EASME.CORE:EXPERIMENT
An EASME experiment applies evolutionary algorithms to protein sequences, iterating through cycles of selection, recombination, and mutation to optimize toward fitness objectives. Each experiment is defined by a configuration that specifies the input proteins, algorithm parameters, and fitness criteria.
To run an experiment: select a configuration below, choose a target system, review the staging details, and execute. The workflow guides you through each step.
Experiments
No registered experiments found. Use the Designer to create one.
Core Operations Reference
20 operations across 6 categories — loaded from EASME.DATA.REGISTRY
Fitness (3)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
calculate_fitness |
experiment | protein, goals, antigoals, fitness_function, targets | evaluate protein fitness using specified fitness function |
calculate_fitness_from_alignment |
experiment | goals, antigoals | calculate fitness based on alignment with goal proteins vs antigoal proteins |
length_penalty |
experiment | observed, target | calculate penalty score based on sequence length deviation from target |
Mutation (7)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
mutate_protein |
experiment | alter_length | apply random mutation (insertion, substitution, or deletion) to protein dna sequence |
insert_sequence |
experiment | dna_sequence, insert_length, random | insert a random or specified subsequence into dna at random position |
substitute_sequence |
experiment | dna_sequence, alter_length, contiguous, allow_premature_stop | substitute nucleotides in dna sequence at random position |
delete_sequence |
experiment | dna_sequence, delete_length | delete nucleotides from dna sequence at random position |
frameshift |
experiment | count | cause random frameshift mutation (insertion/deletion not multiple of 3) changing reading frame |
inframe |
experiment | count | cause random in-frame mutation (insertion/deletion multiple of 3) preserving reading frame |
mutate_amino_acids |
experiment | alter_length, contiguous | substitute random amino acids in protein sequence directly |
Protein Creation (1)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
create_protein |
formulate | dna_sequence, amino_acid_sequence | create a new protein object from dna or amino acid sequence |
Recombination (2)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
crossover_point |
experiment | parents_sequences, parents | recombine two parent sequences at random crossover point |
uniform_crossover |
experiment | parents_sequences, parents, swap_probability | create offspring by selecting each allele randomly from either parent |
Selection (6)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
select_uniform_random |
experiment | n | select n parents uniformly at random from population (with replacement) |
k_tournament_with_replacement |
experiment | n, k | select n parents using k-tournament selection where parents may be selected more than once |
fitness_proportionate_selection |
experiment | n | select n parents with probability weighted by fitness (roulette wheel) |
stochastic_universal_sampling |
experiment | n | select n parents using evenly spaced pointers on fitness wheel for less bias |
truncation |
experiment | n | select the n most fit individuals from the population (survival selection) |
k_tournament_without_replacement |
experiment | n, k, elitism | select n survivors using k-tournament where each individual can only be selected once |
Simulation (1)
| Operation | Stage | Parameters | Description |
|---|---|---|---|
thermostability_eval |
experiment | pdb_file, temperature, timestep, duration, random_seed | evaluate protein thermostability via molecular dynamics simulation at multiple temperatures |