convert_org_into_seq |
Converts a genome instruction sequence into a digital organism file |
convert_seq_into_org |
Converts a genome instruction sequence into a digital organism file |
get_db_summary |
Get database summary |
get_docker_image_from_experiment_id |
Get docker image from experiment |
get_doi_from_experiment_id |
Get doi from experiment |
get_experiment_id_from_organism_id |
Get experiment from organism |
get_genome_id_from_genome_seq |
Get genome from genome sequence |
get_genome_id_from_logic_operation |
Get genome from logic operations |
get_genome_id_from_phenotype_id |
Get genome from phenotype |
get_genome_id_from_transcriptome_id |
Get genome from transcriptome |
get_genome_id_of_wild_type_organisms |
Get genomes of wild-type organisms |
get_genome_seq_from_genome_id |
Get genome sequence from genome |
get_logic_operation_from_phenotype_id |
Get the logic operations computed by a digital organism whose genome encodes a specific phenotype |
get_mutant_at_pos |
Get single-point mutants of wild-type organisms |
get_phenotype_id_from_genome_id |
Get phenotype from genome |
get_phenotype_id_from_genome_seq |
Get phenotype from genome sequence |
get_phenotype_id_from_logic_operation |
Get phenotype from logic operations |
get_phenotype_id_from_transcriptome_id |
Get phenotype from transcriptome |
get_tandem_id_from_genome_id |
Get tandem repeat from genome |
get_tandem_id_from_genome_seq |
Get tandem repeat from genome sequence |
get_tandem_id_from_logic_operation |
Get tandem repeat from logic operations |
get_tandem_id_from_phenotype_id |
Get tandem repeat from phenotype |
get_tandem_seq_from_tandem_id |
Get the tandem repeat sequence from tandem repeat |
get_transcriptome_id_from_genome_id |
Get transcriptome from genome |
get_transcriptome_id_from_genome_seq |
Get transcriptome from genome sequence |
get_transcriptome_id_from_logic_operation |
Get transcriptome from logic operations |
get_transcriptome_id_from_phenotype_id |
Get transcriptome from phenotype |
get_transcriptome_seq_from_transcriptome_id |
Get transcriptome sequence from transcriptome |
instruction_set |
Get the genetic language of Avida |
logic_operation |
Get the list of logic operations that a digital organism can compute |
plot_transcriptome |
Get a plot of the transcriptome as a chord diagram |
triplestore_access |
Class to manage triplestore access options |