to display it in the main Cytoscape window. The Cytoscape DAG display will also allow for the linking of web-based resources (e.g., gene annotations), in order to provide more information for the user.

Difficulty level: 2

Prior experience with Cytoscape app development or extensive Java and graph theory experience highly recommended.

Technologies Involved

Cytoscape, RServe, R.

Potential Mentors

Marco Antoniotti (marco.antoniotti@unimib.it)

[srikanthBezawada]

Hi @marcoxa ,

I am interested in this app.

[marcoxa]

Hi Srikanth

the app is still "in fieri". That's the reason for the GSoC project. However, at this point the application period is closed I fear.

Marco

[srikanthBezawada]

Hi again @marcoxa ,

I am interested in developing cyTRON project as a Cytoscape app through NRNB academy. Please let me know..

[khanspers]

Hi @srikanthBezawada! Please start by completing our NRNB Academy Admissions form: http://nrnb.org/academy-admissions.html

[marcoxa]

Hi Srikanth

thanks for the interest. Looks like you missed the GSoC deadline. You'll have to check in with the NRNB regarding the academy. Note that I am not part of it.

Marco

On Wed, May 11, 2016 at 2:18 AM, srikanthBezawada notifications@github.com wrote:

Hi again @marcoxa https://github.com/marcoxa ,

I am interested in developing cyTRON project as a Cytoscape app through NRNB academy. Please let me know..

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/52#issuecomment-218329383

Marco Antoniotti Somewhere over the Rainbow

[rohit12]

I am interested in this and some other projects on the nrnb page. I feel that I could learn something interesting by contributing to this project. Can I contribute to this outside of GSoC?

[khanspers]

Hi Rohit, it is indeed possible to contribute to NRNB projects outside of GSoC. However, this particular project is already ongoing with another student. I will contact you directly with more information on other opportunities.

[marcoxa]

Thanks for the interest Rohit.

As Kristina said. We already have a student working on it.

Please do keep track of our announcements. There will be other opportunities in the future.

All the best

Marco

On Tue, Jul 5, 2016 at 2:12 PM, Rohit Shinde notifications@github.com wrote:

I am interested in this and some other projects on the nrnb page. I feel that I could learn something interesting by contributing to this project. Can I contribute to this outside of GSoC?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/52#issuecomment-230461262, or mute the thread https://github.com/notifications/unsubscribe/AAfZWgFkMBX5qazVGaMEM3NdRyab1wUBks5qSkohgaJpZM4HRy67 .

Marco Antoniotti Somewhere over the Rainbow

[AdrianBZG]

Hi @marcoxa ,

I'm a senior Computer Science university student from Spain, and I feel interested on this project for GSoC'17.

After reading the project goal I have some questions:

1. The main idea is to provide a better graphical interpretation of the read DAG data-structure, that currently is being visualized using R graphviz, the objective is to 'port' the visualization to the main cyTRON window. Am I right about this?

2. You mention "The Cytoscape DAG display will also allow for the linking of web-based resources (e.g., gene annotations), in order to provide more information for the user.", I'm a little bit confused about the exact desired behaviour of this feature, can you please illustrate me with a simple/tiny example?

3. I have also noted on the "Technolovies Involved" the mention of R, is it really neccesary for this project to know about R? I haven't worked with R yet so I'm not profficient with it, but I am an easy learner so I'll have no problem if it's needed (Currently I'm most comfortable with Java).

Thank you!

[marcoxa]

Hi Adrian

your interpretation of the project specs are correct.

1. Yes. That is correct. One of the problems is to find the proper Cytoscape layout engine (or reuse one) to display DAGs.
2. This is rather simple in principle, but it could easily expand. Once you have a node displaying a gene name, by (let's say) right-click on the node name, you should, at a minimum, get gene related information about it in a pop-up web page.
3. Knowledge of R is necessary, as many of the backend functionalities will require a back-and-forth with a running R instance.

Hope this helps

Marco

On Thu, Mar 16, 2017 at 12:44 AM, Adrián Rodríguez Bazaga < notifications@github.com> wrote:

Hi @marcoxa https://github.com/marcoxa ,

I'm a senior Computer Science university student from Spain, and I feel interested on this project for GSoC'17.

After reading the project goal I have some questions:

1.

The main idea is to provide a better graphical interpretation of the read DAG data-structure, that currently is being visualized using R graphviz, the objective is to 'port' the visualization to the main cyTRON window. Am I right about this? 2.

You mention "The Cytoscape DAG display will also allow for the linking of web-based resources (e.g., gene annotations), in order to provide more information for the user.", I'm a little bit confused about the exact desired behaviour of this feature, can you please illustrate me with a simple/tiny example? 3.

I have also noted on the "Technolovies Involved" the mention of R, is it really neccesary for this project to know about R? I haven't worked with R yet so I'm not profficient with it, but I am an easy learner so I'll have no problem if it's needed (Currently I'm most comfortable with Java).

Thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/52#issuecomment-286914811, or mute the thread https://github.com/notifications/unsubscribe-auth/AAfZWhaGQ2qx7_du0n5ZgIAYpHlAxiuqks5rmHf2gaJpZM4HRy67 .

-- Marco Antoniotti Somewhere over the Rainbow

[AdrianBZG]

Hi @marcoxa ,

Ok, it's clearer now :)

I would love to know how to write a good proposal for this programme based on this project goal, I would like to know who I can discuss this with (here or by mail, IRC...)

Thank you!

[khanspers]

Selected as GSoC 2017 project