rnavagamuwa
commented
7 years ago Hi , I am Randika Navagamuwa and I am a final year undergraduate of Department of Computer Science and Engineering, University of Moratuwa, Srilanka. Last year also I participated and completed GSoC with Eclipse foundation [1]. This year I thought of applying for this project. Since there is plenty of time before applying as a student, I thought of getting familiar with the project. As the initial step what should I be doing.
[1] https://summerofcode.withgoogle.com/archive/2016/projects/4930443140923392/
Thank you, Randika Navagamuwa (randika.12@cse.mrt.ac.lk)
kapilkd13
funasoul
khanspers
AlexanderPico
Introduction
Today SBML has several extension packages to extend its capability. One of its extension is called Spatial Processes (spatial) which supports for describing processes that involve a spatial component, and describing the geometries involved. In spatial package, there are several ways (analytic geometry, sampled field geometry, parametric geometry, CS geometry, mixed geometry) to describe the spatial geometries in a model. Currently, most of the spatial simulator which supports SBML spatial package supports analytic geometry and sampled field geometry. While we just focus on developing a spatial simulator with FDM (Finite Difference Method) or FVM (Finite Volume Method) as a numerical integrator, supporting analytic geometry and sampled field geometry will be enough. But if we want to implement our spatial simulator with a more stable integrator such as FEM (Finite Element Method), then the model should be described with parametric geometry. Creating a spatial model with parametric geometry from scratch is quite tough, especially if we want to create a spatial model from microscope image.
This summer, we would like to mentor a student in developing a converter which will convert spatial SBML models with different spatial geometries.
Goal
The project could be split down into following 3 tasks.
Student requirements
Students should be familiar with the Java™ programming and handling XML documents with their favorite APIs. If the student are interested in creating a simple GUI application to visualize their converted spatial models, he/she should have some experience on creating a GUI application using Swing or JavaFX.
Potential Mentors