From a7624bf2e762004683463147e3c17328c7477725 Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 22 Jun 2020 21:15:56 +0100 Subject: [PATCH 1/7] minor changes email, copyright etc. --- UserGuide/package.mo | 38 ++++++++++++++++++-------------------- UserGuide/package.order | 2 +- 2 files changed, 19 insertions(+), 21 deletions(-) diff --git a/UserGuide/package.mo b/UserGuide/package.mo index 2400210..1a5087a 100644 --- a/UserGuide/package.mo +++ b/UserGuide/package.mo @@ -1,11 +1,12 @@ within GenKinetics; + package UserGuide "user guide" extends Modelica.Icons.Information; model Overview extends Modelica.Icons.Information; - annotation ( - Documentation(info=" + annotation( + Documentation(info = "

About


GenKinetics contains an implementation of a specific set of reaction kinetics, namely, generalized simplified kinetic formats. It follows many of the guidelines recommended by the Biochem library. The underlying simplified kinetics formats are represented by generalized structured kinetics formulas suitable for arbitrary biochemical reactions with arbitrary number of substrates, products, inhibitors and activators. In this way, matabolic reaction networks can be easily assembled using a few number of reaction kinetics.


Structure of the Library

@@ -61,27 +62,25 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet model Contributors extends Modelica.Icons.Information; - annotation ( - Documentation(info=" -

Author: Atiyah Elsheikh

+ annotation( + Documentation(info = " +

Author: Atiyah Elsheikh, Mathemodca.com

Contact details: GenKinetics.UserGuide.Contact

")); end Contributors; model Contact extends Modelica.Icons.Contact; - annotation ( - Documentation(info=" -

Atiyah Elsheikh : atiyah.m.g.elsheikh at gmail.com

-")); + annotation( + Documentation(info = "

Atiyah Elsheikh : atiyah.elsheikh at mathemodica.com

+")); end Contact; model ReleaseNotes extends Modelica.Icons.ReleaseNotes; - annotation ( - Documentation(info=" -

V1.0-alpha (7.12.2018) : First version containing Biochem-like structure and implementation of Convenience and LinLog kinetics

-")); + annotation( + Documentation(info = "

+")); end ReleaseNotes; model References @@ -90,15 +89,14 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet model CopyRight extends Modelica.Icons.Information; - annotation ( - Documentation(info=" -

Licensed under the Modelica License 2

-

Copyright © <2018>, <Atiyah Elsheikh>.

+ annotation( + Documentation(info = "

Licensed under the Modelica License 2

+

Copyright © <2018-2020>, <Mathemodica.com>.

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica BSD 3-Clause License. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.License 

-")); +")); end CopyRight; - annotation ( - Documentation); + annotation( + Documentation); end UserGuide; diff --git a/UserGuide/package.order b/UserGuide/package.order index b26b2fb..9b00f41 100644 --- a/UserGuide/package.order +++ b/UserGuide/package.order @@ -1,7 +1,7 @@ Overview Contributors Contact -License ReleaseNotes References CopyRight +License From abe9edde41be70b626f5fe50bbf38f5cb22425e6 Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 22 Jun 2020 22:04:55 +0100 Subject: [PATCH 2/7] GenKinetics version 1.0.1 --- package.mo | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/package.mo b/package.mo index 16bc4cf..1f895ae 100644 --- a/package.mo +++ b/package.mo @@ -7,5 +7,6 @@ annotation ( Documentation(info = "

This package contains an implementation of generalized simplified kinetic formats following the guidelines recommended by the Biochem library. Matabolic reaction networks can be easily assembled using a few number of reaction kinetics. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought.


Licensed under the Modelica License 2


Copyright © GenKinetics.UserGuide.CopyRight

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.ModelicaLicense2 or visithttp://www.modelica.org/licenses/ModelicaLicense2.

"), - uses(Modelica(version = "3.2.3"))); + uses(Modelica(version = "3.2.3")), + version = "1.0.1"); end GenKinetics; From 9b4cf2a5aa59da4dfd272893187ef4b3fad347c1 Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 22 Jun 2020 22:06:17 +0100 Subject: [PATCH 3/7] uses Biochem Version 1.0.2 --- package.mo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.mo b/package.mo index 1f895ae..a49147f 100644 --- a/package.mo +++ b/package.mo @@ -7,6 +7,6 @@ annotation ( Documentation(info = "

This package contains an implementation of generalized simplified kinetic formats following the guidelines recommended by the Biochem library. Matabolic reaction networks can be easily assembled using a few number of reaction kinetics. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought.


Licensed under the Modelica License 2


Copyright © GenKinetics.UserGuide.CopyRight

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.ModelicaLicense2 or visithttp://www.modelica.org/licenses/ModelicaLicense2.

