UsersGuide package#21
Merged
AtiyahElsheikh merged 24 commits intoOpenModelica:developfrom Apr 7, 2021
Merged
Conversation
… the documentation
…m Icons when available
Usage of MSL 4.0.0 after applying the conversion script
The Modelica grammar does not allow annotations except at the end of a class.
* Convert to MSL 4.0.0 * Update version number to 1.0.3
MSL 4.0.0
# Conflicts: # BioChem/Interfaces/Reactions/Basics/FourSubstrates.mo # BioChem/Units/package.mo
Collaborator
Author
|
Sorry for the high number of commits. Only the last two commits can be considered for review. The other commits are due to merging from previous pull requests. |
sjoelund
reviewed
Apr 7, 2021
BioChem/UsersGuide/CopyRight.mo
Outdated
| class CopyRight | ||
| extends Modelica.Icons.Information; | ||
| annotation( | ||
| Documentation(info = "<html><head></head><body>Copyright © 2005-2015 MathCore Engineering AB, Linköpings universitet and Modelica Association</body></html>")); |
Member
There was a problem hiding this comment.
You could probably bump that to 2021 and add your own name
Collaborator
Author
There was a problem hiding this comment.
Done and have added your name as well under ReleaseNotes
BioChem/UsersGuide/References.mo
Outdated
| class References | ||
| extends Modelica.Icons.References; | ||
| annotation( | ||
| Documentation(info = "<html><head></head><body><h2>References</h2><p><b>BioChem - A Biological and Chemical Library for Modelica (Conference paper)</b><br>Emma Larsdotter Nilsson, Peter Fritzson. Proceedings of the 3rd International Modelica Conference (November 3-4, Linköping, Sweden) 2003, pp. 215-220 <br><br><b>A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase</b><br>Albert Goldbeter. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 9107-9111, October 1991 Cell Biology <br><br><b>Hierarchical modeling of diabetes</b><br>Elin Nyman. ISRN:LiU-IKE-EX-09/14. Linköping University 2009. <br><br><b>A Minimal Generic Model of Bacteria-Induced Intracellular Ca<sup>2+</sup> Oscillations in Epithelial Cells</b><br>Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemo. Biophysical Journal Volume 88 April 2005 2976-2981. <br><br><b>A mathematical model of metabolic insulin signaling.</b><br>A. Sedaghat, R, A. Sherman, and J. Quon, Michael. American Journal of Physiology - Endocrinology and Metabolism, 283:1048-1101, Jul 2002. <br><br><b>Modeling the cell division cycle: cdc2 and cyclin interactions</b><br>John J. Tyson. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 7328-7332, August 1991 Cell Biology <br><br><b>Modeling Feedback Loops of the Mammalian Circadian Oscillator</b><br>Becker-Weimann S, Wolf J, Herzel H, Kramer A. Biophysical Journal Volume 87 November 2004 3023-3034 </p></body></html>")); |
Member
There was a problem hiding this comment.
Since it's HTML, perhaps add links to the papers while changing things?
sjoelund
reviewed
Apr 7, 2021
BioChem/UsersGuide/References.mo
Outdated
| extends Modelica.Icons.References; | ||
| annotation( | ||
| Documentation(info = "<html><head></head><body><h2>References</h2><p><b>BioChem - A Biological and Chemical Library for Modelica (Conference paper)</b><br>Emma Larsdotter Nilsson, Peter Fritzson. Proceedings of the 3rd International Modelica Conference (November 3-4, Linköping, Sweden) 2003, pp. 215-220 <br><br><b>A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase</b><br>Albert Goldbeter. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 9107-9111, October 1991 Cell Biology <br><br><b>Hierarchical modeling of diabetes</b><br>Elin Nyman. ISRN:LiU-IKE-EX-09/14. Linköping University 2009. <br><br><b>A Minimal Generic Model of Bacteria-Induced Intracellular Ca<sup>2+</sup> Oscillations in Epithelial Cells</b><br>Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemo. Biophysical Journal Volume 88 April 2005 2976-2981. <br><br><b>A mathematical model of metabolic insulin signaling.</b><br>A. Sedaghat, R, A. Sherman, and J. Quon, Michael. American Journal of Physiology - Endocrinology and Metabolism, 283:1048-1101, Jul 2002. <br><br><b>Modeling the cell division cycle: cdc2 and cyclin interactions</b><br>John J. Tyson. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 7328-7332, August 1991 Cell Biology <br><br><b>Modeling Feedback Loops of the Mammalian Circadian Oscillator</b><br>Becker-Weimann S, Wolf J, Herzel H, Kramer A. Biophysical Journal Volume 87 November 2004 3023-3034 </p></body></html>")); | ||
| Documentation(info = "<html><head></head><body><h2>References</h2><p><b>BioChem - A Biological and Chemical Library for Modelica </b><br>Emma Larsdotter Nilsson, Peter Fritzson. Proceedings of the 3rd International Modelica Conference (November 3-4, Linköping, Sweden) 2003, pp. 215-220 <b>(<a href=\"https://www.researchgate.net/publication/237321637_BioChem_-_A_Biological_and_Chemical_Library_for_Modelica\">link</a>)</b><br><br><b>A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase </b><br>Albert Goldbeter. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 9107-9111, October 1991 Cell Biology (<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC52661/\">link</a>) <br><br><b>Hierarchical modeling of diabetes</b><br>Elin Nyman. ISRN:LiU-IKE-EX-09/14. Linköping University 2009 (<a href=\"http://liu.diva-portal.org/smash/record.jsf?pid=diva2%3A231708&dswid=mainwindow\">link</a>)<br><br><b>A Minimal Generic Model of Bacteria-Induced Intracellular Ca<sup>2+</sup> Oscillations in Epithelial Cells</b><br>Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemo. Biophysical Journal Volume 88 April 2005 2976-2981 (<a href=\"https://www.sciencedirect.com/science/article/pii/S000634950573349X\">link</a>)<br><br><b>A mathematical model of metabolic insulin signaling.</b><br>A. Sedaghat, R, A. Sherman, and J. Quon, Michael. American Journal of Physiology - Endocrinology and Metabolism, 283:1048-1101, Jul 2002 (<a href=\"https://pubmed.ncbi.nlm.nih.gov/12376338/\">link</a>)<br><br><b>Modeling the cell division cycle: cdc2 and cyclin interactions </b><br>John J. Tyson. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 7328-7332, August 1991 Cell Biology <b>(<a href=\"https://pubmed.ncbi.nlm.nih.gov/1831270/\">link</a>)</b><br><br><b>Modeling Feedback Loops of the Mammalian Circadian Oscillator </b><br>Becker-Weimann S, Wolf J, Herzel H, Kramer A. Biophysical Journal Volume 87 November 2004 3023-3034 (<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304775/\">link</a>)</p></body></html>")); |
Member
There was a problem hiding this comment.
researchgate? Why not the source? https://www.modelica.org/events/Conference2003/papers/h21_Larsdotter_Nilsson.pdf
And http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-19076 is the "permanent link" according to the second URL
sjoelund
approved these changes
Apr 7, 2021
Member
|
Squash and merge will let you combine all commits into one |
AtiyahElsheikh
added a commit
to AtiyahElsheikh/BioChem
that referenced
this pull request
Apr 7, 2021
UsersGuide package (OpenModelica#21)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
An initial package for UsersGuide following common guidelines. I have simply moved existing documentation to the UsersGuide package