Completed Feature List

1. Organization of biological entities from chromosome, genome (consisting of one or more chromosomes), organism (consisting of one genome), population (consisting of one or more organisms). Reference: Foundational paper; Lim et al., 2010.
2. Random mutation operators - point, insertion, deletion, inversion, duplication, and translocation. Reference: Foundational paper; Lim et al., 2010.
3. Regional (known mutation) mutation operators - point, insertion, deletion, inversion, duplication, and translocation. Reference: Foundational paper; Lim et al., 2010.
4. Separation of background mutation rate and additional (on top of background mutation rate) mutation rate. Reference: Foundational paper; Lim et al., 2010.
5. 32-character random name generated for each organism. Reference: version 1.0.0.
6. Organism status - alive, vitality, parents, age, gender, lifespan, fitness, blood, identity, deme, location, and death reasons. Reference: Foundational paper; Lim et al., 2010; and version 1.0.0.
7. Population freeze and revival. Reference: Foundational paper; Lim et al., 2010.
8. Crossover operator between 2 chromosomes. Reference: Foundational paper; Lim et al., 2010.
9. 3-dimensional cubic/rectangular world of one or more ecological cells. Reference: Foundational paper; Ling, 2012.
10. Rajaraga interpreter to decode/express genome. Reference: Foundational paper; Ling, 2012.
11. Bury and excavate the 3-dimensional world. Reference: Foundational paper; Ling, 2012.
12. Organism status - new identity generated for each organism and descendants. Reference: Example 01.
13. Organism status - location of descendant recorded. Reference: Example 01.
14. Organism status - deme of descendant recorded. Reference: Example 01.
15. List of 29 parameters for a simulation - simulation_name, population_names, population_locations, deployment_code, chromosome_bases, background_mutation, additional_mutation, mutation_type, chromosome_size, genome_size, max_tape_length, clean_cell, interpret_chromosome, max_codon, population_size, eco_cell_capacity, world_x, world_y, world_z, goal, maximum_generations, fossilized_ratio, fossilized_frequency, print_frequency, ragaraja_version, ragaraja_instructions, eco_buried_frequency, database_file, and database_logging_frequency. Reference: Example 01.
16. List of 15 functions for a simulation - organism_movement, organism_location, ecoregulate, update_ecology, update_local, report, fitness, mutation_scheme, prepopulation_control, mating, postpopulation_control, generation_events, population_report, database_report, and deployment_scheme. Reference: Example 01.
17. Simulation parameters - simulation_name to store name of simulation. Reference: Example 01.
18. Simulation parameters - population_names to store one or more population names. Reference: Example 01.
19. Simulation parameters - population_locations to define the centroid location of population(s). Reference: Example 01.
20. Simulation parameters - deployment_code to define how population(s) are deployed into the world. Reference: Example 01.
21. Simulation parameters - chromosome_bases to define allowable characters for use as chromosomal bases. Reference: Example 01.
22. Simulation parameters - background_mutation to define background mutation rate. Reference: Example 01.
23. Simulation parameters - mutation_type to define default type of mutation. Reference: Example 01.
24. Simulation parameters - chromosome_size to define initial size of a chromosome. Reference: Example 01.
25. Simulation parameters - genome_size to define the initial number of chromosome(s) for each organism. Reference: Example 01.
26. Simulation parameters - max_tape_length to define the number of cells to act as cytoplasm. Reference: Example 01.
27. Simulation parameters - clean_cell to define whether a new cytoplasm is needed for each expression. Reference: Example 01.
28. Simulation parameters - interpret_chromosome to define whether the genome is expressed (interpreted by Rajaraga). Reference: Example 01.
29. Simulation parameters - max_codon to define the maximum number of codons to express. Reference: Example 01.
30. Simulation parameters - population_size to define the initial number of organisms for each population. Reference: Example 01.
31. Simulation parameters - eco_cell_capacity to define the initial capacity of each ecological cell. Reference: Example 01.
32. Simulation parameters - world_x, world_y, world_z to define the size of world in x, y, and z coordinates. Reference: Example 01.
33. Simulation parameters - maximum_generations to define the maximum number of generations to simulate. Reference: Example 01.
34. Simulation parameters - fossilized_ratio to define the proportion of populations for each fossilization. Reference: Example 01.
35. Simulation parameters - fossilized_frequency to define the interval of fossilization. Reference: Example 01.
36. Simulation parameters - ragaraja_version to define the version of Ragaraja instructions to use. Reference: Example 01.
37. Simulation parameters - ragaraja_instructions to define a specific list of Ragaraja instructions to use. Reference: Example 01.
38. Simulation parameters - eco_buried_frequency to define the interval of ecological burial. Reference: Example 01.
39. Simulation parameters - database_file to define the file name of logging database. Reference: Example 01.
40. Simulation parameters - database_logging_frequency to define the interval of database logging. Reference: Example 01.
