PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

https://petab.readthedocs.io

PEtab-dev/PEtab Issues

Handling of events on parameters that are subject to condition specific values.
Closed 7 days ago4
Specifying units
Updated 21 days ago1
Support time dependent changes in conditions
Updated 21 days ago3
Time-dependent changes in component values
Updated 21 days ago6
Allow formulas in condition table
Updated 21 days ago1
No Noise
Closed 21 days ago13
Clarification/specification of order of condition changes required
Updated a month ago5
Update editorial board page
Closed 2 months ago
No reference to paper in repository
Closed 6 months ago1
Allow species in `yValues` of the visualization table
Updated 7 months ago2
Global vs local SBML parameters
Closed 7 months ago1
PEtab extension for NLME
Updated 7 months ago15
Update PETab to be model format agnostic
Updated 8 months ago4
Add tool using PEtab
Closed a year ago
Allow using observables in noiseFormula
Updated a year ago2
Fix sphinx doc
Closed a year ago
Specification of model time in observables file unclear
Closed 2 years ago2
Bounds documentation needs clairification
Closed 2 years ago2
Extensions: required/optional
Updated 2 years ago2
Clarification of condition table what happens if NaN is provided as a value
Updated 2 years ago
Clarification for condition table what happens if a parameter ID is provided as value
Updated 2 years ago1
Condition table not specified for parameters governed by rate rules
Updated 2 years ago3
Change main branch name "master"->"main"
Closed 2 years ago2
Petab Yaml: Include petabId / modelId
Closed 2 years ago3
Clarify reinitialization for parameters in the condition table
Updated 2 years ago7
Add support for non-SBML models
Updated 2 years ago6
Proposed new column in measurementData.tsv: datapointId
Closed 2 years ago4
False positive invalid condition ID.
Updated 3 years ago6
observable table vs observables table
Updated 3 years ago1
optimization vs estimation
Updated 3 years ago1
PEtab Extensions
Updated 3 years ago
Specification for formula format
Updated 3 years ago1
Separate repositories for PEtab format specification and library
Closed 3 years ago3
Cleanup repository after splitting off PEtab library
Closed 3 years ago
Add link to arxiv manuscript to Readme file
Closed 3 years ago
Can we take the nominalValue in the parameters table from SBML?
Closed 3 years ago5
Prior definition still in feature branch
Closed 3 years ago2
Visualization: add option to scale data
Updated 3 years ago
Extension to correlated observables
Updated 3 years ago
Visualization specification: Is tsv the right choice?
Updated 3 years ago2
Visualization: allow grouping plots?
Updated 3 years ago
PriorParameters in sampling are not transformed for parameterScaleUniform
Closed 3 years ago7
Questions regarding setting initial concentrations via condition table
Updated 4 years ago7
petablint does not check if parameter value in SBML matches parameter table
Closed 4 years ago1
Priors for functions of parameters
Updated 4 years ago
Delimiter issues in empty lines: tab-only line produces regex error with petablint
Closed 4 years ago1
PEtab's petablint validator doesn't seem to actually recognize .sbml files?
Closed 4 years ago3
objectivePriorType vs. priorType
Closed 4 years ago1
`petab.calculate_llh` and `petab.calculate_chi2` with observableParameters
Closed 4 years ago7
Error in merge_preeq_and_sim_pars_condition
Closed 4 years ago1