Hackathon 2014

HBM Hackathon – June 5-7, 2014 – Berlin, Germany

OHBM_K_TextCheck out the updated projects!

More information on the OHBM website available here Register now!
Due to the great response received from last year’s Hackathon event in Seattle, OHBM is pleased to announce that registration is now open for the 2nd Annual OHBM Hackathon taking place at c-base, a hacker/artists space, in Berlin, Germany from June 5-7, 2014.

This three day Hackathon aims to encourage project development and open neuroscience through collaborative projects. The spirit of the Hackathon will continue into the OHBM Annual Meeting, June 8-12, 2014,  in Hamburg through an on-site meeting space that will be available throughout the conference.

The OHBM Hackathon, is a pre-meeting analysis and resource building competition designed to accelerate the connection between open neuroscience and cloud computing.

Dates: June 5 – 7, 2014
Location: c-base, Rungestraße 20, 10179 Berlin, Germany
Registration cost (including all meals): 177.24 Euros ($245 US)

Organizers

Pierre Bellec
Cameron Craddock
Tom Grabowski
Sean Hill
Daniel Margulies
Nolan Nichols
JB Poline
OHBM 2014 Local Organizing Committee

Sponsors

Thank you to our sponsor:
Have an open neuroscience resource to contribute to the Hackathon? We’ll be happy to include you as a sponsor! Just contact us: hbm.hackathon@gmail.com

 

Suggestions for hotels/hostels:

Hostels:

Ostel – Das DDR Hostel

Wriezener Karree 5
10243 Berlin
~30-40 euros/night

A&O Berlin Mitte

Koepenicker Straße 127-129
10179 Berlin
~20 Euros/night for shared dorm room

Singer109 – Hostel Berlin

Singerstraße 109
10179 Berlin
~20 Euros/night for shared dorm room

Hotels:

Art’otel Berlin Mitte

Wallstraße 70-73
10179 Berlin
~100 Euros/night

NH Berlin Heinrich Heine

Heinrich-Heine-Platz 11
10179 Berlin
~80 Euros/night

Ibis am Ostbahnhof

An der Schillingbrücke 2
10243 Berlin
~100 Euros/night

15 Minute DSI Project

Posted by on Jun 11, 2014 in data, Hackathon 2014 | 0 comments

15 Minute DSI Project

Summary: The 15 Minute DSI Project first began at the 2013 Hackathon in Paris, France. Siemens MR sponsored/attended the meeting and brought along a 15min DSI data set using the latest advanced in MR technology: MAGNETOM Prisma 3T scanner with 80 mT/m gradients, 64 channel head/neck coil and slice accelerated (3x) diffusion imaging. Here we would like to make the data set available to the neuroimaging community with the aim of providing a state of the art reference data set for advanced visualization techniques. Included is a half...

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Flasking Neurosynth

Posted by on Jun 2, 2014 in Hackathon 2014 | 0 comments

Flasking Neurosynth

Summary: The Neurosynth website is currently supported by a Rails back-end. There’s nothing wrong with Rails, but since the rest of the Neurosynth codebase is written in Python, and the scientific computing as a whole is pretty Python-centric, it would be much more productive to move the web app to a Python framework. The goal for the Hackathon is to rewrite the back-end in Flask and have a working prototype ready by the end of the event. If time allows, we also plan to add a number of new bells and whistles. Contact: Name:...

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Alzheimer’s Disease Big Data DREAM8.5 Challenge #1

Posted by on Jun 1, 2014 in Hackathon 2014 | 0 comments

Alzheimer’s Disease Big Data DREAM8.5 Challenge #1

Summary: The goal of the Alzheimer’s Disease Big Data DREAM8.5 Challenge #1 (AD#1) is to apply an open science approach to rapidly identify accurate predictive AD biomarkers that can be used by the scientific, industrial, and regulatory communities to improve AD diagnosis and treatment. AD#1 will be the first in a series of Alzheimer’s Big Data Challenges to leverage genetics and brain imaging data in combination with cognitive assessments, biomarkers and demographic information from cohorts ranging from cognitively normal...

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NI-DM Apps

Posted by on May 31, 2014 in Hackathon 2014 | 0 comments

NI-DM Apps

Summary: The NIDASH Data Model (NI-DM) is a set of specifications (http://nidm.nidash.org/specs/) to convey neuroimaging  data and meta-data, developed by the INCF Neuroimaging Task Force  (http://wiki.incf.org/mediawiki/index.php/Neuroimaging_Task_Force) (and the allied BIRN Derived Data Working Group: https://wiki.birncommunity.org/display/FBIRN/Derived+Data+Working+Group). The ultimate scope of NI-DM is all types of neuroimaging data, encompassing provenance from raw data to final statistical inference, but is presently...

