GSoC projects 2012

We participated as a mentoring organization in 2012, for our 2th consecutive year, with 6 projects proposed and mentored by our Nodes and international community.

A simulator-independent Python API for multi-compartmental modeling
A simulator-independent, neuroML-compliant python API for multi-compartmental models to allow standardization of multi-compartmental model simulators. The API will also permit cross-checking of results between different simulators, ease of porting between simulators, access to many scientific Python libraries and encourage a more modular approach towards simulator development.

Student: Michael Vella
Mentor: Andrew Davison (French INCF Node) and the NineML and NeuroML developers

An automated electronic lab notebook for reproducible computational research
The concept of Sumatra is very appealing to any researcher who has already thought about replicability of the results and methods. It begins more and more evident that presenting scientific paper is not only about sharing the results of simulation in the form of ’static’ images, flowcharts and algorithms. Today, the reader expects to be more involved in computation process. Sumatra is a tool which makes it possible and the software that aides in reproduction of the results.

Student: Dmitry Samarkanov
Mentor: Andrew Davison (French INCF Node)

GPU-Based Neural Simulator
The main project idea is to utilize the parallel processing capabilities of modern GPU devices for the modeling of biological neuronal systems by implementing a OpenCL-based simulation framework based on the Hodgkin-Huxley model.

Student: Benjamin Wild
Mentor: Stanislav Stankovic (Finnish INCF Node

NERD - NEuRonalDatabase
Main project goal is to provide solution of successful mapping neuronal data, annotated in "open metadata Markup Language" format to document oriented database, such as MongoDB, so it could be queried with existing REST API . It's part of project "NERD" that aims at popularization of sharing data in neuroscience. 

Student: Lukasz Mokrzycki
Mentor: Christian Kellner and Christian Garbers (German INCF Node)

Parallelization of the Multiple Interacting Instances of Neuronal Dynamics (MIIND) software.
I want to implement parallelization in the Multiple Interacting Instances of Neuronal Dynamics (MIIND) software, to allow the simulation of larger neuron population networks. To achieve this I first want to implement a parallelization on the level of individual neuron populations. As a second step I want to investigate if an additional parallelization on the population algorithm level will bring further benefits.

Student: David Sichau
Mentor: Marc de Kamps (UK INCF Node)

Spatial Queries in CATMAID
Student: Oliver Uvman
Mentor: Stephan Gerhard (Swiss INCF Node)