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Develop and deploy cyTRON: an application to show and explore cancer progression models #52

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marcoxa opened this Issue Feb 2, 2016 · 12 comments

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@marcoxa

marcoxa commented Feb 2, 2016

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)

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srikanthBezawada May 2, 2016

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Hi @marcoxa ,

I am interested in this app.

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srikanthBezawada commented May 2, 2016

Hi @marcoxa ,

I am interested in this app.

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marcoxa May 3, 2016

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

marcoxa commented May 3, 2016

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

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srikanthBezawada May 11, 2016

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Hi again @marcoxa ,

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

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srikanthBezawada commented May 11, 2016

Hi again @marcoxa ,

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

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khanspers May 11, 2016

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

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khanspers commented May 11, 2016

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

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marcoxa May 15, 2016

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
#52 (comment)

Marco Antoniotti
Somewhere over the Rainbow

marcoxa commented May 15, 2016

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
#52 (comment)

Marco Antoniotti
Somewhere over the Rainbow

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rohit12 Jul 5, 2016

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?

rohit12 commented Jul 5, 2016

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?

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khanspers Jul 5, 2016

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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.

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khanspers commented Jul 5, 2016

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.

@khanspers khanspers closed this Jul 5, 2016

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marcoxa Jul 5, 2016

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
#52 (comment),
or mute the thread
https://github.com/notifications/unsubscribe/AAfZWgFkMBX5qazVGaMEM3NdRyab1wUBks5qSkohgaJpZM4HRy67
.

Marco Antoniotti
Somewhere over the Rainbow

marcoxa commented Jul 5, 2016

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
#52 (comment),
or mute the thread
https://github.com/notifications/unsubscribe/AAfZWgFkMBX5qazVGaMEM3NdRyab1wUBks5qSkohgaJpZM4HRy67
.

Marco Antoniotti
Somewhere over the Rainbow

@khanspers khanspers reopened this Jan 6, 2017

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AdrianBZG Mar 15, 2017

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!

AdrianBZG commented Mar 15, 2017

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!

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marcoxa Mar 16, 2017

marcoxa commented Mar 16, 2017

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AdrianBZG Mar 19, 2017

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!

AdrianBZG commented Mar 19, 2017

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!

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khanspers May 12, 2017

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Selected as GSoC 2017 project

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khanspers commented May 12, 2017

Selected as GSoC 2017 project

@khanspers khanspers closed this May 12, 2017

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