Brainhack Americas

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Brainhack Americas

Brainhack is a unique conference that convenes researchers from across the globe and a myriad of disciplines to work together on innovative projects related to neuroscience. Year after year, global Brainhack events have brought together researchers to participate in open collaboration, and regional Brainhack events keep the momentum going throughout the year.

Brainhack Americas will unite several regional Brainhack events throughout North, Central, and South Americas during October 23, 24 & 25, 2015. Having several simultaneous events will help build a critical mass for the regional Brainhack movement and will provide opportunities for inter-Brainhack collaboration. Local events will be connected by videoconference to expand collaborative opportunities so that smaller sites can plug into the content and energy generated at larger sites.

Sites in Ann Arbor, MI, Berkeley, CA, Los Angeles, CA, Miami, FL, New York City, NY, Porto Alegre, Brazil, Querétaro, Mx, and Seattle, WA have signed on, and we hope to partner with additional sites throughout North, Central, and South America. Please contact Alex Franco or Cameron Craddock if you are interested in hosting a Brainhack in your area.

Every attempt will be made to minimize the cost of attendance at these events.

 

GigaScience Proceedings from Brainhack

 

Brainhack has partnered with GigaScience and BioMed Central to publish a Proceedings from Brainhack Americas. Each Brainhack attendee will have the option to submit a project report describing the work that they performed during the event. Project reports will be peer reviewed and edited by members of the Brainhack community. Reports should be written in Markdown and posted as a github repository, be no more than 650 words, contain a single figure, at most two tables and citations (not included in word count). The report should be divided into the following sections: Introduction, Approach, Results / Discussion, Conclusions. Reviews will be open and conducted through the posting of issues within the github repository. The submission deadline is November 23, 2015.

The submission form can be found here.

We are also excited to announce the “Brainhack Thematic Series – Open Tools for Neuroscience”, which will be also published in conjunction with GigaScience. This exciting series will highlight new tools and pipelines produced from past and future Brainhack events, in order to improve data sharing and reproducibility of results within neuroscience. In addition to open review and open-access publication of your Research Articles, Technical Notes, and Data Notes, all supporting tools, materials, methods and results will also be openly available in the GigaScience repository, GigaDB.

Submission is open, just indicate your intention to publish in the Brainhack thematic series in the cover letter. Included manuscripts will receive a 15% discount on GigaScience’s article processing charges.

gigascience-07

Amazon AWS Credits

Amazon AWS is once again supporting Brainhack through an Education Research Grant award. 100 attendees will receive $50 in AWS credits for their Brainhack projects. These credits will be allocated on a first come first serve basis.

Schedule

A synchronized schedule for all events is available at https://tinyurl.com/brainhack-amx-schedule. The schedule is still a work in progress and may change over the next few days.

Collaboration Resources

Regional Event Details

 

Ann Arbor, MI

  • Location: University of Michigan, North Campus, 2203 LBME
  • Dates: October 23 – 25, 2015
  • Organizers:
    • Scott Peltier, PhD, Technical Director and Associate Research Scientist, Functional MRI Laboratory, Associate Research Scientist, Biomedical Engineering, University of Michigan, Ann Arbor, MI
    • Robert Welsh, PhD, Research Associate Professor, Department of Psychiatry, Research Associate Professor, Department of Radiology, University of Michigan, Ann Arbor, MI
  • Registration and Information: Attendance is free, please email brainhacka2 at umich dot edu to RSVP or more information. A website with full details is available at https://sites.google.com/a/umich.edu/brainhack2015.

 

Atlanta, GA – this event has been cancelled.

 

Berkeley, CA

Los Angeles, CA

  • Location: Room 109, USC Center for Health Professions, 1540 Alcazar St., Los Angeles, CA 90089-9003
  • Dates: October 23 – 24, 2015
  • Organizers:
    • Yonggang Shi, PhD, Assistant Professor of Neurology and Electrical Engineering, Laboratory of Neuro Imaging, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC
    • Lei Liew, PhD, OTR/L Assistant Professor, Division of Occupational Science and Occupational Therapy, Division of Biokinesiology and Physical Therapy, Department of Neurology and Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC
    • Gautam Prasad, PhD, Assistant Professor of Research, Laboratory of Neuro Imaging, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC
  • Registration and Information: Attendance is free, please fill out the form at http://tinyurl.com/brainhack-la-2015 to register. Please email npnl at usc dot edu for more information.

