Max component size can not be changed in FBMN workflow

[IngvildRyde]

Hi

Thank you for GNPS2! :)

I have a problem.

When I run a task with the parameter setting "Max Component Size" set to 150, the task runs without any error messages and I can see under the "Workflow Task Parameters" that it has used 150 as max component size. However, when I open the network in the molecular network browser and go to "ReCompute network", it is listed as having a max component size of 100. If I then re-compute with 150 max component size my network changes in the network browser. Similarly, if I "Download Network with Singletons GraphML" or "Export Network in Cytoscape with Singletons", the network with 100 max component size is imported into Cytoscape. I have not been able to find a way to export my network generated with 150 max component size to Cytoscape.

Can you please help me?

Best wishes,
Ingvild

[mwang87]

I'm not sure if I understand the issue. Does running with 150 max component size not work on GNPS2? Ming

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On Mon, Feb 3, 2025 at 6:46 AM IngvildRyde ***@***.***> wrote: Hi Thank you for GNPS2! :) I have a problem. When I run a task with the parameter setting "Max Component Size" set to 150, the task runs without any error messages and I can see under the "Workflow Task Parameters" that it has used 150 as max component size. However, when I open the network in the molecular network browser and go to "ReCompute network", it is listed as having a max component size of 100. If I then re-compute with 150 max component size my network changes in the network browser. Similarly, if I "Download Network with Singletons GraphML" or "Export Network in Cytoscape with Singletons", the network with 100 max component size is imported into Cytoscape. I have not been able to find a way to export my network generated with 150 max component size to Cytoscape. Can you please help me? Best wishes, Ingvild — Reply to this email directly, view it on GitHub <#887>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXSEAX2KL5O2UO7Z4BB6L2N56NBAVCNFSM6AAAAABWMJERS2VHI2DSMVQWIX3LMV43ASLTON2WKOZSHAZDONZSHAYTMMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[IngvildRyde]

Thank you for your answer

Yes, that is correct. It seems like no matter what value I set the max component size to, GNPS2 uses a max component size of 100. So at the moment, I can't export my GNPS2 files with other than a max component size of 100. This is not optimal for me because it looks like a max component size of 150 is more suitable for my data.

I hope that made it more clear?

Ingvild

[mwang87]

Thanks for the update, yes we'll have to look into it! Ming

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On Tue, Feb 4, 2025 at 5:54 AM IngvildRyde ***@***.***> wrote: Thank you for your answer Yes, that is correct. It seems like no matter what value I set the max component size to, GNPS2 uses a max component size of 100. So at the moment, I can't export my GNPS2 files with other than a max component size of 100. This is not optimal for me because it looks like a max component size of 150 is more suitable for my data. I hope that made it more clear? Ingvild — Reply to this email directly, view it on GitHub <#887 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAXSEBM4DODOECFN2W3ZO32ODBBJAVCNFSM6AAAAABWMJERS2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMZUGAZTONJUGM> . You are receiving this because you commented.Message ID: ***@***.***>

[IngvildRyde]

Thank you

Ingvild