Tuesday, June 28, 2016

First week for converting Layout to CellDesigner Annotation

Hello all,

Last week, I  have mentioned that there are still few attributes in the CellDesigner annotation to be converted. Before working the conversion for the other direction, I have implemented the conversions for links and bezier curves.

As for the conversion of SBML Layout to CellDesigner Annotation,  I have been working on the APIs for SBML objects such as Species and for inputs/outputs. The basic algorithm for the conversions with be as follow.

  1. Read model with JSBML
  2. Downgrade 1. to Level 2 Version 4
  3. Unmarshal 2. as string
  4. From 1. convert the Layout attributes to 3.
So far, I have created the basic algorithms above and have created model with empty CellDesigner annotation. Below are the progress I have made so far. For next week, I will be starting on converting each type of glyphs.

Wednesday, June 22, 2016

Half way through

Hello all,

This week is midterm evaluation week. Which means that I am half way through the GSoC program. This week, I have been working on the conversion of complex species and edit points for branched reactions.

Since it's midterm week, I have created a diagram to show how much of the conversion from CellDesigner Annotation to SBML layout has been completed. All items in blue are the ones that have been covered and are able to convert. Items in red are annotations that have not yet been implemented.  From this diagram, you can tell that I still need to work with reactant / product links, residues, beziers, and boolean. 

For my initial plan, I had my midterm goal set as completing the conversion of CellDesigner Annotation to SBML Layout.  The converter still have some missing features, but I have roughly accomplished my goal.  As for my next goal, I will be working on the conversion from SBML Layout to CellDesigner Annotation and will have a converter that converts both ways.

Tuesday, June 14, 2016

Hello everyone,

Since last week,  I have been working with the conversion of reactions.  This week, I have been mainly working on edit points (reaction with bending lines) and modifiers. Here are some diagrams that I have accomplished .

For next week, I will continue working on the conversion of reaction. Heterodimers, dissociation, and truncation reaction with edit points, species complex,  bezier curves, and residue are the things left to be completed. And since it is midterm evaluation next week, I am hoping to complete the CellDesigner annotation conversion to SBML Layout by then.

Wednesday, June 8, 2016

Hi everyone,

Last week,  I have successfully converted the compartment and species from CellDesigner annotation to SBML Layout.  Since then, I have been working on converting the reaction. So far, I have partial completed converting reaction.

For now, I have completed conversions reactions with straight lines and heterodimer association, dissociation. and truncation. Below are some of the models I have successfully converted.

original model  1                                   converted model 1

original model  2                                   converted model 2

heterodimer original                               heterodimer converted

dissociation original                                  dissocation converted

truncation original                                  truncation converted

combined original                                                      combined converted

For next week, I will be working on reactions with bending lines, reactions with modifiers, bezier lines and complexes.  And I am hoping to complete the conversion from CellDesigner annotation to SBML Layout  before the midterm evaluation.