Metabolic Component Library

Merging to remove the extra head

Tommy Yu — 2015-02-12

Merging to remove the extra head - Since the title is changed and in the interest of maintaining the current structure we keep it as is.

Further work on the HTML documentation.

Matthias K?nig — 2013-05-17

Further work on the HTML documentation.

Work on the automatic HTML rendering.

Matthias K?nig — 2013-05-17

Work on the automatic HTML rendering.

HTML Documentation updated.

Matthias K?nig — 2013-05-17

HTML Documentation updated.

Some work on tutorial.

Matthias K?nig — 2013-05-15

Some work on tutorial.

wolf_heinrich_2000 SBGN overview added

Matthias K?nig — 2013-04-21

wolf_heinrich_2000 SBGN overview added

Nazaret 2009 example implemented and integratable.

Matthias K?nig — 2013-04-21

Nazaret 2009 example implemented and integratable. Results between normal and MCL implementation not identical ! Problems with original model implementation (no steady state)!

Merge

Matthias K?nig — 2013-04-19

Merge

Working on Koenig 2012 Glucose Metabolism Example.

Matthias K?nig — 2013-04-19

Working on Koenig 2012 Glucose Metabolism Example.

Removed duplicate cmeta:id attribute that was causing an XML error, and changed metadata to use the more human readable ID.

2013-04-19

Removed duplicate cmeta:id attribute that was causing an XML error, and changed metadata to use the more human readable ID.

Wolf Heinrich Example implemented and working !

Matthias K?nig — 2013-04-18

Wolf Heinrich Example implemented and working !

Example Full 1 working!

Matthias K?nig — 2013-04-18

Example Full 1 working!

Changes in Ingegrator and file hierarchy.

Matthias K?nig — 2013-04-18

Changes in Ingegrator and file hierarchy.

Merge Example 2 changes.

Matthias K?nig — 2013-04-18

Merge Example 2 changes.

Changes in Ingegrator and file hierarchy.

Matthias K?nig — 2013-04-18

Changes in Ingegrator and file hierarchy.

Trivial whitespace changes, and moved import to be adjacent to peer import.

2013-04-17

Trivial whitespace changes, and moved import to be adjacent to peer import.

To "clone" an imported component, the top level import element needs to be duplicated, not just the component reference within an existing import. The rationale is that all connections within a top-level import are kept intact, as dictated by the encapsulation in the imported model.

2013-04-17

To "clone" an imported component, the top level import element needs to be duplicated, not just the component reference within an existing import. The rationale is that all connections within a top-level import are kept intact, as dictated by the encapsulation in the imported model.

CellML Java API source code first commit.

Matthias K?nig — 2013-04-16

CellML Java API source code first commit.

Project summary updated and first manuscript draft for CellML-MCL.

Matthias K?nig — 2013-04-15

Project summary updated and first manuscript draft for CellML-MCL.

Components definition Excel added.

Matthias K?nig — 2013-04-12

Components definition Excel added.

Example reaction mechanisms in SBGN updated.

Matthias K?nig — 2013-04-12

Example reaction mechanisms in SBGN updated.

Example files with documentation generated.

Matthias K?nig — 2013-04-12

Example files with documentation generated.

OpenCell output of Mass Action examples 1 & 3.

Matthias K?nig — 2013-04-12

OpenCell output of Mass Action examples 1 & 3.

Example 3 Mass Action working.

Matthias K?nig — 2013-04-12

Example 3 Mass Action working.

Second mass action example A <-> B <-> C.

Matthias K?nig — 2013-04-12

Second mass action example A <-> B <-> C. Not working due to sharing of B ?

First working example using the library components !

Matthias K?nig — 2013-04-12

First working example using the library components !

Some smaller updates in the documentation. Not critical.

Matthias K?nig — 2013-04-12

Some smaller updates in the documentation. Not critical.

Compact library for import generated.

Matthias K?nig — 2013-04-12

Compact library for import generated. Components and Units are collected from the individual LibraryModelComponents. This is the file imported and should be kept locally with the used model.

Proper encapsulation of all the example files with separation into network/reaction/librarycomponent structure.

Matthias K?nig — 2013-04-10

Proper encapsulation of all the example files with separation into network/reaction/librarycomponent structure. Some smaller bugfixes in mapping between components.

Naming error fixed in HillIrrev.