Miami, FL

  • Location: Activities Room North on the 3rd floor of the Student Center Complex at the University of Miami.
  • Dates: October 23, 2015 9:30 – 16:30
  • Organizers:
    • Angie Laird, PhD, Associate Professor, Department of Physics, Florida International University, Miami, FL
    • Lucina Uddin, PhD, Assistant Professor of Psychology, University of Miami, Miami, FL
  • Registration and Information: The meeting will be devoted to open sessions during which attendees will be breaking into smaller groups to discuss ways to enhance the neuroimaging community in South Florida. New this year will be a data blitz where trainees will present a project (completed or ongoing) in 5 minutes, with 2 minutes for questions. A panel of faculty members will decide on the best presentation, and the winner will be awarded a $500 prize. Please refer to the event flyer for more details. To reserve your spot, submit your data blitz presentation title, or if you would like more information, please send an email to l.uddin at miami dot edu. Attendance is free and open to the public.
  • Invited Speakers: Faculty from University of Miami and Florida International University, TBD
  • Sponsors: University of Miami Flipse Funds

New York, NY

  • Location: Translational & Molecular Imaging Institute, 1st floor of the Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai 1470 Madison Ave (at E102nd St) New York, NY 10029
  • Dates and Times: October 23 – 24, 2015
  • Organizers:
    • Prantik Kundu, PhD, Assistant Professor of Radiology and Psychiatry, Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai
    • Christopher J. Cannistraci, MS, Technical Operations Manager, Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai
    • Ting Xu, PhD, Postdoctoral Fellow, Center for the Developing Brain, Child Mind Institute, New York, NY
    • David O’Connor, MS, Research Assistant, Center for the Developing Brain, Child Mind Institute, New York, NY
    • Cameron Craddock, PhD, Director, Computational Neuroimaging Lab, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY and Director of Imaging, Center for the Developing Brain, Child Mind Institute, New York, NY
  • Registration and Information: Attendance is free, please fill out the form at http://tinyurl.com/brainhack-nyc-2015 to register. Please email Cameron Craddock for more information. You will need to present yourself to the security desk once you arrive on location. Tell the guard that you are there for the Brianhack and they will show you to the rooms.

Porto Alegre, Brazil

  • Location: Computer Science Building (#32) – Room 107 @ Pontifícia Universidade Católica do Rio Grande do Sul
  • Dates: October 24 – 25, 2015
  • Organizers:
    • Alex Franco, PhD, Coordenador de Pesquisa em Neuroinformática e Pós-Processamento, Instituto do Cérebro do Rio Grande do Sul, Associate Professor, Department of Electrical Engineering, Pontifícia Universidade Catòlica do Rio Grande do Sul, Porto Alegre, Brazil
    • Felipe Meneguzzi, PhD, Associate Professor, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
  • Registration and Information: Please register at the eventbrite webpage. Please contact Alex Franco with questions.

Querétaro, Mexico

  • Location: TBD @ Instituto De Neurobiología, Universidad Nacional Autónoma de México
  • Dates and times: October 23 – 25, 2015
  • Organizers:
    • Fernando Barrios, PhD, Associate Professor and Basic Research Chairman of the MRI Unit, Instituto De Neurobiología, Universidad Nacional Autónoma de México, Qeurétaro, México
    • Sarael Alcauter, PhD, Investigador Asociado, Instituto De Neurobiología, Universidad Nacional Autónoma de México, Qeurétaro, México
    • Erick H. Pasaye, PhD, Neuroradiology, Instituto De Neurobiología, Universidad Nacional Autónoma de México, Qeurétaro, México
    • Cameron Craddock, PhD, Director, Computational Neuroimaging Lab, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY and Director of Imaging, Center for the Developing Brain, Child Mind Institute, New York, NY
  • Registration and Information: Please email Sarael Alcauter and Fernando Barrios to RSVP or for more information.

 

Rio de Janeiro, Brazil – this event has been cancelled.

 

Seattle, Washington

  • Location: The WRF Data Science Studio, University of Washington
  • Dates and times: October 24 – 25, 2015, 9 AM – 6 PM PST
  • Organizers:
    • Ariel Rokem, Data Scientist, The University of Washington eScience Institute, Seattle, WA
  • Registration and Information: Attendance is free, please fill out the form at http://tinyurl.com/brainhack-sea-2015 to register. Please email Ariel Rokem for more information.

 

What will happen at local Brainhack events?

Brainhack is unconventional – the event eschews a prearranged schedule of scientific sessions and instead structures activities onsite based on the interests of the community. This model encourages active participation and interaction between attendees.

Regional Brainhack events will span 1 to 3 days and are comprised of several unique components:
• Welcome reception and icebreaker: Opportunity for attendees to get to know each other and to identify scientific challenges they would like to tackle during Brainhack.
• Ignite sessions: Brief talks to inspire attendees and set the pace for the rest of the day
• Open hacking sessions: Most conference time will be devoted to these sessions during which attendees collaborate on neuroscientific projects.
• Unconference sessions: Oral presentations by attendees that are dynamically scheduled onsite.
• Presentations and wrap up: Reporting on progress made on each project and a summary of the event.

