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Dooders
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Pyology
A metaphorical model of a biological cell
MIT License
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Standardizing the naming conventions for metabolites
#49
csmangum
closed
3 weeks ago
0
PR: Glycolysis validation
#48
csmangum
closed
3 weeks ago
0
Issue: Implement Metabolite Energy Balance Comparison for Glycolysis Simulation
#47
csmangum
closed
3 weeks ago
0
Each step should be enzymatically controlled, following the biological sequence.
#46
csmangum
closed
3 weeks ago
0
Glycolysis: Converts glucose into pyruvate, generating ATP and NADH.
#45
csmangum
closed
3 weeks ago
0
Pathways to model
#44
csmangum
opened
3 weeks ago
0
Issue: Review and Correct the Stoichiometry and Thermodynamics of Krebs Cycle Reactions
#43
csmangum
opened
3 weeks ago
0
Expanding metabolite data
#42
csmangum
closed
4 weeks ago
0
Add Tracker class for monitoring simulation metrics
#41
csmangum
opened
4 weeks ago
0
Feature Request: Create a `Tracker` Class for Monitoring Simulation Metrics
#40
csmangum
opened
4 weeks ago
2
Key Metabolites for Krebs Cycle
#39
csmangum
opened
4 weeks ago
0
Bug: Energy Conservation Issue in Krebs Cycle Simulation
#38
csmangum
opened
4 weeks ago
1
Issue: Implement Structured Logging Using `structlog`
#37
csmangum
opened
1 month ago
0
PR: Comprehensive Documentation Update and ATP Data Adjustment for Enzyme, Organelle, and SignalTransductionCascade Classes
#36
csmangum
closed
1 month ago
0
Enhance Enzyme class with advanced kinetics and catalysis
#35
csmangum
closed
1 month ago
0
PR: Enhance Enzyme class and update glycolysis simulation
#34
csmangum
closed
1 month ago
0
Issue: Implement Activation States and Cascades in Enzyme Class
#33
csmangum
closed
1 month ago
0
Issue: Enhance `Enzyme` Class to Model Signal Transduction Cascades and Feedback Loops
#32
csmangum
closed
1 month ago
0
PR: Improving the glycolysis pathway implementation
#31
csmangum
closed
1 month ago
0
Enhance Reaction class, improve error handling
#30
csmangum
closed
1 month ago
0
Merge pull request #28 from Dooders/dev
#29
csmangum
closed
1 month ago
0
Refactoring the reaction execution logic
#28
csmangum
closed
1 month ago
1
Issue: Optimize and Improve `Reaction` Class Implementation
#27
csmangum
closed
1 month ago
0
Stoichiometry Verification Test
#26
csmangum
closed
1 month ago
0
Implement Async Functionality for `execute_command` Function
#25
csmangum
opened
1 month ago
0
PR: Generic Function for Executing Commands with Attribute Tracking and Validation
#24
csmangum
closed
1 month ago
0
Accurate ATP Accounting
#23
csmangum
closed
1 month ago
0
Generic Function for Executing Commands with Attribute Tracking and Validation
#22
csmangum
closed
1 month ago
0
Improve adenine nucleotide balance and energy conservation tracking
#21
csmangum
closed
1 month ago
0
Ensure Mass and Energy Conservation
#20
csmangum
closed
1 month ago
0
Implement Log Hashing for Simulation Consistency Verification
#19
csmangum
opened
1 month ago
1
Correct Initial Metabolite Levels
#18
csmangum
closed
1 month ago
0
Glycolysis accuracy issues
#17
csmangum
closed
1 month ago
0
Refactor ATP production and adenine nucleotide balance
#16
csmangum
closed
1 month ago
0
Improve adenine nucleotide balance and add assertions
#15
csmangum
closed
1 month ago
0
Go through the existing simulation code to understand the flow and identify key variables involved in critical computations.
#14
csmangum
closed
1 month ago
1
Identify critical variables and add assertions accordingly.
#13
csmangum
closed
1 month ago
3
Enhance Continuous Testing and Monitoring in Glycolysis Simulation
#12
csmangum
closed
1 month ago
0
Improve adenine nucleotide balance and ATP production tracking
#11
csmangum
closed
1 month ago
0
Incorrect Adenine Nucleotide Balance Post-Glycolysis
#10
csmangum
closed
1 month ago
0
Enhance Simulation Process with Improved SimulationController and Reporter, Type Annotations, and New Unit Tests
#9
csmangum
closed
1 month ago
1
Inconsistent Initial ATP Levels
#8
csmangum
closed
1 month ago
1
Rebranding and Glycolysis Simulation Enhancements for Pyology: New Features, Documentation Updates, and Improved State Logging
#7
csmangum
closed
1 month ago
0
Enhance pyology Package with Improved Logging, Metabolite Adjustments, and Enzyme Refinements
#6
csmangum
closed
1 month ago
0
Enhance `pyology` Module: Updated Metabolite Data, Refactored `Cell` Class, and Defined Glycolysis Enzymes & Reactions
#5
csmangum
closed
1 month ago
0
Expand Reaction model
#4
csmangum
closed
1 month ago
0
Enzyme model
#3
csmangum
closed
1 month ago
0
Model comments
#2
csmangum
opened
1 month ago
1
organelle metaclass
#1
csmangum
closed
1 month ago
0