Instruction to Evolutionary Constructor script language
The software package “Evolutionary constructor” (EC) provides modeling scenarios with the use of the special script language.
Any scenario of EC model consists of two consequent sections:
1) Model declaration section;
2) Calculation section.
The comment lines may begin with the following symbols: // (C-style), ! (Fortran-style), and % (Matlab-style). The script language is case insensitive.
Model declaration section
This section starts with the declare statement and ends with the end declare statement. The other statements setting up model parameters in the declaration section are shown in the table below (synonyms are also shown if available):
Table 1. Model declaration statements
| Statement | Description/model parameter set up | Example |
| volume | Environmental volume | volume = 1e-1 |
| flow | Flow rate (from 0 to 1.0) | flow = 0.1 |
| nonspec (ns) | Number of non-specific substrates in the model | nonspec = 2 |
| spec (ss) | Number of specific substrates in the model | spec = 3 |
| init_ns
(substrates_ns) |
Initial concentrations of non-specific substrates in environment (list) | init_ns = 1.5e-3, 2e-3 |
| init_ss
(substrates_ss) |
Initial concentrations of specific substrates in environment (list of comma-separated values) | init_ss = 0.1,0.2,0.3 |
| inflow_ns
(comsub) |
Concentration of non-specific substrates in the in-flow (list of comma-separated pairs – substrate number:substrate concentration) | inflow_ss = 1:0.1, 4:0.2 |
| mut_probability
(mut_prob) |
Mutation probability | mut_prob = 1e-8 |
| hgt_probability (hgt_prob) | Horizontal gene transfer probability | hgt_prob = 1e-10 |
| population
(pop, p) |
Opens the population declaration section (see Table 2) | pop = 1 |
| end population
(end pop, end p) |
Closes the population declaration section (see Table 2) | end pop |
Each population in the declaration section is given by the particular subsection. That subsection is opened with population (pop, p) statement, and is closed with end_population (end pop, end p) statement. The only parameter of pop statement is the number of population. The statements setting up population’s parameters are listed in the Table 2:
Table 2. Population declaration statements
| Statement | Description/model parameter set up | Example |
| size | Initial size of a population | size = 4e+8 |
| increaser
(strategy, trophic) |
Trophic strategy of a population (argument is the name of strategy, for example, rubel, liebig, inhibitory, chaotic etc.) | increaser = rubel |
| k_death | Death parameter | k_death = 1e-30 |
| k_flow | Flow parameter | k_flow = 0.05 |
| cprod | Synthesis ratio for specific products | cprod = 1e+5 |
| ccons_nsp
(ccons_ns) |
Utilization ratio for non-specific substrates | ccons_nsp = 1e+7 |
| ccons_sp
(ccons_ss) |
Utilization ratio for specific substrates | ccons_sp = 1e+5 |
| genes_n | Adds a new gene of non-specific substrate utilization to the generalized genome of a population. Arguments: substrate number : list of alleles values : list of alleles frequencies in a population | genes_n = 1;
allele_values:3,5,6; allele_concentrations: 0.1,0.6,0.3 |
| genes_s | Adds a new gene of specific substrate utilization to the generalized genome of a population. Arguments: substrate number : list of alleles values : list of alleles frequencies in a population | genes_s = 2;
allele_values:3,5,6; allele_concentrations: 0.1,0.6,0.3 |
| genes_p | Adds a new gene of specific substrate synthesis to the generalized genome of a population. Arguments: substrate number : list of alleles values : list of alleles frequencies in a population | genes_p = 3;
allele_values:3,5,6; allele_concentrations: 0.1,0.6,0.3 |
The actual values of traits determining corresponding utilization rates, i.e. ri and ci, (see Trophic strategies description) are calculated as a quotient of the following parameters: fixed component – utilization ratio (ccons_ns, ccons_ss) and variable components taken from allele_values list in genes_n and genes_s statements.
The actual values of traits determining corresponding synthesis rates, i.e. di (see Metabolism simulation description) are calculated as a product of analogical parameters: fixed component – synthesis ratio (cprod), and variable one set up with genes_p statement.