Matthias K?nig — 2013-04-09

Naming error fixed in HillIrrev. Components documentation updated: - Variables of Components parsed - CellML library components validated with cellml-API

Documentation of Reaction Mechanism.

Matthias K?nig — 2013-04-09

Documentation of Reaction Mechanism. Images for basic mechanisms created.

Reaction Mechanisms in SBGN created.

Matthias K?nig — 2013-04-05

Reaction Mechanisms in SBGN created.

Minor bugs in naming conventions removed.

Matthias K?nig — 2013-04-04

Minor bugs in naming conventions removed.

Formula images created.

Matthias K?nig — 2013-04-04

Formula images created. Minor bugs in naming conventions removed.

Fixed case and only the title is needed.

Tommy Yu — 2013-03-27

Fixed case and only the title is needed.

Need title tag.

Tommy Yu — 2013-03-27

Need title tag.

tags where appropriate.

Matthias K?nig — 2013-03-26

tags where appropriate.

replaced with
due to missing support of
element.

Matthias K?nig — 2013-03-26

replaced with

due to missing support of
element.

CellML files changed from CellML v1.0 -> v1.1 to support import of the components.

Matthias K?nig — 2013-03-26

CellML files changed from CellML v1.0 -> v1.1 to support import of the components. Additional header added to CellML files for metabolic component library.

Documentation moved to the HTML document from the README.

Matthias K?nig — 2013-03-26

Documentation moved to the HTML document from the README.

First draft of a library documentation.

Matthias K?nig — 2013-03-26

First draft of a library documentation.

Link to a model.

Matthias K?nig — 2013-03-26

Link to a model.

Created Test HTML page for Exposure.

Matthias K?nig — 2013-03-26

Created Test HTML page for Exposure.

Folder structure rearranged. Moving of library components to library.

Matthias K?nig — 2013-03-26

Folder structure rearranged. Moving of library components to library.

Changing of folder structure to distinguish between references, examples, the actual component library and documentation.

Matthias K?nig — 2013-03-25

Changing of folder structure to distinguish between references, examples, the actual component library and documentation.

Initial commit.

Matthias K?nig — 2013-03-25

Initial commit. COPASI 4.8 (Build 35) kinetic equations with test cases implemented.

Metabolic Component Library

Merging to remove the extra head

Further work on the HTML documentation.

Work on the automatic HTML rendering.

HTML Documentation updated.

Some work on tutorial.

wolf_heinrich_2000 SBGN overview added

Nazaret 2009 example implemented and integratable.

Merge

Working on Koenig 2012 Glucose Metabolism Example.

Removed duplicate cmeta:id attribute that was causing an XML error, and changed metadata to use the more human readable ID.

Wolf Heinrich Example implemented and working !

Example Full 1 working!

Changes in Ingegrator and file hierarchy.

Merge Example 2 changes.

Changes in Ingegrator and file hierarchy.

Trivial whitespace changes, and moved import to be adjacent to peer import.

To "clone" an imported component, the top level import element needs to be duplicated, not just the component reference within an existing import. The rationale is that all connections within a top-level import are kept intact, as dictated by the encapsulation in the imported model.

CellML Java API source code first commit.

Project summary updated and first manuscript draft for CellML-MCL.

Components definition Excel added.

Example reaction mechanisms in SBGN updated.

Example files with documentation generated.

OpenCell output of Mass Action examples 1 & 3.

Example 3 Mass Action working.

Second mass action example A <-> B <-> C.

First working example using the library components !

Some smaller updates in the documentation. Not critical.

Compact library for import generated.

Proper encapsulation of all the example files with separation into network/reaction/librarycomponent structure.

Naming error fixed in HillIrrev.

Documentation of Reaction Mechanism.

Reaction Mechanisms in SBGN created.

Minor bugs in naming conventions removed.

Formula images created.

Fixed case and only the title is needed.

Need title tag.

tags where appropriate.

replaced with due to missing support of element.

CellML files changed from CellML v1.0 -> v1.1 to support import of the components.

Documentation moved to the HTML document from the README.

First draft of a library documentation.

Link to a model.

Created Test HTML page for Exposure.

Folder structure rearranged. Moving of library components to library.

Changing of folder structure to distinguish between references, examples, the actual component library and documentation.

Initial commit.

replaced with
due to missing support of
element.