ModelEngineering/SBMLLint issues and pull requests

#55 - dealing with non-unit stoichiometry, e.g., S1 + 2S1 -> S2

Pull Request - State: closed - Opened by woosubs over 3 years ago

#54 - added lines to test repeated species

Pull Request - State: closed - Opened by woosubs over 3 years ago

#53 - fixed issue in stoichiometry matrix

Pull Request - State: closed - Opened by woosubs over 3 years ago

#52 - Update documentation for using moiety analysis

Issue - State: open - Opened by joseph-hellerstein over 3 years ago
Labels: bug

#51 - Model readability checks

Issue - State: open - Opened by joseph-hellerstein over 4 years ago
Labels: enhancement

#50 - Moiety name structures

Issue - State: open - Opened by joseph-hellerstein over 4 years ago
Labels: enhancement

#49 - Add checking for kinetics expressions

Issue - State: open - Opened by joseph-hellerstein over 4 years ago
Labels: enhancement

#48 - updated stoichiometry_matrix: variable names

Pull Request - State: closed - Opened by woosubs over 4 years ago

#47 - finished analysis. cleaning up notebooks

Pull Request - State: closed - Opened by woosubs over 4 years ago

#46 - updated rounding once again; only rounding lower_inverse

Pull Request - State: closed - Opened by woosubs over 4 years ago

#45 - finalised roundup (U matrix, and lower_inverse rounded by 3)

Pull Request - State: closed - Opened by woosubs over 4 years ago

#44 - isolation set to reaction isolation set

Pull Request - State: closed - Opened by woosubs over 4 years ago

#43 - Update biomodels data

Pull Request - State: closed - Opened by woosubs over 4 years ago

#42 - Update biomodels data

Pull Request - State: closed - Opened by woosubs over 4 years ago

#41 - Updated biomodels.zip

Pull Request - State: closed - Opened by woosubs over 4 years ago

#40 - Explain threshold (games)

Pull Request - State: closed - Opened by woosubs over 4 years ago

#39 - explain_detials=False if unexplainable

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#38 - updating games report (explain_details option in echelon/type3 errors)

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#37 - switched to .loc for GAMES.getStoichiometryMatrix()

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#36 - updated GAMES.getStoichiometryMatrix() by using .loc for stoichiometry

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#35 - started MILP analysis & GAMESReport update

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#34 - created run_stoichiometry_matrix.ipynb

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#33 - added run_stoichiometry_matrix.ipynb

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#32 - deleted old notebooks

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#31 - Analyze BiGG initial commit

Pull Request - State: closed - Opened by woosubs almost 5 years ago

#30 - Report errors detected in SBML when parsing

Pull Request - State: open - Opened by dacb about 5 years ago

#29 - implementation of implicit species in GAMES

Pull Request - State: closed - Opened by woosubs about 5 years ago

#28 - Reaction._getCategory to Reaction.getCategory

Pull Request - State: closed - Opened by woosubs about 5 years ago

#27 - added simple.remove()

Pull Request - State: closed - Opened by woosubs about 5 years ago

#26 - updated games_example for size

Pull Request - State: closed - Opened by woosubs about 5 years ago

#25 - games_example updated

Pull Request - State: closed - Opened by woosubs about 5 years ago

#24 - sbmllint reporting games

Pull Request - State: closed - Opened by woosubs about 5 years ago

#23 - GAMES statistics; updated reportCancelingError

Pull Request - State: closed - Opened by woosubs about 5 years ago

#22 - Calculated ISS and nISS

Pull Request - State: closed - Opened by woosubs about 5 years ago