Ecosyste.ms: Issues

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GitHub / biosustain/Maud issues and pull requests

#373 - Bug: make dgf script work with specified but non-existing csvs

Pull Request - State: closed - Opened by teddygroves almost 3 years ago
Labels: bug

#372 - Install cmdstan from github develop branch

Pull Request - State: closed - Opened by teddygroves almost 3 years ago
Labels: bug

#371 - BUG: Incorrect working directory

Issue - State: closed - Opened by carrascomj almost 3 years ago - 3 comments

#370 - Bug: add missing "sample" argument to function call in dgf script

Pull Request - State: closed - Opened by teddygroves almost 3 years ago
Labels: bug

#369 - Experiment slicing

Pull Request - State: closed - Opened by NicholasCowie almost 3 years ago

#368 - Adjoint Algebraic hybrid

Issue - State: open - Opened by NicholasCowie almost 3 years ago

#367 - Modular flux refactor

Pull Request - State: closed - Opened by teddygroves almost 3 years ago

#366 - Flux decomposition

Pull Request - State: closed - Opened by NicholasCowie almost 3 years ago

#359 - Versioning

Issue - State: closed - Opened by teddygroves about 3 years ago

#358 - Case study: comparison with a non-fully-Bayesian method.

Issue - State: closed - Opened by teddygroves about 3 years ago - 1 comment

#357 - Decide whether to fall back to the bdf solver.

Issue - State: closed - Opened by teddygroves about 3 years ago - 1 comment

#356 - Pathway visualisation

Issue - State: closed - Opened by teddygroves about 3 years ago

#354 - feat: add parser and builder for SBML models

Pull Request - State: open - Opened by Midnighter about 3 years ago

#353 - Bug: fix wrong index in enzyme concentration likelihood function

Pull Request - State: closed - Opened by teddygroves about 3 years ago
Labels: bug

#352 - Bug: make arviz disable numba when loading InferenceData

Pull Request - State: closed - Opened by teddygroves about 3 years ago
Labels: bug

#351 - Save an InferenceData when sampling and simulating

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

#350 - Bug: replace obsolete jsondump calls

Pull Request - State: closed - Opened by teddygroves about 3 years ago
Labels: bug

#349 - Prior confidence intervals

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

#345 - chore: updating default timepoints to satisfy steady states

Pull Request - State: closed - Opened by NicholasCowie over 3 years ago - 1 comment

#344 - Case study doc update

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

#340 - Bug: make steady state check look for max concentration change

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

#339 - Easier debugging and optional rejection of non-steady states

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

#337 - feat: changing steady state evaluation to relative

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

#336 - Update plotting

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

#335 - Generate init from run

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

#316 - Simple Methionine DOE

Issue - State: closed - Opened by teddygroves over 3 years ago - 1 comment

#309 - Update scripts

Pull Request - State: closed - Opened by teddygroves almost 4 years ago
Labels: bug

#308 - Bug fix: drain priors are wrong

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#307 - Do profiling analysis to look for easy Stan speedups

Issue - State: closed - Opened by teddygroves almost 4 years ago

#305 - Fix flux checking

Pull Request - State: closed - Opened by NicholasCowie almost 4 years ago

#302 - Make Maud input and output folders

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#301 - Windows installation instructions

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#298 - Streamline automatic testing

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#296 - Case study: calibration

Issue - State: closed - Opened by teddygroves almost 4 years ago

#295 - Case study: extrapolation

Issue - State: closed - Opened by teddygroves almost 4 years ago

#294 - Case study: discovery

Issue - State: closed - Opened by teddygroves almost 4 years ago

#293 - Add KALE on scale data to the Maud repository

Issue - State: closed - Opened by teddygroves almost 4 years ago

#292 - Linear tests

Pull Request - State: closed - Opened by NicholasCowie almost 4 years ago

#289 - Linear integration test

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#286 - Documentation for phosphorylation

Issue - State: closed - Opened by NicholasCowie almost 4 years ago
Labels: documentation

#285 - Linear phosphorylation

Pull Request - State: closed - Opened by NicholasCowie almost 4 years ago

#282 - Improve and document workflow around input files and maudeller

Issue - State: closed - Opened by teddygroves almost 4 years ago
Labels: BLOCKED

#276 - Theory document with essential background papers

Issue - State: closed - Opened by teddygroves almost 4 years ago

#275 - Feat: makefile command for removing auxiliary Stan files

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#271 - Update copyright notices

Issue - State: closed - Opened by teddygroves almost 4 years ago
Labels: bug

#270 - Prior percentiles

Pull Request - State: closed - Opened by teddygroves almost 4 years ago

#269 - Rescale params

Pull Request - State: closed - Opened by teddygroves almost 4 years ago - 1 comment

#265 - Document plan for implementing a single simulation study.

Pull Request - State: closed - Opened by teddygroves about 4 years ago

#263 - Refactoring Drain Code

Issue - State: closed - Opened by NicholasCowie about 4 years ago - 1 comment
Labels: internal

#259 - In progress check to stop bad runs quickly

Issue - State: closed - Opened by teddygroves about 4 years ago

#254 - Investigate how to set priors for allosteric parameters

Issue - State: closed - Opened by teddygroves about 4 years ago

#217 - Bug: deal with new argument names for CmdStanModel.sample

Pull Request - State: closed - Opened by teddygroves over 4 years ago - 1 comment
Labels: bug

#216 - Run maud sample from any directory

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

#213 - Removing unb from ode

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

#212 - Update steady state arguments

Pull Request - State: closed - Opened by NicholasCowie almost 5 years ago - 1 comment

#209 - Remove non-modular rate laws

Pull Request - State: closed - Opened by teddygroves almost 5 years ago - 4 comments

#206 - More reliable indexing

Pull Request - State: closed - Opened by teddygroves almost 5 years ago - 2 comments
Labels: bug

#199 - Expand documentation page about statistical issues

Pull Request - State: closed - Opened by teddygroves almost 5 years ago - 2 comments

#197 - Formation energy

Pull Request - State: closed - Opened by teddygroves almost 5 years ago - 1 comment

#193 - Put output data in the same file that maud sample was run from

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

#192 - Add preamble to documentation landing page (and a bit of doc tidying)

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

#190 - Conserved quantities (e.g adp + atp)

Issue - State: open - Opened by teddygroves about 5 years ago - 2 comments
Labels: NEXT

#189 - demo model

Pull Request - State: closed - Opened by teddygroves about 5 years ago - 1 comment

#184 - Validation: does the ode system have a single steady state?

Issue - State: closed - Opened by teddygroves about 5 years ago