Universal Property Display in Cytoscape

AlexanderPico commented 4 years ago

Background

Cytoscape is a highly popular open source bioinformatics software platform for visualizing, analyzing, and publishing graphs or networks representing molecular interactions, gene expression, other biological data. As a desktop platform, Cytoscape is one of the most successful open source projects in biology, and it is capable of integrating observational data from numerous sources.

Currently, when you click on a node in a Cytoscape networks (e.g., representing a gene or protein), you reciprocally filter the Node Table to display the selected row. This is helpful, but we could provide more informative data displays for selected nodes. There is already a designated Results Panel to the right of the network. Imagine displaying nicely formatted propersheet in that panel, updating as the user selects different nodes. The display could include:

Standard display of name field
Custom displays of columns with discrete and continuous values, e.g., position of selected node's value in the context of the full distribution of values.
Particular visual property values for the selected node, e.g., the precise color within a gradient and associated numeric value.
Identifiers (e.g., if recognized as a molecule) and links to primary databases with more information
PDB structures (e.g., if a protein identifier is found)
and much more...

Goal

Create a Cytoscape app that generates a property sheet per node to be interactively displayed in the Results Panel. The app, if successful, would be later nominated to be included in the core distribution of future Cytoscape versions.

Technologies

A Cytoscape app is a Java/Swing-based plugin that adds functionality to the Cytoscape core, though it's possible that this project could be executed as a mix of Java/Swing and service-oriented Java, C++, Python, Javascript or other language. The panel content would likely be formatted as HTML. The process for writing an app is documented in the Cytoscape App Ladder. For this app, it would be necessary to learn a bit about typical properties for biological molecules, but no prior biology experience is required.

Difficulty level: 1

Familiarity with modern Java development is critical. Prior experience with Cytoscape app development is a plus.

Potential Mentors

Alex Pico
Scooter Morris

mehumaija commented 4 years ago

hey! what do you mean by modern java development? I have skills at Java programming, but I am not sure what is modern Java and what is obsolete. I have done things like javafx GUI and data visualization and know fors and ifs and whiles and lambdas etc.. Is this something related to this or completely different?

Thank you!

scootermorris commented 4 years ago

That should be fine. The only area you may need to come up to speed on is OSGi, but that should be pretty straightforward and we can help you get over that hurdle.

laurenli17 commented 4 years ago

Hey guys,

This is Lauren Li who are interested to join GSOC 2020 development with NRNB.

I looked at the project ideas posted on the website, and really interested in the idea of "Universal Property Display in Cytoscape".

I am now an undergraduate student at the Ohio State university studying computer science. I have programming experience in Java, HTML, XML Trees, etc. I also have some experience of R. It will be really awesome if I can join the community and learn from you guys.

I have set up Cytoscape on my own computer and have spent some time on it. As a user who has troubles to visualizing and understanding the networking, I feel like the networks visualized by Cytoscape are very useful, and that's the reason I choose to reach out.

I am just a starter at computer science and I’m eager to learn from outside of the classrooms. So is there any advice and recommendations for a starter to reach this project?

Looking forward to hearing from you!

Thanks a lot, Lauren

scootermorris commented 4 years ago

Hi Lauren, Great! You've already taken the first step by setting up Cytoscape. The next steps are to get set up to develop apps. To do that, you should look at the Cytoscape App Ladder and try to get your environment set up. Don't hesitate to ask questions!

scootermorris commented 4 years ago

hey! what do you mean by modern java development? I have skills at Java programming, but I am not sure what is modern Java and what is obsolete. I have done things like javafx GUI and data visualization and know fors and ifs and whiles and lambdas etc.. Is this something related to this or completely different?

Thank you!

As I mentioned to Lauren, you should definitely set up using Cytoscape and take a look at the Cytoscape App Ladder also.

laurenli17 commented 4 years ago

Hi Lauren, Great! You've already taken the first step by setting up Cytoscape. The next steps are to get set up to develop apps. To do that, you should look at the Cytoscape App Ladder and try to get your environment set up. Don't hesitate to ask questions!

Copy that! Definitely will go through it. Thanks!

ShigapovRinat commented 4 years ago

Hello, I'm Rinat Shigapov, second-year student from Kazan, Russia.

I have programming experience in Java, HTML, CSS and etc. Also I installed Cytoscape and set up enviroment. Cytoscape App Ladder - it's really useful thing.

I have never worked on an open source project before, but very want to try it. Previous students wrote great reviews about NRNB and mentors, so I would want to work exactly here. Project "Universal Property Display in Cytoscape" is interesting for me and I want join GSoC 2020 with this project.

Please guide me how should I proceed.

Thank you, Rinat!

mehumaija commented 4 years ago

@scootermorris Thanks for the tips. Will take a look after my exams this week!

scootermorris commented 4 years ago

On 3/4/20 4:29 AM, mehumaija wrote:

@scootermorris https://github.com/scootermorris Thanks for the tips. Will take a look after my exams this week!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/151?email_source=notifications&email_token=AAXTJ6FFYFXAOD6SF2GDMIDRFZCQ7A5CNFSM4K66ARY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENXTWXI#issuecomment-594492253, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXTJ6H3VEX62TTWXEPGDILRFZCQ7ANCNFSM4K66ARYQ.

