mauriceling dose issues

mauriceling / dose

Digital Organism Simulation Environment (DOSE)

https://github.com/mauriceling/dose/wiki

GNU General Public License v3.0

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Improved DOSSIER's functionality (refactors + new additions)

#93 ghost closed 2 years ago
0
2 minor fixes (enzymatic_genes to enzymatic_reactions; nx.diameter() to nx.density())

#92 ghost closed 3 years ago
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Problems with finding diameter of network prior to implementation of Diameter() in dossier.py

#91 ghost opened 3 years ago
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3 changes made

#90 ghost closed 3 years ago
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3 additions

#89 ghost closed 3 years ago
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Made requested changes + Added PerceptionSum() and EnzymaticSum() to dossier.py + Added 2 files

#88 ghost closed 3 years ago
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4 changes made

#87 ghost closed 3 years ago
0
Three additions/changes - 1 file for enzymatic reactions, 1 file for local efficiency and added LocalEfficiency()

#86 ghost closed 3 years ago
1
Khadija.py

#85 khadijashahrukh closed 5 years ago
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Simulation script

#84 Sharlene98 closed 5 years ago
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Simulations - B.subtilis 168

#83 keerthana-d closed 5 years ago
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merge from appultaart/pandas_datastructure

#82 mauriceling closed 6 years ago
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Merge from appultaart/master

#81 mauriceling closed 6 years ago
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Fixed unpredictable exec lines in database_calls when run on py3 and optimised file writing in analytics

#80 clarencecastillo closed 8 years ago
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Python3 functional

#79 appultaart closed 9 years ago
2
Merge pull request #14 from mauriceling/master

#78 clarencecastillo closed 9 years ago
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Initial commit of example 18

#77 clarencecastillo closed 9 years ago
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Is our point mutation operator biologically sound?

#76 mauriceling opened 10 years ago
0
wiki - Clarence's short biography

#75 mauriceling closed 10 years ago
1
Implement get_status_by_generation function in analytics.py

#74 clarencecastillo opened 10 years ago
1
Update documentation for examples 13, 14, 15 and 16 under Examples and Case Studies

#73 clarencecastillo opened 10 years ago
0
Rewritten example 13

#72 clarencecastillo closed 10 years ago
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Initial commit of example 13

#71 clarencecastillo closed 10 years ago
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Initial commit of examples 11 and 12

#70 clarencecastillo closed 10 years ago
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dose shell - convert objects (from results dictionary) to Python objects (in userdata dictionary)

#69 mauriceling opened 10 years ago
0
link up database_calls.db_list_xxx functions for calls from DOSE shell

#68 mauriceling closed 10 years ago
1
Reconstructed writing of parameters to print all keys in sim_parameters of all simulations

#67 clarencecastillo closed 10 years ago
0
list the main means of how to analyze simulations #03, 04, 05

#66 mauriceling closed 10 years ago
0
write brief in-file documentation for examples

#65 mauriceling closed 10 years ago
1
Implemented logging of parent's identities through a list in simulations...

#64 clarencecastillo closed 10 years ago
0
Restructured 'value' in line 585 of database_calls.py

#63 mauriceling closed 10 years ago
0
Reconstruct write_parameters() to handle all kinds of simulation

#62 clarencecastillo closed 10 years ago
1
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

#61 clarencecastillo closed 10 years ago
0
Reconstructed simulate() and revive_simulation() in dose.py

#60 clarencecastillo closed 10 years ago
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08_revive_simulation_03.py returns a TypeError exception when reconstructing World

#59 clarencecastillo closed 10 years ago
1
Refactor revive_simulation() and simulate() to call simulation_core()

#58 clarencecastillo closed 10 years ago
1
offsprings to store parents' identity in offsprings' status as list in status['parents']

#57 mauriceling closed 10 years ago
1
extract() support methods

#56 clarencecastillo closed 10 years ago
1
add population name into Organism.status dictionary

#55 mauriceling closed 10 years ago
1
Split deploy functions in simulation_calls.deploy() into their own separate functions

#54 clarencecastillo closed 10 years ago
0
refactoring simulation_calls.deploy() function

#53 mauriceling closed 10 years ago
1
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

#52 clarencecastillo closed 10 years ago
0
Renamed max_cell_population into tape_length

#51 clarencecastillo closed 10 years ago
0
Rename max_cell_population in simulation_parameters into tape_length

#50 clarencecastillo closed 10 years ago
1
writing function documentation for dose.simulate() function

#49 mauriceling closed 10 years ago
1
add database logging in examples 3, 4 and 5

#48 mauriceling closed 10 years ago
1
Removed all unused modules in COPADS

#47 mauriceling closed 10 years ago
1
Implemented database logging function and parameters to all simulations

#46 clarencecastillo closed 10 years ago
0
Updated dose.py to support revival of frozen populations/buried worlds

#45 clarencecastillo closed 10 years ago
0
Updated database_report_world() function in dose.py and added 'blood' key in organism's status dictionary

#44 clarencecastillo closed 10 years ago
0