41. Simulation functions - mutation_scheme to specify the mutation scheme for each organism. Reference: Example 01.
42. Simulation functions - population_report to generate simulation text report. Reference: Example 01.
43. Simulation functions - database_report to log organisms and ecological system into the logging database at specified intervals. Reference: Example 01.
44. Logging all population details into database. Reference: Example 01.
45. Logging entire ecological details into database. Reference: Example 01.
46. Sequential simulation - organism by organism mutation and mating within a cell, cell by cell processing until all ecological cells are processed. Reference: Example 01.
47. Deployment scheme - deployment code 1 to deploy all organisms into one eco cell specified in simulation parameter population_locations. Reference: Example 01.
48. Deployment scheme - deployment code 3 to deploy all organisms evenly into the different eco cells specified in simulation parameter population_locations. Reference: Example 02.
49. Simulation functions - mating function to define mating behavior of organisms in each generation. Reference: Example 03.
50. Simulation functions - organism_movement to trigger organism movement from current ecological cell to an adjacent ecological cell. Reference: Example 04.
51. Simulation functions - organism_location to trigger organism movement from current ecological cell to a distant ecological cell. Reference: Example 05.
52. Simulation revival parameters - sim_folder to define location of simulation files to be revived. Reference: [Example 06] (https://github.com/mauriceling/dose/blob/master/examples/06_revive_simulation_01.py).
53. Simulation revival parameters - eco_file to specify which *.eco file to be excavated for re-simulation. Reference: [Example 06] (https://github.com/mauriceling/dose/blob/master/examples/06_revive_simulation_01.py).
54. Simulation revival parameters - pop_files to specify which *.gap files to be revived for re-simulation, wherein each *.gap file specified would be considered as one population. Reference: [Example 06] (https://github.com/mauriceling/dose/blob/master/examples/06_revive_simulation_01.py).
55. Simulation revival parameters - extend_gen to define the number of generations in continued simulation. Reference: [Example 06] (https://github.com/mauriceling/dose/blob/master/examples/06_revive_simulation_01.py).
56. Database extraction functions - connect_database to prepare the specified database in simulation parameter database_file for data extraction Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
57. Database extraction functions - db_list_simulations to list simulations inside a database by extracting starting times of the simulations Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
58. Database extraction functions - db_list_generations to list all logged generations within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
59. Database extraction functions - db_list_population_name to list all logged population's name within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
60. Database extraction functions - db_list_datafields to list all logged types of data within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
61. Database extraction functions - db_get_ecosystem to get a specific field of the ecosystem or the entire ecosystem for one or more generations within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
62. Database extraction functions - db_get_organisms_status to get a specific field of the organism's status dictionary or the entire dictionary for one or more generations within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
63. Database extraction functions - db_get_organisms_chromosome_sequences to get chromosomal sequences of entire genome of organisms for one or more generations within a simulation specified by its own starting time Reference: [Example 07] (https://github.com/mauriceling/dose/blob/master/examples/07_logging_database_extraction.py).
64. Simulation revival parameters - database_source to specify the file name of which database file to revive a simulation from. Reference: [Example 08] (https://github.com/mauriceling/dose/blob/master/examples/08_revive_simulation_03.py).
65. Simulation revival parameters - simulation_time to identify which simulation within the specified database file is to be revived. Reference: [Example 08] (https://github.com/mauriceling/dose/blob/master/examples/08_revive_simulation_03.py).
66. Simulation revival parameters - rev_start to specify at which generation(s) are the populations to be revived in the simulation. Reference: [Example 08] (https://github.com/mauriceling/dose/blob/master/examples/08_revive_simulation_03.py).
67. Simulation parameters - additional_mutation to influence mutation per base above background mutation. Reference: [Example 11] (https://github.com/mauriceling/dose/blob/master/examples/11_no_migration_natural_selection.py).
68. Simulation parameters - goal to be reached by the population through the fitness scheme. Reference: [Example 11] (https://github.com/mauriceling/dose/blob/master/examples/11_no_migration_natural_selection.py).
69. Simulation functions - fitness to calculate the fitness of an organism. Reference: [Example 11] (https://github.com/mauriceling/dose/blob/master/examples/11_no_migration_natural_selection.py).
70. Simulation functions - prepopulation_control to trigger population control events before mating event in each generation. Reference: [Example 11] (https://github.com/mauriceling/dose/blob/master/examples/11_no_migration_natural_selection.py).
71. Simulation functions - postpopulation_control to trigger population control events after mating event in each generation. Reference: [Example 11] (https://github.com/mauriceling/dose/blob/master/examples/11_no_migration_natural_selection.py).