natural_constants/
biology.rs

1//! Biology related constants
2//!
3//! Taken from http://bionumbers.hms.harvard.edu/search.aspx?task=searchbypop
4//!
5//! Every organism is it's own module, so we don't have overlapping values.
6//!
7//! TODO: Needs some more documentation and usage examples
8
9mod generic {
10    pub struct BioInfo {
11        pub value: Option<f64>,
12        pub value_min: Option<f64>,
13        pub value_max: Option<f64>,
14    }
15}
16
17pub mod human_homo_sapiens {
18    pub struct BioInfo {
19        pub value: Option<f64>,
20        pub value_min: Option<f64>,
21        pub value_max: Option<f64>,
22    }
23
24    /// [kb / min]
25    pub const rate_dna_replication: BioInfo = BioInfo {
26        value: Some(2.0),
27        value_min: Some(0.0),
28        value_max: Some(2.0),
29    };
30
31    /// [kb]
32    pub const spacing_between_origins_dna_replication: BioInfo = BioInfo {
33        value: Some(100.0),
34        value_min: None,
35        value_max: None,
36    };
37
38    /// [µm]
39    pub const diameter_hek_293_cell: BioInfo = BioInfo {
40        value: Some(13.0),
41        value_min: None,
42        value_max: None,
43    };
44}
45
46pub mod unspecified {
47    pub struct BioInfo {
48        pub value: Option<f64>,
49        pub value_min: Option<f64>,
50        pub value_max: Option<f64>,
51    }
52
53    /// [nm]
54    pub const excitation_maximum_of_rfp: BioInfo = BioInfo {
55        value: Some(587.0),
56        value_min: None,
57        value_max: None,
58    };
59} /* unspecified */
60
61pub mod bacteria_escherichia_coli {
62    pub struct BioInfo {
63        value: Option<f64>,
64        value_min: Option<f64>,
65        value_max: Option<f64>,
66    }
67
68    /// mM
69    pub const affinity_of_allolactose_and_lacz: BioInfo = BioInfo {
70        value: Some(1.9),
71        value_min: None,
72        value_max: None,
73    };
74
75    /// μM
76    pub const affinity_of_allolactose_and_laci: BioInfo = BioInfo {
77        value: Some(6.0),
78        value_min: None,
79        value_max: None,
80    };
81
82    /// Molecules / minute
83    pub const velocity_of_allolactose_hydrolysis_by_lacz: BioInfo = BioInfo {
84        value: Some(20_000.0),
85        value_min: None,
86        value_max: None,
87    };
88
89    /// µM
90    pub const maximal_amount_of_lacy: BioInfo = BioInfo {
91        value: Some(50.0),
92        value_min: None,
93        value_max: None,
94    };
95
96    /// µM
97    pub const maximal_amount_of_lacz: BioInfo = BioInfo {
98        value: Some(50.0),
99        value_min: None,
100        value_max: None,
101    };
102
103    /// µM
104    pub const total_amount_of_laci_repressor: BioInfo = BioInfo {
105        value: Some(0.01),
106        value_min: None,
107        value_max: None,
108    };
109
110    /// %
111    pub const percent_of_cell_total_dry_weight_that_is_lipopolysaccharide: BioInfo = BioInfo {
112        value: Some(3.4),
113        value_min: None,
114        value_max: None,
115    };
116
117    /// Unitless
118    pub const number_of_proteins_in_50s_subunit: BioInfo = BioInfo {
119        value: Some(36.0),
120        value_min: None,
121        value_max: None,
122    };
123
124    /// Unitless
125    pub const number_of_proteins_in_30s_subunit: BioInfo = BioInfo {
126        value: Some(22.0),
127        value_min: None,
128        value_max: None,
129    };
130
131    /// Unitless
132    pub const number_of_protein_types_to_make_ribosome: BioInfo = BioInfo {
133        value: Some(56.0),
134        value_min: None,
135        value_max: None,
136    };
137
138    /// Unitless
139    pub const number_of_lipids_per_cell: BioInfo = BioInfo {
140        value: Some(22000000.0),
141        value_min: None,
142        value_max: None,
143    };
144
145    /// Unitless
146    pub const number_of_lipopolysaccharide_per_cell: BioInfo = BioInfo {
147        value: Some(1430000.0),
148        value_min: None,
149        value_max: None,
150    };
151
152    /// Unitless
153    pub const number_of_all_rna_per_cell: BioInfo = BioInfo {
154        value: Some(255000.0),
155        value_min: None,
156        value_max: None,
157    };
158
159    /// %
160    pub const volume_occupied_by_water: BioInfo = BioInfo {
161        value: Some(70.0),
162        value_min: None,
163        value_max: None,
164    };
165
166    /// µm^2/sec
167    pub const apparent_diffusion_constant_of_protein_along_dna_segments: BioInfo = BioInfo {
168        value: Some(0.4),
169        value_min: Some(0.38),
170        value_max: Some(0.42),
171    };
172
173    /// Molecules / cell
174    pub const reca_molecules_per_cell: BioInfo = BioInfo {
