Skills › Scientific Agent Skills › 13c-metabolic-flux › branch-model.json
branch-model.json
122 lines · skills/13c-metabolic-flux/assets/branch-model.json at 5f2bc03
1{
2 "schema_version": 1,
3 "name": "Two-route positional-label demonstration",
4 "flux_unit": "relative units; uptake fixed to 100",
5 "provenance": "Original analytical demonstration. Generic carbon rearrangement, not an organism-specific pathway.",
6 "metabolites": [
7 {
8 "id": "S",
9 "carbons": 2,
10 "boundary": "source",
11 "symmetric": false
12 },
13 {
14 "id": "A",
15 "carbons": 2,
16 "boundary": "internal",
17 "symmetric": false
18 },
19 {
20 "id": "B",
21 "carbons": 2,
22 "boundary": "internal",
23 "symmetric": false
24 },
25 {
26 "id": "Out",
27 "carbons": 2,
28 "boundary": "sink",
29 "symmetric": false
30 }
31 ],
32 "reactions": [
33 {
34 "id": "uptake",
35 "substrates": [
36 [
37 "S",
38 "AB"
39 ]
40 ],
41 "products": [
42 [
43 "A",
44 "AB"
45 ]
46 ],
47 "lower": 0.001,
48 "upper": 200,
49 "fixed": 100
50 },
51 {
52 "id": "straight",
53 "substrates": [
54 [
55 "A",
56 "AB"
57 ]
58 ],
59 "products": [
60 [
61 "B",
62 "AB"
63 ]
64 ],
65 "lower": 0.001,
66 "upper": 300
67 },
68 {
69 "id": "swap",
70 "substrates": [
71 [
72 "A",
73 "AB"
74 ]
75 ],
76 "products": [
77 [
78 "B",
79 "BA"
80 ]
81 ],
82 "lower": 0.001,
83 "upper": 300
84 },
85 {
86 "id": "export",
87 "substrates": [
88 [
89 "B",
90 "AB"
91 ]
92 ],
93 "products": [
94 [
95 "Out",
96 "AB"
97 ]
98 ],
99 "lower": 0.001,
100 "upper": 300
101 }
102 ],
103 "fragments": [
104 {
105 "id": "Bfirst",
106 "metabolite": "B",
107 "carbons": [
108 1
109 ],
110 "provenance": "Synthetic position-specific carbon-1 measurement; not an experimentally established fragment assignment."
111 },
112 {
113 "id": "Bwhole",
114 "metabolite": "B",
115 "carbons": [
116 1,
117 2
118 ],
119 "provenance": "Synthetic complete two-carbon pool measurement."
120 }
121 ]
122}