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Real-life cognition contest

Posted by on May 28, 2014 in Hackathon 2014 | 0 comments

Real-life cognition contest

Summary: The human brain is designed to process vast amounts of input that are continuously gathered through the senses. However, most experiments study the brain via simplified stimuli that do not resemble the complexity of a natural environment — a mismatch that needs to be addressed in order to better understand how the brain works in its daily, stimuli-rich environments. This project aims to provide essential components to enable inter-disciplinary research to study the brain’s natural behavior and the versatile interactions...

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Aural Neuroanatomy

Posted by on May 15, 2014 in Hackathon 2014 | 0 comments

Aural Neuroanatomy

Summary: What if there was a neuroanatomy not meant to be seen, but to be listened? Eyes and the ears have evolved to detect different types of data regularities. This project aims at discovering this new types of representations of brain imaging data using sound. You can already play (and fork!) with our web application that lets you hear the neocortex of different species: http://siphonophore.org/auralbrain/. Join us at BrainHack to help develop this new branch of neuroanatomy! Contact: Roberto Toro e-mail: rto (at)...

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Pixel Shader Livecoding

Posted by on May 14, 2014 in Hackathon 2014 | 0 comments

Pixel Shader Livecoding

Summary: LIvecoding on the GPU–no geometry, just texture convolution–represents a uniquely satisfying way of feeling your way into a visualization. So far it’s being developed mainly as a form of improvisatory performance art and rapid prototyping. Does it have something to offer Serious Scientific Visualization? Let’s find out. I’ll show preliminary sketches from Zeitgeber, an interactive video projection installation going up in Mumbai next year and talk about how shader livecoding figures into the artistic...

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1000 Functional Connectomes Project/INDI: Future Consortiums

Posted by on May 14, 2014 in Hackathon 2014 | 0 comments

1000 Functional Connectomes Project/INDI: Future Consortiums

Summary: The 1000 Functional Connectomes Project and its International Neuroimaging Data-sharing Initiative (INDI) actively promote the formation of grassroots open data-sharing initiatives in the neuroimaging community. Examples include the classic 1000 Functional Connectomes Project dataset, the ADHD-200, the Autism Brain Imaging Data Exchange (ABIDE), and coming soon – the Consortium for Reliability and Reproducibility (CoRR) and the Addiction Connectome Preprocessed Initative (ACPI). HOW CAN YOU GET INVOLVED? 1. Suggest a new...

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BrainBrowser

Posted by on May 14, 2014 in Hackathon 2014 | 0 comments

BrainBrowser

Summary: BrainBrowser is a set of open source, web-based, 3D visualization tools primarily targetting neuroimaging. Using open web-standard technologies, such as WebGL and HTML5, it allows for real time manipulation and analysis of 3D imaging data. Source code: https://github.com/aces/brainbrowser API Docs: https://brainbrowser.cbrain.mcgill.ca/docs/ Contact: Tarek Sherif e-mail: tsherif (at) gmail.com website:...

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Calculating effect sizes and their CIs

Posted by on May 12, 2014 in Hackathon 2014 | 0 comments

Calculating effect sizes and their CIs

Summary: It is becoming obvious that the the black and white world of reporting effects as significant or not is causing serious problems with reproducibility in science. One of the ways to battle this is to report effect sizes and their confidence intervals. With this project we will look into how effect sizes and their CIS can be calculated for various analyses popular in neuroimaging as well as how to perform those calculations post-hoc with external tools such as NeuroVault. Contact: Chris Gorgolewski e-mail:...

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MRI Quality Control

Posted by on May 12, 2014 in Hackathon 2014 | 0 comments

MRI Quality Control

Summary: MRI QC https://github.com/chrisfilo/mriqc is a set of plotting routines useful for creating quality control reports. Currently it supports plotting information about tSNR, coregistration and motion. In this hacking session we will improve documentation and add more plots. Contact: Chris Gorgolewski e-mail: krzysztof.gorgolewski (at) gmail.com website: https://github.com/chrisfilo/mriqc

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NeuroVault.org + NI-DM

Posted by on May 12, 2014 in Hackathon 2014 | 0 comments

NeuroVault.org + NI-DM

Summary: NI-DM is a format of describing neuroimaging experiments results. NeuroVault is a database for storing unthresholded statistical maps. We will try to integrate it into NeuroVault as part of the upload and download API as well as the internal data model. This will set a common standard for third party applications to integrate with NeuroVault. Contact: Chris Gorgolewski e-mail: krzysztof.gorgolewski (at) gmail.com website:...

