Monday, August 22, 2016

Final Report

Hello everyone,

As the GSoC come to an end, I would like to sum up what I have done for the past 4 months. For my GSoC project, I have been working on the Interconvertible Layout program for CellDesigner. This project implements a converter that turns CellDesigner annotation into SBML Layout package and vice versa, preserving the biochemical network layouts when handling the model in different softwares.

Here is a link to this project's repository.

For my last result, I will present the conversion of influenza model (Matsuoka,Y. BMC systems biology 7.1 (2013): 1.) and Core metabolism model of E.coli ( converted with EscherConverter.

CellDesigner to SBML Layout

Influenza model original

Influenza model converted

SBML Layout to CellDesigner

E.coli model original

E.coli model converted

Finally, I would like to thank Google Summer of Code, NRNB, and SBML team for giving me this opportunity and my mentors Dr. Dräger and Dr. Funahashi for their support.

Wednesday, August 17, 2016

Final week (week 16)

Hi all,

Only few more days are left until I submit my work. And last week, I left off with some unfinished tasks. Here are the todo list from last week. Darker blue means for the conversion from SBML Layout to CellDesigner Annotation and lighter blue means  for the conversion from CellDesigner Annotation to SBML Layout.

For this week, I have mainly worked on 1st, 3rd, and 4th tasks. As for the conversion of bezier curve,  I have converted the bezier curve into line segments, since CellDesigner does not allow a bezier curve with the reaction with one reactant and one product.

Bezier original

Bezier converted

For the 3rd task, I have added conversion for reaction with modifiers with branches.

Modifier with branches original

Modifier with branches converted

Also, for the 4th task, adjusting the arrowhead, I have moved the end point of the line segment to go to the boundary of the glyph.

arrowhead before

arrowhead after

Additionally, I have fixed the conversion for FBC package. I have added the conversion for reaction with boolean logic operators.

boolean model

boolean model converted 

So for the next few days, I have to work on the 2nd task and wrap up the project.

Wednesday, August 10, 2016

week 15

Hello everyone,

Last week, I left off with the following tasks. So, this week I have been working on these. In particular, I have been working on the 1st, 2nd, 3rd, 5th, and 6th tasks from the top.


For the first three tasks, it is still in progress.  I am struggling with the conversion of edit points. But I managed to complete the conversion for some of the reaction.

heterodimer association

heterodimer association converted

For the 5th task (adjusting text glyph), the text for the reaction is adjusted to go in the center of reaction. The previous implementation laid the text glyph near a reactant, but now I have changed that to go into center of the reaction

before adjustment            after adjustment

For the 6th task, I have added the conversion of gene on CellDesigner Annotation to the SBML fbc package.

fbc converted model

Here is the diagram of how much of the conversion is covered. Blue means it's completed, red means it's not yet completed, green means it's unconvertable.

Next week is going to be the last week of Google Summer of Code. Below is the tasks that I still need to work on. I am hoping to complete at least the top 5 tasks before the deadline.

Wednesday, August 3, 2016

Week 14

Hello everyone,

This week, I have been working on reactions with branches. I was able to convert the branched reactions only with the one that have single reactant and product. For the reaction with multiple reactants/products,  the conversion for connecting point is a bit off. I assume there is something wrong in the algorithm.

So far, for the conversion from SBML Layout to CellDesigner annotation, I have completed the following shown in the chart below. Blue is completed, red is incomplete, and green is inconvertable.

Also, the remaining tasks for this project is as below.  The dark blue is for conversion from SBML Layout to CellDesigner annotation, and the light blue if for conversion from CellDesigner annotation to SBML Layout. For next week, I will be working on the tasks on the top.