Snorre Sulheim
Snorre Sulheim
It would be very nice if it was possible to change the bigg_ids directly in the map. The reason for this is that I reuse old maps to draw one...
#### Problem description The title says it all: It would be nice if memote could recognize a reaction annotated with SBO:0000630 as the NGAM - reaction. http://www.ebi.ac.uk/sbo/main/display?sboId=SBO:0000630 System Information ==================...
#### Problem description It is not obvious from the current documentation what the keys "data" and "metric" are used for and what the difference is in the current documentation. I...
Information on how accurately the Kcat-values extracted from BRENDA is matched to the chosen organism is important metadata. While it is possible to get this information by running run lines...
Not super-important, but I suggest to rescale the biomass equations so they sum exactly to 1 :) The one for bacteria sums to 1.03
The threshold for when pathways are considered complete seems to be hardcoded into the R scripts. Would it be possible to make this an input parameter so that it can...
A simple question. I use the albacore output directory as input folder for porechop, but then the failed reads seemes to be included. Should i only use the "pass" folder...
Reframed currently only parses the human readable part of the annotations in an SBML model file. ## Example ``` model = reframed.load_cbmodel('bigg_universe.xml') print(model.reactions.R_G1PP.metadata) OrderedDict([('SBOTerm', 'SBO:0000176'), ('XMLAnnotation', '\n \n \n \n...