175        value: Some(1000.0),
176        value_min: Some(800.0),
177        value_max: Some(1200.0),
178    };
179
180    /// µmol / g
181    pub const imp_pool_size: BioInfo = BioInfo {
182        value: Some(0.38),
183        value_min: Some(0.37),
184        value_max: Some(0.39),
185    };
186
187    /// µmol / g
188    pub const carbamoyl_aspartate_pool_size: BioInfo = BioInfo {
189        value: Some(0.84),
190        value_min: Some(0.56),
191        value_max: Some(1.12),
192    };
193
194    /// µmol / g
195    pub const valine_pool_size: BioInfo = BioInfo {
196        value: Some(2.41),
197        value_min: Some(2.14),
198        value_max: Some(2.68),
199    };
200
201    /// µmol / g
202    pub const tyrosine_pool_size: BioInfo = BioInfo {
203        value: Some(0.41),
204        value_min: Some(0.16),
205        value_max: Some(0.66),
206    };
207
208    /// µmol / g
209    pub const threonine_pool_size: BioInfo = BioInfo {
210        value: Some(1.34),
211        value_min: Some(1.50),
212        value_max: Some(1.18),
213    };
214
215    /// µmol / g
216    pub const proline_pool_size: BioInfo = BioInfo {
217        value: Some(1.1),
218        value_min: Some(0.95),
219        value_max: Some(1.25),
220    };
221
222    /// µmol / g
223    pub const methionine_pool_size: BioInfo = BioInfo {
224        value: Some(0.29),
225        value_min: Some(0.22),
226        value_max: Some(0.36),
227    };
228
229    /// µmol / g
230    pub const aspartate_pool_size: BioInfo = BioInfo {
231        value: Some(6.45),
232        value_min: Some(9.9),
233        value_max: Some(2.91),
234    };
235
236    /// µmol / g
237    pub const asparagine_pool_size: BioInfo = BioInfo {
238        value: Some(2.02),
239        value_min: Some(1.56),
240        value_max: Some(2.48),
241    };
242
243    /// µmol / g
244    pub const alanine_pool_size: BioInfo = BioInfo {
245        value: Some(6.81),
246        value_min: Some(5.102),
247        value_max: Some(8.51),
248    };
249
250    /// µmol / g
251    pub const glutamate_pool_size: BioInfo = BioInfo {
252        value: Some(100.55),
253        value_min: Some(83.001),
254        value_max: Some(118.09),
255    };
256
257    /// µmol / g
258    pub const glutamine_pool_size: BioInfo = BioInfo {
259        value: Some(3.92),
260        value_min: Some(3.75),
261        value_max: Some(4.09),
262    };
263
264    /// fg
265    pub const mass_in_excess_of_displaced_buffer: BioInfo = BioInfo {
266        value: Some(110.0),
267        value_min: Some(80.0),
268        value_max: Some(140.0),
269    };
270
271    /// nm
272    pub const outer_membrane_thickness: BioInfo = BioInfo {
273        value: Some(13.0),
274        value_min: Some(12.0),
275        value_max: Some(14.0),
276    };
277
278    /// µm^3
279    pub const cell_total_volume: BioInfo = BioInfo {
280        value: Some(1.1),
281        value_min: Some(0.44),
282        value_max: Some(1.79),
283    };
284
285    /// [µm]
286    pub const concentration_pyruvate: BioInfo = BioInfo {
287        value: Some(390.0),
288        value_min: None,
289        value_max: None,
290    };
291
292    /// [g / liter]
293    pub const ratio_cell_dry_weight: BioInfo = BioInfo {
294        value: Some(0.36),
295        value_min: None,
296        value_max: None,
297    };
298} /* bacteria_escherichia_coli */
299
300pub mod chinese_hamster_ovary {
301    pub struct BioInfo {
302        pub value: Option<f64>,
303        pub value_min: Option<f64>,
304        pub value_max: Option<f64>,
305    }
306
307    /// [µm]
308    pub const diameter_cell: BioInfo = BioInfo {
309        value: None,
310        value_min: Some(14.02),
311        value_max: Some(15.21),
312    };
313
314} /* chinese_hamster_ovary */
315
316pub mod budding_yeast_saccharomyces_cerevisiae {
317    pub struct BioInfo {
318        pub value: Option<f64>,
319        pub value_min: Option<f64>,
320        pub value_max: Option<f64>,
321    }
322
323    /// [pg / cell]
324    pub const mass_protein_diploid_cell: BioInfo = BioInfo {
325        value: Some(8.0),
326        value_min: None,
327        value_max: None,
328    };
329} /* budding_yeast_saccharomyces_cerevisiae  */
330
331pub mod green_algae_chlorella_vulgaris {
332    pub struct BioInfo {
333        pub value: Option<f64>,
334        pub value_min: Option<f64>,
335        pub value_max: Option<f64>,
336    }
337
338    /// [µm]
339    pub const size_diameter_green_algea: BioInfo = BioInfo {
340        value: Some(3.0),
341        value_min: Some(2.0),
342        value_max: Some(4.0),
343    };
344} /* green_algae_chlorella_vulgaris */
345
natural_constants/biology.rs

natural_constants/
biology.rs
