mauriceling/dose issues and pull requests

#93 - Improved DOSSIER's functionality (refactors + new additions)

Pull Request - State: closed - Opened by ghost over 2 years ago

#92 - 2 minor fixes (enzymatic_genes to enzymatic_reactions; nx.diameter() to nx.density())

Pull Request - State: closed - Opened by ghost about 3 years ago

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

Issue - State: open - Opened by ghost about 3 years ago

#90 - 3 changes made

Pull Request - State: closed - Opened by ghost about 3 years ago

#89 - 3 additions

Pull Request - State: closed - Opened by ghost about 3 years ago

#88 - Made requested changes + Added PerceptionSum() and EnzymaticSum() to dossier.py + Added 2 files

Pull Request - State: closed - Opened by ghost about 3 years ago

#87 - 4 changes made

Pull Request - State: closed - Opened by ghost about 3 years ago

#86 - Three additions/changes - 1 file for enzymatic reactions, 1 file for local efficiency and added LocalEfficiency()

Pull Request - State: closed - Opened by ghost about 3 years ago - 1 comment

#85 - Khadija.py

Pull Request - State: closed - Opened by khadijashahrukh over 5 years ago

#84 - Simulation script

Pull Request - State: closed - Opened by Sharlene98 over 5 years ago

#83 - Simulations - B.subtilis 168

Pull Request - State: closed - Opened by keerthana-d over 5 years ago

#82 - merge from appultaart/pandas_datastructure

Pull Request - State: closed - Opened by mauriceling over 6 years ago

#81 - Merge from appultaart/master

Pull Request - State: closed - Opened by mauriceling over 6 years ago

#80 - Fixed unpredictable exec lines in database_calls when run on py3 and optimised file writing in analytics

Pull Request - State: closed - Opened by clarencecastillo almost 9 years ago

#79 - Python3 functional

Pull Request - State: closed - Opened by appultaart almost 10 years ago - 2 comments

#78 - Merge pull request #14 from mauriceling/master

Pull Request - State: closed - Opened by clarencecastillo almost 10 years ago

#77 - Initial commit of example 18

Pull Request - State: closed - Opened by clarencecastillo almost 10 years ago

#76 - Is our point mutation operator biologically sound?

Issue - State: open - Opened by mauriceling over 10 years ago
Labels: examples

#75 - wiki - Clarence's short biography

Issue - State: closed - Opened by mauriceling over 10 years ago - 1 comment
Labels: documentation

#74 - Implement get_status_by_generation function in analytics.py

Issue - State: open - Opened by clarencecastillo over 10 years ago - 1 comment

#73 - Update documentation for examples 13, 14, 15 and 16 under Examples and Case Studies

Issue - State: open - Opened by clarencecastillo over 10 years ago

#72 - Rewritten example 13

Pull Request - State: closed - Opened by clarencecastillo over 10 years ago

#71 - Initial commit of example 13

Pull Request - State: closed - Opened by clarencecastillo over 10 years ago

#70 - Initial commit of examples 11 and 12

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

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

Issue - State: open - Opened by mauriceling almost 11 years ago
Labels: enhancement, high-priority

#68 - link up database_calls.db_list_xxx functions for calls from DOSE shell

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement, high-priority

#67 - Reconstructed writing of parameters to print all keys in sim_parameters of all simulations

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

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

Issue - State: closed - Opened by mauriceling almost 11 years ago
Labels: enhancement, examples, documentation, high-priority

#65 - write brief in-file documentation for examples

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: documentation

#64 - Implemented logging of parent's identities through a list in simulations...

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#63 - Restructured 'value' in line 585 of database_calls.py

Pull Request - State: closed - Opened by mauriceling almost 11 years ago

#62 - Reconstruct write_parameters() to handle all kinds of simulation

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment
Labels: enhancement, high-priority

#61 - 1. Fixed TypeError when calling org.status['location'] 2. Population[pop_name].generation is now equal to generation count in simulation level to cater both revive and normal simulations 3. Updated 08_revive_simulation_03.py

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#60 - Reconstructed simulate() and revive_simulation() in dose.py

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#59 - 08_revive_simulation_03.py returns a TypeError exception when reconstructing World

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment
Labels: bug, high-priority

#58 - Refactor revive_simulation() and simulate() to call simulation_core()

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment

#57 - offsprings to store parents' identity in offsprings' status as list in status['parents']

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement

#56 - extract() support methods

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment

#55 - add population name into Organism.status dictionary

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement, wontfix

#54 - Split deploy functions in simulation_calls.deploy() into their own separate functions

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#53 - refactoring simulation_calls.deploy() function

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement

#52 - 1. Moved 01_basic_funtions_one_cell_deployment_2013-10-13-1281664013.83 to test_data 2. .gitignore updated to ignore everything inside examples/Simulations

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#51 - Renamed max_cell_population into tape_length

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#50 - Rename max_cell_population in simulation_parameters into tape_length

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment
Labels: enhancement, high-priority

#49 - writing function documentation for dose.simulate() function

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: documentation, high-priority

#48 - add database logging in examples 3, 4 and 5

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: examples

#47 - Removed all unused modules in COPADS

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement

#46 - Implemented database logging function and parameters to all simulations

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#45 - Updated dose.py to support revival of frozen populations/buried worlds

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#44 - Updated database_report_world() function in dose.py and added 'blood' key in organism's status dictionary

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#43 - Possible infinite loop in Ragaraja interpreter

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: bug, high-priority

#42 - Means to continue simulation from database logs

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: enhancement

#41 - resolved Issue #40 (https://github.com/mauriceling/dose/issues/40)

Pull Request - State: closed - Opened by mauriceling almost 11 years ago

#40 - report(World) and deployment_scheme() in dose.dose_functions class appears syntactically wrong

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: bug, duplicate, high-priority

#39 - Initial commit of adjacent-migration and no-migration isolated mating simulations

Pull Request - State: closed - Opened by clarencecastillo almost 11 years ago

#38 - mixed licensing in DOSE

Issue - State: closed - Opened by mauriceling almost 11 years ago - 1 comment
Labels: documentation

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

Issue - State: closed - Opened by clarencecastillo almost 11 years ago - 1 comment
Labels: enhancement

GitHub / mauriceling/dose issues and pull requests