SED-ML sed-ml issues - Githubissues

SED-ML / sed-ml

Simulation Experiment Description Markup Language (SED-ML)

http://sed-ml.org

5 stars 2 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Add examples/pictures for curve types, especially the surface ones.

#122 luciansmith opened 3 years ago
3
Add description of DataRange

#121 luciansmith closed 3 years ago
2
Support external definitions of parameter estimation tasks (PETab)

#120 jonrkarr opened 3 years ago
0
Separate SED into several modules, breaking out a core that has a low barrier to entry

#119 jonrkarr opened 3 years ago
2
Enable external definitions of data visualizations

#118 jonrkarr opened 3 years ago
0
Clarify whether all tasks are intended to be executed or just those that contribute to outputs

#117 jonrkarr closed 3 years ago
6
Encourage simulation tools optionally be able to output changed models

#116 jonrkarr opened 3 years ago
3
Define a canonical, reproducible order of execution

#115 jonrkarr closed 3 years ago
4
Redesign model changes and variable targets to address fundamental flaws with XML XPATHs, changes, and namespaces

#114 jonrkarr opened 3 years ago
7
When sub-tasks involve different models, optionally use an additional dimension to encode their results

#113 jonrkarr closed 3 years ago
1
Require sub-tasks of a repeated task to reference the same model (or a model with the same variables)

#112 jonrkarr closed 3 years ago
4
Replace symbol URNs with KiSAO terms

#111 jonrkarr closed 3 years ago
6
Clarify the semantics of resetModel of repeatedTask and simplify its intended behavior

#110 jonrkarr closed 3 years ago
28
Discuss the complexity implied by using symbols in ComputeChange and other calculations

#109 jonrkarr closed 3 years ago
3
Modify or remove the setting of symbols (via SetValue)

#108 jonrkarr closed 3 years ago
6
Disallow data generators for outputs of specific subtasks of repeated tasks

#107 jonrkarr closed 3 years ago
5
Simplify the interpretation of internal targets by requiring targets to be more explicit

#106 jonrkarr closed 3 years ago
4
Clarify the capabilities of repeated tasks to execute multiple models in the specifications

#105 jonrkarr opened 3 years ago
3
Standardize names of abstract classes

#104 jonrkarr opened 3 years ago
1
Clarify the semantics of the interaction of repeated tasks with reports and plots

#103 jonrkarr closed 3 years ago
5
Enable simulation experiments to indicate whether basic tasks referenced by repeated tasks should be run individually or not

#102 jonrkarr closed 3 years ago
14
What is the rationale for SetValue in addition to FunctionalRange?

#101 jonrkarr closed 3 years ago
7
Support factorial RepeatedTasks for more abstraction in descriptions of complex simulation experiments

#100 jonrkarr opened 3 years ago
4
Allow instances of the base Simulation class to better support other modeling formalisms and other analyses of models

#99 jonrkarr opened 3 years ago
2
Allow SetValue to set attributes of simulations to allow the execution of variants of simulations (in addition to variants of models)

#98 jonrkarr opened 3 years ago
16
Allow more data type flexibility with UniformRange, VectorRange and other classes for logical and other modeling formalisms

#97 jonrkarr opened 3 years ago
1
Standardize names of reference attributes

#96 jonrkarr opened 3 years ago
0
Require `SubTask.order` to be unique within a task to provide clear, reproducible execution orders for subtasks

#95 jonrkarr closed 3 years ago
23
Support EDAM terms as an alternative to URNs for indicating model languages

#94 jonrkarr opened 3 years ago
4
Encourage the labels of data sets to be unique within a report

#93 jonrkarr closed 3 years ago
4
What are the conventions for namespaces of content of NewXML?

#92 jonrkarr closed 3 years ago
5
Decide whether to update old specs

#91 luciansmith closed 3 years ago
3
Remove/Deactivate http://sed-ml.sourceforge.net/

#90 matthiaskoenig closed 3 years ago
1
Compute changes are intended to be able to retrieve values from multiple models. Does any tool support this?

#89 jonrkarr closed 3 years ago
7
XPATHs for sbml:parameter are not consistent throughout the L1V3 specifications

#88 jonrkarr closed 3 years ago
4
More explanation about "XPATH"s with more explicit examples would be informative

#87 jonrkarr closed 3 years ago
2
Replace resolution of "MIRIAM URNs" with resolution of modelXchange ids

#86 jonrkarr closed 3 years ago
7
`name` attributes should be removed from tables 2.10, 2.11 of L1V3 specs because change elements don't have names

#85 jonrkarr closed 3 years ago
4
`id` attribute is missing from tables 2.22-2.24 of L1V3 specs of plot2d, plot3d, report attributes

#84 jonrkarr closed 3 years ago
3
Clarify the semantics of mathematical expressions of data generators

#82 jonrkarr closed 3 years ago
3
Add note to specifications that KiSAO terms be referenced by KISAO: rather than KISAO_

#81 jonrkarr closed 3 years ago
2
Clarify the semantics of internal/relative references to models

#80 jonrkarr closed 3 years ago
3
In general, how can MIRIAM URNs be resolved to specific model files?

#79 jonrkarr closed 3 years ago
8
MIRIAM URNs should be renamed to Identifiers.org

#78 jonrkarr closed 3 years ago
1
What do simulation tools do when the variables of a data generator or the data generators of an output have different shapes?

#77 jonrkarr closed 3 years ago
16
When the source of a model is defined by reference to another model should the changes be inherited?

#76 jonrkarr closed 3 years ago
6
What is the intended semantics of addXML, changeXML, and removeXML when targets match multiple elements and/or NewXML has multiple children?

#75 jonrkarr closed 3 years ago
21
Create URNs for SBML fbc, multi, and qual packages

#74 jonrkarr opened 3 years ago
16
Support global parameters of simulation experiments

#73 jonrkarr closed 2 years ago
5
More clearly handle multiple predictions per model element

#72 jonrkarr closed 3 years ago
8

Previous Next