Load some simple bio-networks

[itsyosef]

Hi all! Just following up from our discussion today. Here is a google doc detailing the types of graphs we have been working with. Specific summaries of the example graphs on Rivanna are included at the top.

Was an action item for Andrew and I to convert these graphs into a format suitable for the current state of CINES? I wrote down PNEANet as a format that may work for this, is that correct?

Thanks! Joseph

[dmachi]

I believe @cckuhlman was suggesting that we explore generating some unlabeled versions of these networks (just edgelists) that would be useful for users who are doing generic network science work. So that would be either a PUNGraph (undirected) or PNGraph (directed). PNEANet is also a possibility.

[itsyosef]

Ok, y'all should be able to access the example graphs in edgelist format (saved from SNAP PUN/PNGraph) at /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/Acaryochloris_gids_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/first_pass_split_0_train_with_pfams_processed_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/LA_County_2020-03-12_2020-03-18_PNGraph_edgelist.txt

[dmachi]

Thanks. I confirmed I can access these. I will get them added to the system soon.

On Jul 30, 2021, at 12:37 PM, Joseph Outten @.***> wrote:

Ok, y'all should be able to access the example graphs in edgelist format (saved from SNAP PUN/PNGraph) at /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/Acaryochloris_gids_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/first_pass_split_0_train_with_pfams_processed_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/LA_County_2020-03-12_2020-03-18_PNGraph_edgelist.txt

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[cckuhlman]

Hey Joseph and Andrew:

How hard would it be to make up about 20 graphs in total?

I'm thinking of the report and stating that we have these graphs. It would be better if we had more than 3. I think something around 20 would be good, and then we can re-evaluate when the graph ingestion system is up and running.

But I do not know the difficulty in what I'm asking for. Is 20 graphs a big pain?

chris

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From: Dustin Machi @.> Sent: Tuesday, August 3, 2021 9:49 AM To: NSSAC/CINES @.> Cc: kuhlman, chris (cjk8gx) @.>; Mention @.> Subject: Re: [NSSAC/CINES] Load some simple bio-networks (#240)

Thanks. I confirmed I can access these. I will get them added to the system soon.

On Jul 30, 2021, at 12:37 PM, Joseph Outten @.***> wrote:

Ok, y'all should be able to access the example graphs in edgelist format (saved from SNAP PUN/PNGraph) at /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/Acaryochloris_gids_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/first_pass_split_0_train_with_pfams_processed_PUNGraph_edgelist.txt /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/LA_County_2020-03-12_2020-03-18_PNGraph_edgelist.txt

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[itsyosef]

Hey Chris.

Not a problem at all. We have a few hundred graphs like the Acaryochloris_gids_PUNGraph_edgelist.txt from different example genomes of different genera. I should be able to get ~20 of those to you in the same format in the next day or so.

[itsyosef]

Chris and Dustin,

I've added 30 more graphs to the folder. The edgelists are at /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/edgelists. Let me know if I can do anything else for this/if anything needs clarification.

[cckuhlman]

Hey Joseph:

Thanks for the networks.

I assume that the metadata for these graphs are in:

/project/biocomplexity/jho5ze/bionetworks/example_graphs/metadata

Thanks a lot.

chris

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From: Joseph Outten @.> Sent: Wednesday, August 4, 2021 11:56 AM To: NSSAC/CINES @.> Cc: kuhlman, chris (cjk8gx) @.>; Mention @.> Subject: Re: [NSSAC/CINES] Load some simple bio-networks (#240)

Chris and Dustin,

I've added 30 more graphs to the folder. The edgelists are at /sfs/qumulo/qproject/biocomplexity/jho5ze/bionetworks/example_graphs/edgelists. Let me know if I can do anything else for this/if anything needs clarification.

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[itsyosef]

That's right! Just wanted to clean it up a bit