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saezlab / cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://saezlab.github.io/cosmosR/
GNU General Public License v3.0
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CBC version #37

Open an-altosian opened 4 months ago

an-altosian commented 4 months ago

Hello,

Could you please specify the CBC version COSMOS uses? I tried to download the latest version, AMPL/cbc Optimizer [2.10.10] (Linux x86_64), driver(20240529), MP(20240529), but I got Error: invalid option '-import' Error in file(file, "rt") : cannot open the connection

Thanks.

an-altosian commented 4 months ago

Ok it seems like we the executables provided by AMPL don't work. I have to download the binary from source and use the bin/cbc directly. Also, LD_LIBRARY_PATH has to be specified.

However, cbc failed to run and reported the following error Error in `dplyr::left_join()`: ! Can't join `x$Node2` with `y$nodes` due to incompatible types. ℹ `x$Node2` is a <double>. ℹ `y$nodes` is a <character>.

Not sure what I can do with it. The head lines of the result file is 

$ head result_t00_48_35d19_07_2024n48.csv 
name,solution
aD1,1
aD2,1
nU1,0
nU2,0
nU3,0
nU4,0
nU5,0
nU6,0
nU7,0
adugourd commented 4 months ago

Hi, I would actually advise to use the last version of cosmos that does not require such solvers anymore, should be much simpler to use.

See https://github.com/saezlab/COSMOS_basic for a simple tutorial on how to use the solver free version of cosmos :)

Cheers,

Aurelien

an-altosian commented 4 months ago

First of all thanks for relying all my questions across different threads/repos ;P.

I am still trying to match the results I got from COSMOS_basic to the tutorials listed on the website. It will be great if those tutorials can be updated as well. my immediate question is, should I expect to replace moon with previous backbone functions like preprocess_COSMOS_metabolism_to_signaling+run_COSMOS_metabolism_to_signaling? Do I still need the auxiliary functions like format_COSMOS_res?

adugourd commented 4 months ago

Hi, yes moon replaces those. Best is you just follow the new tutorial :)