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AutoSeg STN

Posted by on May 8, 2014 in Hackathon 2014 | 0 comments

AutoSeg STN

Summary: Deep-Brain-Stimulation (DBS) is a widely used and highly-effective treatment in various diseases, the most common of which is Parkinson’s Disease (PD). In DBS-surgery of PD patients, an electrode is implanted into the subthalamic nucleus, a small subcortical structure of the brain. After surgery, it is important to ensure correct placement of DBS electrodes within the nucleus. To do so, a MATLAB® toolbox has been developed that is capable to localize DBS electrodes based on postoperative MR or CT data (LEAD-toolbox, Horn et al....

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The ModelGUI Project

Posted by on May 7, 2014 in Hackathon 2014 | 0 comments

The ModelGUI Project

Summary: The ModelGUI Project is a Java-based, free, open source, platform-independent desktop GUI application for reading/writing, organizing, manipulating, and visualizing neuroscientific datasets. The software has mature implementations of 2D and 3D visualization (surfaces, volumes, graphs, pointsets, vectorsets), databasing (via JDBC), and I/O for common neuroscience formats as well as a native compressable XML format. Developing features include organization of datasets into intuitive projects, dynamic (time-varying) shapes,...

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NITRC Resources Registry, Image Repository, and Computational Environment

Posted by on May 6, 2014 in Hackathon 2014 | 0 comments

NITRC Resources Registry, Image Repository, and Computational Environment

Summary: The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) suite of services have facilitated 1.8 million downloads across the globe and include: 1) NITRC Resources Repository (NITRC-R), the “go to” collaboration environment that enables the worldwide distribution, enhancement, and adoption of over 650 neuroinformatics tools and resources, 2) NITRC Image Repository (NITRC-IR), a curated repository of nine studies distributing a total of 20,579 DICOM and NIfTI scanned images searchable by metadata such as...

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Nipype for XNAT

Posted by on May 4, 2014 in Hackathon 2014 | 0 comments

Nipype for XNAT

Summary: Nipype has the potential to be a great feature in XNAT. For this project, we will add UI and infrastructure in XNAT to manage and run nipype pipelines. We will also add new capabilities in nipype to seamlessly transmit pipeline output (data files, provenance, etc) to XNAT and to update XNAT workflow tracking as pipelines execute. Contact: Dan Marcus e-mail: dmarcus (at) wustl.edu website: www.xnat.org

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Data sharing: Making it work

Posted by on May 2, 2014 in Hackathon 2014 | 0 comments

Data sharing: Making it work

Summary: Brain imaging lags behind other disciplines in data sharing. But to make data sharing in neuroimaging commonplace we need the coordination of many different players. The purpose of this workshop is to bring together key constituents in neuroimaging data including: (1) Informatics teams, principally the joint collective of the INCF Neuroimaging Data Sharing Task Force (NI-DASH) and the BIRN Derived Data Working Group, who have been actively developing NI-DM, a data model for sharing data across analysis software platforms; (2)...

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neurostars.org

Posted by on Apr 28, 2014 in Hackathon 2014 | 0 comments

neurostars.org

Summary: As part of INCF’s Google Summer of Code, neurostars.org, a question and answer site will incorporate new features: https://github.com/brainstorm/biostar-central/issues?state=open A semantic backend will be prototyped so that all sites can potentially relate data from questions to publications, datasets or code. Contact information: Roman Valls Guimera: roman (at) incf (dot) org Paolo Coffetti: coffetti (at) gmail (dot) com website:...

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BrainSpell Tagging Sprint

Posted by on Apr 27, 2014 in Hackathon 2014 | 0 comments

BrainSpell Tagging Sprint

Summary: More than 1 neuroimaging paper is published every hour. But we can keep up with the literature if we do it all together! BrainSpell is a web portal where we can annotate the papers extracted by NeuroSynth (>9,000!) using ontologies from CognitiveAtlas and BrainMap. Your task will be to read the full text, tell us if you agree or not with the tags already entered, give us information about the stereotaxic space used by the article, and an approximation of the number of subjects in the study. Let’s annotate the 1st 10% of...

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LORIS

Posted by on Apr 26, 2014 in Hackathon 2014 | 0 comments

LORIS

Summary: Longitudinal Online Research and Imaging System (LORIS ; Das et al., 2011) is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from management of  the acquisition of heterogeneous data (imaging, clinical, behavior, and genetics) to storage, processing, and ultimately dissemination. LORIS began as the infrastructure for the NIH MRI Study of Normal Brain Development (Evans et al., 2006)  and later became the data management system for numerous multi-center...

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