 

Brainhacking 101

New at the Brainhack Americas event will be an educational track called “Brainhacking 101”. Modeled after Software Carpentry, these courses aim to introduce brain enthusiasts to basic software skills to enable their research. They will be taught by experts via video broadcast and local proctors will be available at each site to answer attendee questions. Courses that will be available at Brainhack Americas include:

  • Installfests: these are opportunities to interact with local experts to get assistance with installing software. Bring your laptop, access to your server, or a portable hard drive that can be re-formatted. Instructions will be provided for installing the software required for the Brainhacking 101 courses.
  • GitHub: GitHub provides a vibrant community for sharing open source software and tools. This tutorial will teach attendees how to access software written by others and how to use GitHub tools to host, backup, and provide revision control for their own software.
  • Python: Python has become a popular programming language for automating data processing tasks and performing data analyses. This tutorial will provide an introduction to the Python programming language and the basic constructs for creating data processing tools.
  • Nibabel: Nibabel is a python library that provides support for reading and writing a variety of different neuroimaging file formats. This tutorial will demonstrate loading and manipulating neuroimaging data with Python.
  • Nilearn and Plotting: Nilearn is a python library that provides a variety of demos for analyzing neuroimaging data along with many beautiful tools for visualizing analysis results. This tutorial will demonstrate using Nilearn to visualize neuroimaging data.
  • Neurodebian: Neurodebian is a one-stop shop for all of your neuroscience research software needs. This tutorial will demonstrate using Neurodebian to install and maintain your research computing platform.
  • AWS: Cloud computing is revolutionizing neuroscience research by democratizing access high-throughput data processing and analysis. This tutorial will explain the cloud computing resources available through Amazon Web Services and provide a demo of using these resources to process nueroimaging data.
  • Meta: A variety of tools are available for performing meta-analyses that combine results from different published experiments to develop and test neuroscientific models. This tutorial will focus on Neurosynth and Neurovault and demonstrate how they can be used to extract consistent findings from the neuroimaging literature.

 

Meet the experts

One of the best aspects of Brainhack is the opportunity to interact with experts from a variety of different backgrounds. The meet the experts series provide an opportunity for Brainhack attendees to tap into the expertise from different sites during the Brainhack Americas event over video conference. Experts who have agreed to participate include:

  • Eleftherios Garyfallidis, PhD – Diffusion MRI and tractography
  • Yaroslav Halchenko, PhD – debian, neurodebian, datalad, MVPA
  • Tal Yarkoni, PhD – Meta-analysis, neurosynth, statistical methods
  • Cameron Craddock, PhD – cloud computing, analysis methods, datasharing
  • Daniel Margulies, PhD – neuroanatomy, data visualization, open science
  • Alex Optiz, PhD – brain stimulation techniques (TACS,TDCS,TMS,Ultrasound)
  • Chris Gorgelewski, PhD – Nipype, data processing, sharing, BIDS, analysis
  • Adriana Di Martino, MD – child and adolescent psychiatric and developmental disorders

Who comes to Brainhack?

Brainhack attendees come from a wide variety of backgrounds and are interested in working together on projects related to brain science. Although the nature of the Brainhack makes it most amenable to projects that can be completed with a computer, effective contribution is not limited to those with computational backgrounds. Brainhack welcomes expertise from all fields, including but not limited to: engineering, math and computer science, neuroscience, psychology, psychiatry, neurology, art, and philosophy – from undergraduate students to established principal investigators. All have found opportunities to make valuable contributions to the Brainhack.

What do people work on at Brainhack?

Attendees are free to work on any project that they like. In order to assist with the process of choosing a project, attendees are encouraged to post project ideas to brainhack.org weeks before the event. A poster session will occur during the welcome reception to offer another opportunity for attendees to discuss their project ideas. Local organizers may also wish to present a “grand challenge” or unifying problem to offer an additional project opportunity for attendees. As the purpose of local Brainhack events is to build new relationships and to set the foundation for longer-term collaborations, the project need not be completed during the course of the Brainhack. Some attendees may not work on a project, but instead use the Brainhack as an opportunity to learn from other attendees about different domains of brain science.

Example projects from previous years of Brainhack can be viewed at brainhack.org and run the gamut from large-scale analyses of cortical thickness in autism, to developing better tools for analyzing and visualizing brain imaging data, to establishing standards for assessing the quality of functional MRI data. These projects have led to ongoing international collaborations and in some cases resulted in scientific publications.

