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ecell / ecell4

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
https://ecell4.e-cell.org/
GNU General Public License v3.0
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DataSource module for modeling in cooperation with databases #40

Open kaizu opened 8 years ago

kaizu commented 8 years ago 
with reaction_rules():
    for pathway in ecocyc().all_pathways():
        for gene in ecocyc().genes_of_pathway(pathway):
            for enzyme in ecocyc().enzymes_of_gene(gene):
                ~gene > enzyme | k

http://bioinformatics.ai.sri.com/ptools/ptools-fns.html

from operator import add
from functools import reduce, partial
join = partial(reduce, add)

with reaction_rules():
    for r, p, k in biomodels('BIOMD0000000019').reactions():
        join(r) > join(p) | k

https://www.ebi.ac.uk/biomodels-main/BIOMD0000000019

kozo2 commented 8 years ago

references

VCell Pathway Commons Tutorial Database Sources in VCell 6.0 (Beta) help

kozo2 commented 8 years ago

datasets

tasklist