chemart / brane-calculi
View on GitHubBrane calculi — Membranes as the active element rather than the container. A system is a nest of membranes, and each membrane carries a program of actions: phagocytosis engulfs a neighbour, exocytosis expels contents and fuses, pinocyto…
{"species": [{"id": "!coexo|!cophago(mate)[!coexo|!comate[],Z],phago.exo[X|!bud[vRNA]]", "structure": "membrane !coexo|!cophago(mate)\n membrane !coexo|!comate\n Z\nmembrane phago.exo\n membrane X|!bud\n vRNA"}, {"id": "!coexo|!cophago(mate)[!coexo|!comate[],Z,mate[exo[X|!bud[vRNA]]]]", "structure": "membrane !coexo|!cophago(mate)\n membrane !coexo|!comate\n Z\n membrane mate\n membrane exo\n membrane X|!bud\n vRNA"}, {"id": "!coexo|!cophago(mate)[!coexo|!comate[exo[X|!bud[vRNA]]],Z]", "structure": "membrane !coexo|!cophago(mate)\n membrane !coexo|!comate\n membrane exo\n membrane X|!bud\n vRNA\n Z"}, {"id": "!coexo|!cophago(mate)[!coexo|!comate[],X|!bud[vRNA],Z]", "structure": "membrane !coexo|!cophago(mate)\n membrane !coexo|!comate\n membrane X|!bud\n vRNA\n Z"}], "reactions": [{"reactants": {"!coexo|!cophago(mate)[!coexo|!comate[],Z],phago.exo[X|!bud[vRNA]]": 1}, "products": {"!coexo|!cophago(mate)[!coexo|!comate[],Z,mate[exo[X|!bud[vRNA]]]]": 1}, "rate": null, "count": null}, {"reactants": {"!coexo|!cophago(mate)[!coexo|!comate[],Z,mate[exo[X|!bud[vRNA]]]]": 1}, "products": {"!coexo|!cophago(mate)[!coexo|!comate[exo[X|!bud[vRNA]]],Z]": 1}, "rate": null, "count": null}, {"reactants": {"!coexo|!cophago(mate)[!coexo|!comate[exo[X|!bud[vRNA]]],Z]": 1}, "products": {"!coexo|!cophago(mate)[!coexo|!comate[],X|!bud[vRNA],Z]": 1}, "rate": null, "count": null}], "status": "complete", "initial_state": {"!coexo|!cophago(mate)[!coexo|!comate[],Z],phago.exo[X|!bud[vRNA]]": 1.0}, "inflow": null, "outflow": null, "extras": {"system": "viral-infection", "program": "# Cardelli 2004, section 3.3 (Semliki Forest virus)\nvirus := phago.exo[nucap]\nnucap := !bud|X[vRNA]\ncell := membrane[cytosol]\nmembrane := !cophago(mate)|!coexo\ncytosol := endosome, Z\nendosome := !comate|!coexo[]\nviral-envelope := cobud(phago.exo)\nenvelope-vesicle := exo.viral-envelope[]\nmain := virus, cell\n", "definitions": {"virus": "phago.exo[nucap]", "nucap": "!bud|X[vRNA]", "cell": "membrane[cytosol]", "membrane": "!cophago(mate)|!coexo", "cytosol": "endosome, Z", "endosome": "!comate|!coexo[]", "viral-envelope": "cobud(phago.exo)", "envelope-vesicle": "exo.viral-envelope[]", "main": "virus, cell"}, "main": "!coexo|!cophago(mate)[!coexo|!comate[],Z],phago.exo[X|!bud[vRNA]]", "reaction_rules": ["phago", "mate", "exo"], "compartments": {"representation": "each species is a whole configuration (canonical nested-membrane text); this is the membrane tree of the initial one", "initial": [{"membrane": "!coexo|!cophago(mate)", "contents": [{"membrane": "!coexo|!comate", "contents": [], "copies": 1}, {"molecule": "Z", "copies": 1}], "copies": 1}, {"membrane": "phago.exo", "contents": [{"membrane": "X|!bud", "contents": [{"molecule": "vRNA", "copies": 1}], "copies": 1}], "copies": 1}]}, "analysis": {"membranes_initial": 4, "infection (fig. 7)": {"configuration": "!coexo|!cophago(mate)[!coexo|!comate[],X|!bud[vRNA],Z]", "reached": true}, "terminal": ["!coexo|!cophago(mate)[!coexo|!comate[],X|!bud[vRNA],Z]"]}}, "chemistry": "brane-calculi", "params": {"system": "viral-infection", "program": "", "max_species": 1000}, "seed": 1}