Sept8

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Contents

First Annual INCF Cross-Task Force Hackathon

IRC

IRC channel - #incf on irc.oftc.net

Shared folder

Shared folder from the meeting

Join the hackers list

Hackers list sign-up page

Venue / directions

A group will meet (with Janis) at 8:30 in the lobby of the Seaport Hotel and then go together to MIT.

What you need to bring

  • Laptop
  • Pointers to your personal projects or projects you are passionate about

About

The INCF is composed of groups around the world that are addressing challenging problems of data integration in the neurosciences. To accomplish this, Senior scientists leading these groups have attracted talented programmers (staff, scientists, graduate students, undergraduates, high school students, etc) who seek to reuse best practices from the open source community to meet this challenge.

Today, the INCF task forces have helped to coordinate individuals like these within subject areas that are relevant to neuroinformatics. Additionally, the INCF has been successful in creating a software center that is increasingly richly populated with open source tools from the broader neuroinformatics community. However, sometimes the best work is done when technical people get excited each other's technology. Because of this, it would be extremely useful for those individuals whose fingers are on the keyboards, driving innovation, to:

  1. Be introduced to and help contribute to a coherent and compelling vision of a global neuroinformatics data integration infrastructure
  2. Build relationships that they can use to call on each other for technical help
  3. Exchange best practices on what open source tools to reuse
  4. Build understanding about the work going on between task forces and between external software projects in order to identify technical connection points.
  5. Kick off interactions by hacking up design documents or small bits of code that prototype technical connection points.

Spirit of the meeting

We are trying something new here. Unlike meetings where the technical goals or outcomes are pre-defined, we are trying to create an interactive environment that will spur creativity and cross-communication. The ideal end products are a brief summary for the group of interactions that occurred that led to an idea that neither party had prior to the session.

Itinerary / Agenda

Agenda of the hackathon

Proposed "Bird of a feather" sessions

The spreadsheet for determining the break out sessions

Projects to seek crossover interactions on

Cross-task force initiatives

  • Streamlining and standardizing use of coding resources used throughout INCF programs
  • INCF Virtual Machine and irods
  • What does a global framework for neuroinformatics looks like that pulls efforts from task forces together?
  • Creation of Waxholm space brain region labels that are identified with ontology terms from PONS group
  • Reconciling ontology-based search (PONS Representation & Deployment) with spatial search (Digital Atlasing infrastructure)
  • How does multi-scale simulation fit into atlasing and ontology?
  • Tools that read the multiple atlas labels (displays or overlays the labels from the different atlases at a given plane?)
  • Generate a consistency volume to see locations where all atlases call a structure the same name. Find non-problematic structures that are identified across all atlases, modalities, and possibly even in different species
  • “plug and play” registration workflow

Task force projects

Confirmed Attendees

  • Brian Avants-- UPenn registration/digital atlasing
  • Alexandra Badea - Digital Atlasing task force
  • Rembrandt Bakker -- Scalable Brain Atlas + CocoMac / Structural Lexicon / Atlasing
  • Janis Breeze -- INCF Secretariat + Data sharing
  • Chris Condit -- Neuroscience Information Framework -- developer of the NIF search interface and index
  • Andrew Davison - Electrophys / Multiscale Modeling
  • Blaise Frederick - NIRS / Datasharing
  • James Gee -- Digital Atlasing
  • Stephan Gerhard -- Connectome Format & Library / Datasharing
  • Satra Ghosh -- NiPyPE / Datasharing
  • Padraig Gleeson -- NeuroML/Neuro Construct / Multi-scale Task Force
  • Chris Gorgolewski - NIPyPE / Datasharing
  • Jeff Grethe -- Atlasing / PONS / Datasharing efforts
  • David Gutman -- Emory U.
  • Yaroslav Halchenko -- Neurodebian / Datasharing
  • David Hamilton -- Neuron Registry
  • Michael Hanke -- Neurodebian/Datasharing
  • Christian Haselgrove -- Atlasing / Datasharing
  • Luis Ibanez -- Digital Atlasing / ITK group within Kitware
  • David Keator -- Datasharing TF
  • Linda Lanyon -- UBC + INCF
  • Stephen Larson -- Digital Atlasing + Structural Lexicon/Neurolex
  • Bengt Ljungquist -- Electrophys task force
  • Piotr Majka -- Common Atlas format, Digital Atlasing task force
  • Roman Mouček -- Electrophys Task Force
  • Lydia Ng -- Digital Atlasing Task Force
  • JB Poline -- Neuroimaging Data sharing
  • Raphael Ritz -- Digital Atlasing + Secretariat
  • Seth Ruffins -- Digital Atlasing
  • Alan Ruttenberg -- Ontology Representation and Deployment
  • Malin Sandström -- INCF secretarian + multi-scale modeling
  • Yannick Schwartz -- PyXNAT / Datasharing
  • Gang Song -- UPenn registration/digital atlasing
  • Richard Stoner -- UCSD Post doc working with Digital Atlasing Infrastructure
  • Jeff Teeters -- Electrophys TF + CRCNS
  • Thomas Wachtler -- Electrophys Task Force
  • Ilya Zaslavsky -- Digital Atlasing Infrastructure
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