"), - uses(Modelica(version = "3.2.3")), + uses(Modelica(version = "3.2.3"),BioChem(version = "1.0.2")), version = "1.0.1"); end GenKinetics; From 509bf175a5a1827acd014eca34845f8236b0fd78 Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Sun, 28 Mar 2021 06:57:18 +0200 Subject: [PATCH 4/7] annotation stuffs --- UserGuide/package.mo | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/UserGuide/package.mo b/UserGuide/package.mo index 1a5087a..c7c090c 100644 --- a/UserGuide/package.mo +++ b/UserGuide/package.mo @@ -1,11 +1,10 @@ -within GenKinetics; - +within GenKinetics; package UserGuide "user guide" extends Modelica.Icons.Information; model Overview extends Modelica.Icons.Information; - annotation( + annotation ( Documentation(info = "

About


GenKinetics contains an implementation of a specific set of reaction kinetics, namely, generalized simplified kinetic formats. It follows many of the guidelines recommended by the Biochem library. The underlying simplified kinetics formats are represented by generalized structured kinetics formulas suitable for arbitrary biochemical reactions with arbitrary number of substrates, products, inhibitors and activators. In this way, matabolic reaction networks can be easily assembled using a few number of reaction kinetics.

@@ -62,7 +61,7 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet model Contributors extends Modelica.Icons.Information; - annotation( + annotation ( Documentation(info = "

Author: Atiyah Elsheikh, Mathemodca.com

Contact details: GenKinetics.UserGuide.Contact

@@ -71,14 +70,14 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet model Contact extends Modelica.Icons.Contact; - annotation( + annotation ( Documentation(info = "

Atiyah Elsheikh : atiyah.elsheikh at mathemodica.com

")); end Contact; model ReleaseNotes extends Modelica.Icons.ReleaseNotes; - annotation( + annotation ( Documentation(info = "

  • V1.0.1-alpha (22.06.2020) : Restarting , MSL 3.2.3
  • V1.0.0-alpha (07.12.2018) : First version containing Biochem-like structure and implementation of Convenience and LinLog kinetics

")); end ReleaseNotes; @@ -89,7 +88,7 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet model CopyRight extends Modelica.Icons.Information; - annotation( + annotation ( Documentation(info = "

Licensed under the Modelica License 2

Copyright © <2018-2020>, <Mathemodica.com>.

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica BSD 3-Clause License. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.License 

@@ -97,6 +96,6 @@ modelica://GenKinetics.Interfaces.Dynamic.Dimension.ReactionDimension\">GenKinet end CopyRight; - annotation( + annotation ( Documentation); end UserGuide; From 3c946148c4b400f6407905d8acc52e64688fb9dd Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 29 Mar 2021 09:41:19 +0200 Subject: [PATCH 5/7] MSL v4.0.0 --- package.mo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.mo b/package.mo index a49147f..316b580 100644 --- a/package.mo +++ b/package.mo @@ -7,6 +7,6 @@ annotation ( Documentation(info = "

This package contains an implementation of generalized simplified kinetic formats following the guidelines recommended by the Biochem library. Matabolic reaction networks can be easily assembled using a few number of reaction kinetics. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought.


Licensed under the Modelica License 2


Copyright © GenKinetics.UserGuide.CopyRight

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.ModelicaLicense2 or visithttp://www.modelica.org/licenses/ModelicaLicense2.

"), - uses(Modelica(version = "3.2.3"),BioChem(version = "1.0.2")), + uses(Modelica(version = "4.0.0"),BioChem(version = "1.0.2")), version = "1.0.1"); end GenKinetics; From 2fe404dce966f72d3b089aabfb0c6be59cdbfbd8 Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 29 Mar 2021 09:42:05 +0200 Subject: [PATCH 6/7] version 1.0.2 --- package.mo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.mo b/package.mo index 316b580..7640699 100644 --- a/package.mo +++ b/package.mo @@ -8,5 +8,5 @@ annotation ( Documentation(info = "

This package contains an implementation of generalized simplified kinetic formats following the guidelines recommended by the Biochem library. Matabolic reaction networks can be easily assembled using a few number of reaction kinetics. Constructed models can also be used for computing parameter sensitivities with little modifications to the used interfaces and by initializing the input Jacobian, i.e. the parameters w.r.t. derivatives are sought.


Licensed under the Modelica License 2


Copyright © GenKinetics.UserGuide.CopyRight

This Modelica package is free software and the use is completely at your own risk; it can be redistributed and/or modified under the terms of the Modelica License 2. For license conditions (including the disclaimer of warranty) see Modelica.UsersGuide.ModelicaLicense2 or visithttp://www.modelica.org/licenses/ModelicaLicense2.

"), uses(Modelica(version = "4.0.0"),BioChem(version = "1.0.2")), - version = "1.0.1"); + version = "1.0.2"); end GenKinetics; From a6ca5df54dddb0b546c3943c812f7c42cb3a3b6c Mon Sep 17 00:00:00 2001 From: Atiyah Elsheikh Date: Mon, 29 Mar 2021 11:13:48 +0200 Subject: [PATCH 7/7] version 1.0.2-alpha --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 32a7f9d..db9f102 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,8 @@ A Modelica library for descriptive modeling of biochemical reaction networks usi #### Release notes +(29.3.2021) v1.0.2-alpha : MSL 4.0.0 + (22.06.2020) v1.0.1-alpha : starting the progress again, MSL 3.2.3 (7.12.2018) v1.0-alpha : Initial implementation containing Biochem-like structure and implementation of Convenience and LinLog kinetics