Develop and deploy cyTRON: an application to show and explore cancer progression models #52
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.
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.
Cytoscape, RServe, R.
Marco Antoniotti (email@example.com)
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thanks for the interest. Looks like you missed the GSoC deadline. You'll
On Wed, May 11, 2016 at 2:18 AM, srikanthBezawada firstname.lastname@example.org
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
All the best
On Tue, Jul 5, 2016 at 2:12 PM, Rohit Shinde email@example.com
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:
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 < ***@***.***> 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 <#52 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAfZWhaGQ2qx7_du0n5ZgIAYpHlAxiuqks5rmHf2gaJpZM4HRy67> .
-- Marco Antoniotti Somewhere over the Rainbow