The example below demonstrates the description of a monomorphic (with relation to utilization of the substrate S1) population, the actual c1 parameter value of which is equal to 2×10-5 (it means that one cell division takes 2×105 of substrate molecules):
pop = 1
ccons_sp = 1e+5
genes_s=1;allele_values:2;allele_concentrations:1.0
// Other parameters of the population
end pop
Model calculation section
Calculation section starts immediately after end declare statement. The statements of this section are listed in the table below:
Table 3 Model calculation statements
| Statement | Description/model parameter set up | Example |
| iterate | Iterate n simulation steps (n is argument). Stochastic operations (mutations, horizontal transfer etc.) are not permitted. | iterate = 400 |
| stochastic (s_iterate) | Iterate n simulation steps (n is argument). Stochastic operations are permitted – possible events are regulated by corresponding probabilities. | stochastic = 400 |
| mutation
(mut) |
Perform mutation in one (or more) cells in a population. Detailed description of this statement is in the text below. | Description is in the text below |
| horizontal_transfer
(ht, hgt) |
Perform horizontal transfer of a gene from a cell of donor population into a cell of acceptor population. Detailed description of this statement is in the text below. | Description is in the text below |
| set_nssc
(set_ns) |
Change the concentration of non-specific substrate in the in-flow. Arguments: substrate number: new concentration | set_ns=1 : 0.5 |
| set_flow
(set_f) |
Change flow rate (the argument range is from 0 to 1) | set_flow = 0.2 |
| buffer_on | Fix concentration(s) of some substrate(s) in environment on a certain level regardless of flow or populations action. Arguments: substrate type (possible values N, S): substrate number : concentration | buffer_on=S:1:0.7 |
| buffer_off | Cancel buffer_on command. Arguments: substrate type (possible values N, S): substrate number | buffer_off=S:1 |
| ns_pattern | Set series of in-flow concentrations for a certain non-specific substrate alternating in time periods, and durations of those periods. Arguments: substrate number; list of concentrations; list of duration periods | ns_pattern = 1;
concentrations:0.1,2,0; durations:10,20,300 |
Mutation statement
The statement mutation (mut) causes the mutation in cell(s) of a population:
mutation= pop:1; gene_type:n; sub_num:0; from:1.0; to:7.0; count:0.01
where
pop – population number;
gene_type – type of a gene to be mutated (possible values: n, s, p);
sub_num – number of substrate corresponding with the mutant gene;
from – initial trait value (only cells having trait of this particular value will mutate);
to – mutant trait value (mutant cells will have this trait value);
count (unnecessary parameter) – fraction of mutants in a whole population. If this parameter missed, the fraction is chosen automatically to get the minimal size of the mutant subpopulation (acceptable with regard to computational accuracy or special parameter).
Horizontal_transfer statement
The statement horizontal_transfer (ht, hgt) causes the horizontal transfer of gene(s) from a cell of donor population into a cell of acceptor population:
hgt=acceptor:2; donor:1; gene_type:n; sub_num:1,2; gene_type:s; sub_num:1,3,4,..; p_size:1e+1; allele:greatest|lowest:1
where
acceptor – acceptor population number;
donor – donor population number;
gene_type – type of transferred gene(s) (possible values: n, s, p);
sub_num – list of numbers of transferred genes;
p_size (unnecessary parameter) – subpopulation size (number of cells incurred horizontal gene transfer). If this parameter missed, the automatically set size is the minimal with regard to computational accuracy or special parameter;
allele (unnecessary parameter) – set the rule of allele selection (for the transfer) and the number of allele in cell(s) (in the order defined with selection rule) of the donor population. Possible values for selection rule: greatest or lowest, determine, whether maximal or minimum trait-valued alleles will be transferred. If this parameter missed, the most presented (in the donor population) allele will be selected for transfer.
Note: it is possible to transfer genes of all types simultaneously per one horizontal gene transfer. To achieve this it is necessary to specify lists of transferred genes in such a manner: point out gene type followed by list of genes numbers, then another gene type followed by list of genes numbers etc (see the example above).