INCF Newsletter with neuroinformatics community activities, new publications, and upcoming events
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Message from the Director

As I enter my 4th year as INCF’s Executive Director, I reflect upon developments within the organisation and the field, especially recent developments in INCF’s 3rd phase. The surge in positivity and commitment within our community this year, despite challenging times financially, has been an inspiration! The inaugural meeting of the new INCF Council for Training, Science and Infrastructure took place in September in Reading, UK, and was attended by all 17 INCF Nodes. The Nodes presented information about their science and infrastructural projects and it was hugely impressive to see the strength of this work across the INCF Network. Forthcoming meetings of the CTSI’s Infrastructure Committee and Training and Education Committee will further efforts in those areas.

The emerging mainstream impact of the field of neuroinformatics was evident at this year’s Neuroinformatics Congress in Reading. Reflecting on the evolution of the field over many years of Congress, attendees commented that it was now clear that neuroinformatics is having major impact in shaping developments in neuroscience. The updated format of this year’s Congress was well received; we welcome further inputs to help shape next year’s event in August in Kuala Lumpur, Malaysia.

Together globally we are helping to ensure successes in neuroinformatics: a field whose time has come! We hope to see many of you at SfN – look out for us at booth 4112!

Seed funding

INCF invites applications for seed funding of collaborative brain research projects. The deadline for submission is November 30, 2016.

Seed funding grants should facilitate community work in collaborative brain research, promote the use of neuroinformatics solutions, and accelerate advances in understanding the brain and treating its illnesses. There are two types of funding available, project funding and travel grants.

Read more:

NI2016 update

Thanks to all of the participants for being a part of our 9th INCF Congress on Neuroinformatics in Reading, UK, on September 3-4. Photos and videos from the meeting are now available, and some posters, too - don't forget to add yours!


New INCF Council for Training, Science and Infrastructure

The new INCF Council for Training, Science and Infrastructure (CTSI) held its inaugural meeting in Reading UK on September 5-6, directly after the INCF Neuroinformatics Congress. The CTSI is one of the governing bodies of INCF in its new organizational structure. It consists of scientific representatives from all countries in the INCF network, and has subcommittees responsible for Training & Education and for Infrastructure. 

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Meet INCF at SfN!

We will exhibit in booth #4112, with demos of community tools Sunday-Tuesday and Q&A about our new seed funding program on all days. This year we will be celebrating our 10th consecutive exhibition!

Two socials will be hosted on November 13 and 14.
Keep an eye out for our 'SfN edition' Newsletter (late October) for more details on INCF and neuroinformatics at SfN!


The EU CENTER-TBI project, which aims to improve diagnostics and treatment of traumatic brain injury (TBI), is halfway through its data collection phase. There are now more than 3300 patients in the core cohort and over 14000 in the registry. Curation of the data has just begun, and will result in a rich dataset for analytics, to be used for improved prognostication, prediction biomarkers, and better healthcare pathways for TBI.

Building on the infrastructure of CENTER-TBI, a number of initiatives for broader TBI applications and more in-depth analysis are currently taking place. These include:
  • A project on integrating clinical features and biomarker assessment;
  • A project on developing a new traumatic axonal injury classification scheme based on improved MR Imaging;
  • A new international collaboration on neuroinflammation in TBI; and
  • A large international study on genetic associations in neurotrauma.
Read more: 

Funding opportunities

Sony Faculty Innovation award
Up to $100K for a North America-based PI

Areas: comp neurosci, knowledge extraction, vision 

BD2K ('Big Data to Knowledge') funding announcements
  • Enhancing the efficiency and effectiveness of digital curation for biomedical big data:
  • Community-based data and metadata standards efforts:
BRAIN Initiative calls
Three inter-related BRAIN Initiative program announcements for FY17. It is expected that the standards developed will be used in the data archive and by the software. INCF is aiming to coordinate proposals under these BRAIN Initiative calls. Let us know by email to if you would like to contribute.

Courses and Conferences

IEEE Brain Hackathon
October 8-9, 2016
Budapest, Hungary

2016 International Conference on Brain Informatics & Health
October 13-16, 2016
Omaha, Nebraska, USA

Brainhack: Anatomy edition
October 24-26
Paris, France
Registration deadline: October 16

Neuroscience 2016
SfN's 46th annual meeting
November 12-16, 2016
San Diego, USA
Early registration deadline: October 4

Workshop on the Neuroscience Gateway Portal
Using the Neuroscience Gateway Portal for parallel simulation
November 12, 2016
San Diego, USA
Registration deadline: October 28

Teaching Neuroscience with Big Data
SfN Workshop
November 14, 2016
San Diego, USA
There is no fee or preregistration

NeuroEng 2016
9th Australasian workshop on neuro-engineering and computational neuroscience
November 28-29, 2016
Brisbane, Australia
Early bird registration: October 3

