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zicanl / NemoMapPy

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Subgraph visualization #1

Open gabipana7 opened 3 years ago

gabipana7 commented 3 years ago

Hello @zicanl I was wondering if there is a way to not just count the total mappings of my motif in the inputGraph, but also to save the edges ( the subgraphs ) of my inputGraph that are indeed the specified motif. I am intersted in visualizing these motifs in my network, not just counting them.

Thank you in advance !

zicanl commented 3 years ago

Go to the website http://bioresearch.css.uwb.edu:83/. After calculating the motifs, click the "NemoCollection" button which will give you a file that includes all the subgraphs counted. I hope it can help.

gabipana7 commented 3 years ago

Thank you for the answer, I used the NemoCollection button to collect but the issue I have is with bigger graphs, the site gets stuck. I wish there was a way to get access to the source code, so that I could run everything on my machine because every single iteration of Nemomap I found on github ( the original in C++ , the python ports etc ), none give the NemoCollection to get the actual motifs, they just count them.

I do not know who to contact for help with this; the original developer of Nemomap, Tien Huynh, no longer works at Bothell; others whom I messaged about the python port, do not really remember how it worked ( since they worked on it more than 2 years ago )..

Thank you in advance for your input !

zicanl commented 3 years ago

Could you please share your input about running NemoMapPy? You have to run NemoMap first before clicking NemoCollection, otherwise, the file will be wrong. If you are looking for the all subgraph collection, you should try this website https://bioresearch.css.uwb.edu/biores/nemo/, with the NemoCollection mode.

gabipana7 commented 2 years ago

Are you by any chance one of the authors/developers of the original article/web app ? I appreciate the help with accesing the NemoSuite wep app, but we would like more than that, we would like to have access to the python (if possible) source code for the motif discovery.

What is available on GitHub, in my experience, only counts the motifs in a graph, but we also want to identify each of the motifs by their nodes (as the webapp did while it was still running, now it seems the website is down ) so we would really find use of the source code of that app in order to run it on our machines !

zicanl commented 2 years ago

Hi, you may contact my director, Dr. Wooyoung Kim. She is the author of NemoSuite app, and here is her website http://faculty.washington.edu/kimw6/