Genemania CyREST call stalled for over 30 mins

[nivedas...@gmail.com]

Hi,

I am using Cytoscape's CyREST API call to run genemania for a list of about 750 genes. I see that for the same dataset Genemania regularly stalls for over 30 mins. This is a random occurrence as the dataset has previously run in about 12-14 mins.

I use the below script for the API call:

'''
join_genes = '|'.join(each_inp_list)

body = dict(attrLimit=str(att_limit), geneLimit=str(limit), genes=join_genes, organism=species)

get_genemania = requests.post('http://localhost:1234/v1/commands/genemania/search', json=body)
uploaded_list = get_genemania.json()
'''

where join_genes = input gene list separated by '|'
att_limit = 0
limit = 100
species = rat

Is there a way to improve performance? Can I change the API call in anyway for this improvement?

Thanks!

[Ruth Isserlin]

By default, the genemania command will search the web version of genemania.  Maybe the random slow down is related to slower network traffic at the time that you do your search.  Have you tried downloading the genemania Rat dataset to your computer and then adding offline=true to the above command to see if it eliminates the stalling?

Thanks, 

Ruth 

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[nivedas...@gmail.com]

Thanks! That does seem to be the cause of the delay