BrainModes 2016
Coordinated brain activity: foundations and applications
December 1-2, 2016
Brussels, Belgium
Abstract submission deadline: November 1st

IEEE Big Data 2016
2016 IEEE international conference on Big Data
December 5-8, 2016
Washington, USA
Early bird registration: November 15

Big NLP 2016
Big data and neural language processing workshop hosted at IEEE Big Data 2016
December 5-8, 2016
Washington, USA
Paper submission deadline: October 3

NIPS 2016
The thirtieth annual conference on neural information processing systems
December 5-10, 2016
Barcelona, Spain
Early registration deadline: October 6

Continual Learning and Deep Networks Workshop NIPS 2016
December 10, 2016
Barcelona, Spain
Abstract submission deadline: October 21

1st HBP Student Conference
Transdisciplinary research linking neuroscience, brain medicine and computer science.
February 8-10, 2017
Vienna, Austria
Abstract submissions deadline: October 7
Registration deadline: January 23

Computation Neurology 2017
Bridging computer science, neuroscience, imaging, modelling and neurology.
February 20-21, 2017
Newcastle, UK
Abstract submission deadline: October 31
Registration opens in November

SAC 2017
The 32nd ACM SIGAPP Symposium On Applied Computing Marrakesh
April 3-7, 2017
Marrakesh, Marocco
Registration opens December 10, 2016

ESANN 2017
April 26-28, 2017
Bruges, Belgium
Submission of papers: November 19, 2016


Publications in brief

BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods
This preprint introduces a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS).

Democratic databases: science on GitHub
This Nature Toolbox article gives a nice overview of how researchers are using GitHub for sharing data, including a list of GitHub-based research projects which is open for community edits.

Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
This paper, occasioned by model-sharing database ModelDB’s 20th anniversary, reviews ModelDB’s origins, its current state, and highlights future plans for its development.

Data publications correlate with citation impact
The authors show that neuroscience or molecular biology articles that come with data shared are more highly cited than otherwise comparable articles. They introduce a new metric, the data article citation index, and report ranking results.

Efficient integration of coupled electrical-chemical systems in multiscale neuronal simulations 
This paper describes an efficient coupling strategy for a multiscale test problem in neuroscience, and introduces an efficient coupling method for multiscale simulations.

Nature Neuroscience toolbox issue
Special focus issue highlighting recent technological advances, approaches and collaborative initiatives in neuroscience.

pypet: A Python Toolkit for Data Management of Parameter Explorations
This paper describes pypet, a new multi-platform Python toolkit for managing numerical simulations. It is designed to allow easy and arbitrary sampling of trajectories through a parameter space, and collects and stores simulation parameters and results in a HDF5 file.

COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data
The authors propose a dynamic, decentralized platform for large scale analyses called the Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC). It allows pooling of both open and “closed” repositories by developing privacy-preserving versions of widely-used algorithms.

Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution
The authors present a functional prototype of a system to integrate Digital Object Identifiers (DOIs) and a standardized metadata schema into a XNAT-based repository workflow, allowing for identification of data at both the project and image level.

Clinical Concepts Emerging from fMRI Functional Connectomics 
This review details how fMRI, while not yet a routine clinical tool, has important influences clinical concepts guiding diagnosis and patient management. It also discusses immediate challenges and potential opportunities for clinically relevant applications of fMRI-based functional connectomics.

Analysis of Neuronal Spike Trains, Deconstructed
This extensive primer teaches techniques for model fitting and spike prediction, and how to judge the success of different methods.
Handling Metadata in a Neurophysiology Laboratory
In this methods article, the authors provide conceptual and technical guidance to overcome the challenges associated with the collection, organization, and storage of metadata in a neurophysiology laboratory. They demonstrate a practical implementation, and detail five use cases that demonstrate the resulting benefits of constructing a well-organized metadata collection.

Proposed Training to Meet Challenges of Large-Scale Data in Neuroscience
Report from the November 2014 iNeuro workshop aiming to identify training needs for the new generation neuroscience workforce

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases
This paper describes NBLAST, a fast and sensitive algorithm to measure pairwise neuronal similarity, able to distinguish between neuronal types without training.
Call for Participation
bioCADDIE 2016 Dataset
Retrieval Challenge

Aim: to accelerate development of search strategies for published biomedical datasets beyond utilization of provider metadata.

Selected participant teams will be awarded a sub-contract ($50,000 direct costs) by UCSD to incorporate their systems into the existing prototype.

Read more:
New Open Science Framework preprint service lets you search across multiple preprint servers
Save the date!
The INCF Neuroinformatics Congress comes to Malaysia in 2017
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Copyright © 2016 INCF (International Neuroinformatics Coordinating Facility), All rights reserved.

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