mauriceling/dose

Issues

• Problems with finding diameter of network prior to implementation of Diameter() in dossier.py

  #91 opened 3 years ago
  0

• wiki - Clarence's short biography

  #75 opened 10 years ago by mauriceling
  1

• Is our point mutation operator biologically sound?

  #76 opened 10 years ago by mauriceling
  0

• Implement get_status_by_generation function in analytics.py

  #74 opened 11 years ago by clarencecastillo
  1

• Update documentation for examples 13, 14, 15 and 16 under Examples and Case Studies

  #73 opened 11 years ago by clarencecastillo
  0

• write brief in-file documentation for examples

  #65 opened 11 years ago by mauriceling
  1

• list the main means of how to analyze simulations #03, 04, 05

  #66 opened 11 years ago by mauriceling
  0

• dose shell - convert objects (from results dictionary) to Python objects (in userdata dictionary)

  #69 opened 11 years ago by mauriceling
  0

• link up database_calls.db_list_xxx functions for calls from DOSE shell

  #68 opened 11 years ago by mauriceling
  1

• Reconstruct write_parameters() to handle all kinds of simulation

  #62 opened 11 years ago by clarencecastillo
  1

• offsprings to store parents' identity in offsprings' status as list in status['parents']

  #57 opened 11 years ago by mauriceling
  1

• 08_revive_simulation_03.py returns a TypeError exception when reconstructing World

  #59 opened 11 years ago by clarencecastillo
  1

• Refactor revive_simulation() and simulate() to call simulation_core()

  #58 opened 11 years ago by clarencecastillo
  1

• Means to continue simulation from database logs

  #42 opened 11 years ago by mauriceling
  1

• extract() support methods

  #56 opened 11 years ago by clarencecastillo
  1

• add population name into Organism.status dictionary

  #55 opened 11 years ago by mauriceling
  1

• refactoring simulation_calls.deploy() function

  #53 opened 11 years ago by mauriceling
  1

• writing function documentation for dose.simulate() function

  #49 opened 11 years ago by mauriceling
  1

• Rename max_cell_population in simulation_parameters into tape_length

  #50 opened 11 years ago by clarencecastillo
  1

• add database logging in examples 3, 4 and 5

  #48 opened 11 years ago by mauriceling
  1

• Removed all unused modules in COPADS

  #47 opened 11 years ago by mauriceling
  1

• Means to continue from frozen population(s) and buried ecosystem

  #17 opened 11 years ago by mauriceling
  2

• function documentation for dose.filter_xxx()

  #36 opened 11 years ago by mauriceling
  1

• Possible infinite loop in Ragaraja interpreter

  #43 opened 11 years ago by mauriceling
  1

• database - log simulation parameters

  #6 opened 11 years ago by mauriceling
  1

• report(World) and deployment_scheme() in dose.dose_functions class appears syntactically wrong

  #40 opened 11 years ago by mauriceling
  1

• Class documentation for dose.dose_functions

  #35 opened 11 years ago by mauriceling
  1

• database - database file

  #18 opened 11 years ago by mauriceling
  1

• mixed licensing in DOSE

  #38 opened 11 years ago by mauriceling
  1

• world_builder class inside dose.py shows an unecessary nesting of classes as initialization of World can be done directly with dose_world.World

  #37 opened 11 years ago by clarencecastillo
  1

• wiki - writing a simulation: parts of a simulation

  #34 opened 11 years ago by mauriceling
  0

• Moving functions called by dose.simulation into simulation_calls.py

  #32 opened 11 years ago by mauriceling
  1

• Genetic distance between long migration / no cross-cell mating

  #33 opened 11 years ago by clarencecastillo
  1

• Genetic distance between adjacent migration / no cross-cell mating

  #31 opened 11 years ago by clarencecastillo
  2

• reporting organism.status['location'] for every organism in the population does not follow deployment schemes

  #14 opened 11 years ago by clarencecastillo
  3

• Genetic distance between no migration / no cross-cell mating

  #23 opened 11 years ago by mauriceling
  1

• Children produced in mating scheme share status dictionaries similar to Issue #14

  #29 opened 11 years ago by clarencecastillo
  1

• Needs simulation_functions class in dose.py for documentation

  #28 opened 11 years ago by mauriceling
  1

• Basic simulation examples

  #25 opened 11 years ago by clarencecastillo
  1

• Rename simulation files (eg. SIM_01.py) into a more detailed name (01_basic_functions_one_cell_deployment.py)

  #24 opened 11 years ago by clarencecastillo
  1

• Incorrect calling of custom functions inside dose.py

  #26 opened 11 years ago by clarencecastillo
  1

• Are the eco_cell dictionaries in World.ecosystem affected by the same issue stated in Issue #14?

  #20 opened 11 years ago by mauriceling
  1

• deployment schemes: user-defined

  #11 opened 11 years ago by mauriceling
  1

• Split the initialization of dose_world from entities class in SIM_01.py

  #21 opened 11 years ago by clarencecastillo
  1

• Renaming "p", "Entities" and "population" in dose.py

  #19 opened 11 years ago by mauriceling
  1

• renaming dose_entities class in dose.py into dose_functions or simulation_functions

  #12 opened 11 years ago by mauriceling
  1

• deployment schemes: [pre-defined] centralized deployment

  #10 opened 11 years ago by mauriceling
  2

• deployment schemes: [pre-defined] even deployment

  #9 opened 11 years ago by mauriceling
  2

• deployment schemes: [pre-defined] random deployment

  #8 opened 11 years ago by mauriceling
  2

• deployment schemes: [pre-defined] all-in-one

  #7 opened 11 years ago by mauriceling
  1