 

Hosting a regional Brainhack

Regional Brainhacks can range in size from just a few participants to something much larger. Depending on the size of the regional Brainhack, two or more individuals may be needed to host the event. Most of the details below are flexible and ultimately left up to the local organizing committee. If you are interested in hosting an event, please contact Cameron Craddock (cameron.craddock@childmind.org).

Some items to take into consideration as you begin planning your Branhack:

Location

The primary requirements for the Brainhack location are Internet, electricity, and sufficient workspace for the attendees. Ideally the facilities will be accessible around the clock to allow attendees to work late into the night. Some level of video conferencing capabilities will be needed to connect with other sites, but a web camera and projector will be sufficient. Having multiple workrooms would be convenient (though not necessary) for the open hacking sessions, and there should be at least one room that is large enough to host the entire group during Unconference sessions and other oral presentations. Limiting the event to a single room will make it easier to link sites via video. We have found that it works best to arrange desks or tables in the workrooms into small clusters that fit 4-6 people, with Internet connections and power available at each cluster.

Ideally, a university or research institution would provide the facilities for free. Community based organizations, such as libraries or hacker spaces, are also good places to find meeting spaces.

Getting the Word Out

Announcements and materials for Brainhack EDT will begin being distributed on relevant web channels and mailing lists starting July 2014. Regional hosts are encouraged to contact brain science researchers at all local Institutions to solicit their involvement. Enlisting high profile researchers from the area for the Ignite sessions can help attendance. The central organizing committee will also help to develop recruitment materials such as web pages and posters.

Welcome reception and icebreaker

The Welcome Reception is the first opportunity for Brainhack attendees to interact with one another and to start self-organizing into project groups. Ideally refreshments would be available during the welcome reception, and if there is any money available for the event it should be spent here. Depending on the size of the attendance, each attendee should be asked to briefly introduce themselves to the group, or another icebreaker activity (such as a poster session, round of 3-min 1-slide introductions, speed dating) could be employed.

Food and Refreshments

All meals are typically catered at global Brainhack events to encourage the attendees to eat together and to minimize interruptions to the working sessions. For the regional Brainhacks this requirement can be forgone to minimize attendee costs, but ideally some refreshments should be available. Attendees are encouraged to sit together during meals, which can be either delivered or takeout. This will require that the Brainhack be located near food vendors.

Ignite Speakers

Ideal speakers for the Ignite sessions are established brain scientists who have a broad view of brain research and understand the long terms goals of the research community. The primary role of these speakers is to set the tone for each day of hacking. Local events will be able to tune in to Ignite sessions from other sites by videoconference.

Unconference Sessions

Unconference sessions offer attendees the ability to dynamically create scientific content at the Brainhack event. Sign up sheets for the Unconference sessions will be hung each morning and will be available up until the time of the Unconference sessions. Based on experience from previous Brainhacks, we anticipate presentations to include: tool demonstrations, explanations of complex concepts in neuroscience and data analysis, clinical background on mental disorders, and open debates about the future of neuroscience. Local events will be connected by videoconference so all can tune in to Unconference talks presented at other locations.

Project Summaries and Wrap-up

Teams will be given an opportunity to provide a 2-5 minute description of their projects and their progress during a lightening talk session at the end of the day on Sunday. Any remaining time should be spent getting feedback from the attendees about their Brainhack experience and making plans for future regional Brainhack events.

Budgetary Concerns

A major goal of Brainhack EDT is to have attendance be as inexpensive as possible (and in some cases completely free). Some local budget will likely be necessary to cover incidental expenses as well as refreshments at the welcome reception and during the working sessions. The primary concern is arranging a location to host the event. In the past, we have had success raising small amounts of funding from local universities and research institutions. We have also had success obtaining corporate sponsorship. The central organizing committee is more than happy to work with regional organizing committees to help them obtain funding.

Attending a local Brainhack

1. Pre-register to make sure that you are accounted for.

2. If you have a project idea, post it to brainhack.org and make sure that you indicate which of the local Brainhacks that you will be attending. This will make other attendees aware of your project idea, so that they can prepare to join your team. If the project involves working with a specific dataset, make sure that it is organized before the Brainhack and consider bringing it on a thumb drive or external hard drive for easy sharing.

3. If you do not have a project idea, read the list of projects occurring at your local Brainhack event at brainhack.org to get an idea of what will be available. If you find a project team, feel free to contact other project members so that you can prepare to work on the projects.

4. Prepare to participate in the icebreaker activity. Depending on the local site this might involve preparing a poster, a single slide, or a brief introduction, that showcases your research and interests to present at the welcome ceremony. This will be a valuable means for introducing yourself to others and to tell them about your project ideas.

5. Come to the Brainhack local event well rested and ready for hardcore collaboration. Bring along any presentations that you may have lying around in case you are called upon to provide a talk at an Unconference session.