International Neuroinformatics Coordinating Facility

Web Page: http://www.incf.org/gsoc

Mailing List: https://lists.incf.org/listinfo/incf-users

The INCF is a professional organization devoted to advancing the field of neuroinformatics. One of its aims is to develop an international neuroinformatics infrastructure, which promotes the sharing of data and computing resources to the international research community.

Projects

• 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.
• 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.
• 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.
• NERD - NEuRonalDatabase, Lukasz Mokrzycki 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. Mentored by members of the German INCF Node (Christian Kellner, Christian Garbers)
• Parallelization of the Multiple Interacting Instances of Neuronal Dynamics 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.
• Spatial Queries in CATMAID I want to implement spatial queries in CATMAID as described in idea one of the example proposals at http://www.incf.org/gsoc#section-13.