GSoC Project Idea 16.4: Open Data for OpenWorm

linux
python

#1

Description: OpenWorm is building the world’s first digital organism in an open source manner. To date, we have developed significant infrastructural components for modeling the C. elegans nematode worm, recently published in a peer-reviewed special issue of the Philosophical Transactions of the Royal Society. Now that our code has reached initial critical milestones, and our scientific directions have been peer reviewed and published, we now embark on the next phase of development. This phase will require a significant increase / improvement in the availability of open data for the purpose of taking the next steps in our simulations. In this project, we will break through the technical and logistical barriers to making these data sets available for research purposes, and make data sets of critical importance for building the simulation publicly available for broader research.

Aims: We will be gathering, packaging, documenting, and writing up data papers for key datasets in the space of understanding the C. elegans. This includes, videos of worm movement, videos of worm neuron behavior, traces of worm cellular behavior, etc. Along the way, code will be written to pull out key features from the data into a manner that can be compared against models. Code will also need to be written to define key metrics that can be calculated from key features. Platforms such as SciUnit and NeuronUnit will be important for this, as well as tools from the Movement Validation set of source code. By the end of the project, we will have made available 3-5 key data sets and posted them online.

Skills: Basic command line skills in Linux Shell, Python scripting, familiarity with open source programming, Desirable to have a background in physics and math to help understand the underlying principles of the data and the metrics being computed

Mentor: Stephen Larson (stephen@openworm.org)