Sounds good. Best of luck on your exams!

-- scooter

laurenli17 commented 4 years ago

Hi! I am getting started and reading the book about git. However, I'm a little bit stuck at the step "Setup Cytoscape App Development", where I want to search for the egit plugin, the pop-up window always reminds me the info as the following picture shows. May I ask how can I fix this problem? (I'm pretty sure that my internet connection is fine.)Thanks for your time. Screen Shot 2020-03-09 at 6 30 26 PM

scootermorris commented 4 years ago

Hi Lauren, Here is an updated guide you can look at: https://github.com/cytoscape/cytoscape/wiki/Launching-Cytoscape-from-Eclipse Sorry it took me so long to get back to you. I don't use Eclipse and had to look up this guide from one of my colleagues.

-- scooter

On 3/9/20 3:35 PM, LaurenLi wrote:

    hey! what do you mean by modern java development? I have
    skills at Java programming, but I am not sure what is modern
    Java and what is obsolete. I have done things like javafx GUI
    and data visualization and know fors and ifs and whiles and
    lambdas etc.. Is this something related to this or completely
    different?
    Thank you!

As I mentioned to Lauren, you should definitely set up using
Cytoscape and take a look at the Cytoscape App Ladder
<https://github.com/cytoscape/cytoscape/wiki/Cytoscape-App-Ladder>
also.
Hi! I am getting started and reading the book about git. However, when I'm a little bit stuck at step "Setup Cytoscape App Development", where when I want to search for the egit plugin, the pop-up window always reminds me as the following picture shows. May I ask how can I fix this problem? Screen Shot 2020-03-09 at 6 30 26 PM https://user-images.githubusercontent.com/55322897/76263232-bef88180-6234-11ea-8300-928d9a3c6fad.jpg

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/151?email_source=notifications&email_token=AAXTJ6A3SEDGXAFNJNXSNLLRGV4MPA5CNFSM4K66ARY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOJJ7KI#issuecomment-596811689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXTJ6GLSG6TBN3KVKIG43LRGV4MPANCNFSM4K66ARYQ.

laurenli17 commented 4 years ago

Hi Lauren, Here is an updated guide you can look at: https://github.com/cytoscape/cytoscape/wiki/Launching-Cytoscape-from-Eclipse Sorry it took me so long to get back to you. I don't use Eclipse and had to look up this guide from one of my colleagues. … -- scooter On 3/9/20 3:35 PM, LaurenLi wrote: hey! what do you mean by modern java development? I have skills at Java programming, but I am not sure what is modern Java and what is obsolete. I have done things like javafx GUI and data visualization and know fors and ifs and whiles and lambdas etc.. Is this something related to this or completely different? Thank you! As I mentioned to Lauren, you should definitely set up using Cytoscape and take a look at the Cytoscape App Ladder https://github.com/cytoscape/cytoscape/wiki/Cytoscape-App-Ladder also. Hi! I am getting started and reading the book about git. However, when I'm a little bit stuck at step "Setup Cytoscape App Development", where when I want to search for the egit plugin, the pop-up window always reminds me as the following picture shows. May I ask how can I fix this problem? Screen Shot 2020-03-09 at 6 30 26 PM https://user-images.githubusercontent.com/55322897/76263232-bef88180-6234-11ea-8300-928d9a3c6fad.jpg — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#151?email_source=notifications&email_token=AAXTJ6A3SEDGXAFNJNXSNLLRGV4MPA5CNFSM4K66ARY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOJJ7KI#issuecomment-596811689>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXTJ6GLSG6TBN3KVKIG43LRGV4MPANCNFSM4K66ARYQ.

Thank you so much Scooter! I already went through the guide, but actually I changed a laptop from a Mac to a windows one yesterday and the problem fixed lol.

aniket328 commented 4 years ago

Is this project still available, can I contribute to this?

khanspers commented 4 years ago

Hi @aniket328 , this project is still available, outside of Google Summer of Code. Please contact the mentors direclty.

gaurlakshya commented 3 years ago

@AlexanderPico hello Sir , I want to work on this issue (#151 ) . I have good knowledge in the field of web development and java .Sir i am a B.tech student of 2nd year (C.S.E. department). Can i work on this issue ??

AlexanderPico commented 3 years ago

Edit and reopen for 2021

mohasseb99 commented 3 years ago

Hi,

I am Mahmoud. I am interested to join GSOC 2021 development with NRNB. I am going through Cytoscape App Ladder. I am asking if there are things should I do to be accepted.

AlexanderPico commented 3 years ago

@mohasseb99. The app ladder is a good place to start. Please submit your application through Google's GSoC website. A good application includes your relevant background, your understanding of the project, your ideas for how to implement the project, mockups for key UI elements, and a detailed timeline. See the "resources" tab at https://nrnb.org/gsoc.html for more GSoC tips.

nrnb / GoogleSummerOfCode