2012 Allen Brain Atlas Hackathon

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The Allen Institute would like to thank the International Neuroinformatics Coordinating Facility (INCF) for cosponsoring the 2012 Allen Brain Atlas Hackathon, as well as everyone who joined us for five days of mining, analyzing, and developing applications using the Allen Brain Atlas API. The projects, ranging from the practical to the whimsical, were inspiring. Please join us in congratulating Rich Stoner, who collected the most buttons for his presentations, and the "People's Choice", Leon French.

The 2012 Allen Brain Atlas Hackathon may be over, but there are opportunities to connect with the Allen Institute throughout the year. If you are interested in attending the next hackathon, or learning about our other events, please follow us on Twitter and Facebook.

Speakers

Speaker Organization Presentation
Chinh Dang Allen Institute for Brain Science The Allen Brain Atlas API
Lydia Ng
Allen Institute for Brain Science
Mouse ISH Informatics Pipeline
Chris Lau
Allen Institute for Brain Science Human Brain Atlas Informatics Pipeline
Mike Hawrylycz
Allen Institute for Brain Science Analyzing Human Microarray Gene Expression Data
Carol Thompson
Allen Institute for Brain Science Allen Developing Mouse Brain Atlas: A Spatiotemporal Atlas of the Mouse Brain
Ed Lein
Allen Institute for Brain Science Human Brain and NHP Developmental Gene Expression Analysis
Stephen Larson
University of California, San Diego
The Allen Brain Atlas open data: integration and hacking experiences
Shuiwang Ji
Old Dominion University
Mining the mouse data: clustering, prediction, and networks
Leon French
University of British Columbia
Tips for mining and integrating the Allen Mouse Brain Atlas data
David Marques
Elsevier
Elsevier Neuro-Atlas API Program

Event Materials

Document Description
Flyer
Announcement
Agenda
Schedule
Allen Brain Atlas Data Model Quick Reference
Data model highlights and lists of commonly required members
Allen Brain Atlas Data Model Diagram
Comprehensive data model diagram
Allen Brain Atlas Structure Ontology Data Model
Subset of data model detailing the structure ontologies
Mouse ISH Data Model
Subset of data model detailing the Mouse projects' ISH experiments
Human/NHP Microarray and RNA Sequencing Data Model
Subset of the data model detailing the human and NHP microarray and RNA sequencing experiments
Age Comparison: Human, NHP and Mouse
Asserted age mappings across species
Allen Mouse Brain to Human Brain Atlas Structure Mappings
Asserted structure mappings from the Mouse Brain to Human Brain ontologies
Allen Human Brain to Mouse Brain Atlas Structure Mappings
Asserted mappings from the Human Brain to Mouse Brain ontologies
Correlative, Differential, and Expression Searches
Reference for correlative, differential and expression searches
Mouse Brain Reference Atlas 1
Mouse Brain reference atlas
Mouse Brain Reference Atlas 2
Mouse Brain reference atlas
Developing Mouse Brain Reference Atlas 1
Developing Mouse Brain reference atlas
Developing Mouse Brain Reference Atlas 2
Developing Mouse Brain reference atlas
Allen Mouse Brain and Developing Mouse Brain Merged Nissl Annotations
Merged annotations from both the Mouse Brain and Developing Mouse Brain reference atlases

Sponsors




Press

Links



Attendees

Attendee Organization Website Github Projects
Andrew Smith Bristol-Myers Squibb

  • Created human and mouse gene expression summaries using bar graphs.
Andrew Zaldivar University of California, Irvine http://sites.uci.edu/andrewzaldivar
  • Viewed multiple genes' expression using the sunburst graph.
  • Gene expression signatures of neuromodulatory system.
Cameron McDonald University of British Columbia

  • Created "Falling Brain Sections" game.
Catherine Ojo Jan & Dan Duncan Neurological Research Institute

  • Developed scripts to retrieve and plot gene expression data in Matlab.
  • Focused on developing models/algorithms that can predict whether genes expressed in a structure map to one ore more networks (i.e. signalling pathways) active in that structure.
  • Work contineus with focus on BrainSpan and Autism studies' data.
Dan Butler University of Washington


David J. Hamilton George Mason University

  • Collaborated with Eric Hamilton.
  • Searched for conserved hippocampal marker genes.
  • Rendered grid data on histology images.
David Marques Elsevier http://www.brainnav.com/
  • Speaker.
Donald G. McLaren Massachusetts General Hospital/Harvard Medical School http://www.martinos.org/~mclaren

Eric Hamilton


  • Collaborated with David Hamilton.
  • Searched for conserved hippocampal marker genes.
  • Rendered grid data on histology images.
Evan Morien University of British Columbia
bradjunswick
  • Created music based on gene expression.
JB Poline University of California, Berkeley
jbpoline
Jingwen Yan Indiana University

  • Viewed the correlation of two genes using a sunburst graph.
Kyle H. Ambert Oregon Health & Science University http://frontalattackonanenglishwriter.com/ ambertk
  • Searched literature for genes in the Allen Brain Atlas.
  • Used supervised classification to identify  publications that would likely contain gene- and neuron-related information, based on the PubMed abstract.
Leon French University of British Columbia
leonfrench
  • Speaker.
  • Created a brain connectivity network between brain regions.
  • Data mined for connectivity.
  • Viewed genes and expression intersecting in different datasets.
Matthew Goodman 3scan http://3scan.com meawoppl
  • Viewed atlas section in a data viewer.
Mi-Youn Brusniak Institute for Systems Biology https://www.systemsbiology.org/mi-youn-brusniak
  • Found brain region-specific syndrome biomarker by inspecting differentially expressed regions.
Nolan Nichols University of Washington http://www.ibic.washington.edu nicholsn
Philip Baldwin Baylor College of Medicine http://www.bcm.edu/psychiatry/labi/
  • Used gene expression to delineate fMRI.
Piotr Majka Nencki Institute of Experimental Biology http://service.3dbar.org pmajka
Pragya Goel Cornell University

  • Modified sunburst graph example to view human gene expression data.
Raul Lozano



Rich Stoner University of California, San Diego http://www.wholeslide.com richstoner
  • Created viewer for Allen Institute images.
  • Created 3-D reconstruction of human autism.
Sabina Pfister Institute of Neuroinformtics, ETH Zurich http://n.ethz.ch/student/sabpfist/ xanibas
Shreejoy Tripathy Carnegie Mellon University http://www.neuroelectro.org
  • Checked for the results of registration with a custom visualization.
Shuiwang Ji Old Dominion University http://www.cs.odu.edu/~sji/
  • Speaker
Sriram Chandrasekaran Institute for Systems Biology & UIUC, Urbana-Champaign https://netfiles.uiuc.edu/chandra6/www/
  • Found glioblastoma marker genes in the Developing Human Brain data.
Stephen Larson University of California, San Diego http://slars0n.com
  • Speaker.
Yundi (Wendy) Shi University of North Carolina, Chapel Hill http://www.niral.unc.edu/
  • Registered a Human Brain MRI to a custom atlas volume.
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