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

Greetings, INCF community members! Most of you know me already, but this is the first you hear from me in a director’s message - I’ve assumed the role as Acting Executive Director while Linda Lanyon is on parental leave.

The Secretariat has worked hard during the spring, focusing on developing the network and organization within the framework of the strategic plan. The development of TrainingSpace, the INCF hub linking neuroinformatics educational materials, is proceeding according to plans. We have a first set of Special Interest Groups, which are open to new members. The second round of INCF Seed Funding is currently under review, and a third round specifically aimed at projects developing training materials is open now - apply latest April 30. We have also formed strategic partnerships with several international organizations to coordinate neuroinformatics training activities and other initiatives, in order to fully utilize available resources. Don't forget that we also have publication services. We manage NPRC, and we have a community channel on F1000 - make sure to utilize them!

The Secretariat is, as always, here to support the INCF Network - don’t hesitate to contact us if you have questions or suggestions about the organization or our activities. We hope to see many of you this spring and summer - at the Nodes Workshop in Oslo in May, at OHBM and Nordic Neuroscience in June, CNS in July, and of course at Neuroinformatics 2017 in Kuala Lumpur in August. Abstract submission for Neuroinformatics 2017 is open, make sure to submit your work! If you want to catch INCF Secretariat staff at an event this year, take a look at the complete list of where to find us.

We wish you all a neuroinformagical spring and summer!

Hacking the brain at Open Data Day.
Blogpost about Brainhack Global by:
Anders Frick, analyst with focus on Open Data and Internet of Things

"A hackathon with focus on the human brain - that’s Sweden’s contribution for Open Data Day 2017. The hackathon was held at the Karolinska Institutet.

International Open Data Day is a grass-root initiative with different events on open data all around the world. This day is coordinated via e-mailing lists and has been arranged since 2010. This year, about 300 different events are being held and over 100 of them are on the map, created by Open Knowledge International.

One of the events is Brainhack Global, an international hackathon within the field of Neuroscience. At the Karolinska Institutet, brain experts with a data-interest and data experts with a brain-interest gather for two days full of presentations, cooperation and exchange of knowledge at a distance.

- We think that Brainhack is a good opportunity for the local Neuro-community in Stockholm to meet, see more of what other people are working on and initiate new collaborations. Those who develop software tools for research are often unsung heroes who work alone with limited resources, but they are vital to the advancement of research, says Malin Sandström, Community Engagement Officer at INCF."

Read the full blogpost about Brainhack Global

INCF Nodes Workshop, May 29-30 in Oslo, Norway

This year's Nodes Workshop has two themes: Tools for teaching & training in neuroinformatics and Integration of neuroscience data through digital brain atlasing. Speakers include: Gaute Einevoll, Arvind Kumar, G. Allan Johnson, Trygve Leergard, James Gee, Anna Kreshuk, Timo Dicksheid and Jan Bjaalie.

Register by May 15 to get free coffee and lunch. 
On March 21, 2017, the Brain/MINDS Data Portal was opened to the public for serving the Brain/MINDS database. The project’s core institute is RIKEN, where the Neuroinformatics Japan Center (NJIC) is located. NIJC contributes to the technical development of the database construction and its management. The first release of the data portal provides representative content of the research themes being conducted in Brain/MINDS. The data portal will be developed further as more data is collected.

Submission for our new round of seed funding is open!

The INCF Training and Education Committee will award funding to facilitate the development of training materials that align with INCF’s mission and strategic objectives. Funding will drive forward the development of training materials, such as tutorials, demos, use of open data, and video recording of courses, and support the inclusion of neuroinformatics-related instruction in existing courses.

In this funding cycle, funds will be awarded in two main categories:

  • Development of neuroinformatics curricula
  • Course grants
More about our seed funding scheme and how to apply

Don't miss these INCF Node courses

Camp @ Bangalore Summer School 2017,
July 19 - August 3

16-day summer school on the theory and simulation of learning, memory and plasticity in the brain with the INCF India Node in Bangalore.
Apply by April 15

Berkeley summer course in mining and modelling neuroscience data, July 10-21
This course is for students and researchers with backgrounds in mathematics and computational sciences who are interested in applying their skills toward problems in neuroscience.The course is arranged by one of the INCF US Nodes; CRCNS.
Apply by April 30th

8th G-Node Short Course on Neural Data Analysis, July 31-August 4 in Munich
The G-Node Course on Neural Data Analysis offers hands-on experience in state-of-the-art methods for analyzing complex neural data to PhD students and postdocs. The course is arranged by the INCF German Node.
Apply by May 15

IBRO-APRC School on Neuroinformatics and Brain Network Analysis, August 2-16
The Malaysia Node is arranging a summer course, in Kuala Lumpur just before the Neuroinformatics 2017, sponsored by IBRO and co-sponsored by INCF

Neurostars is an online question & answer resource for the neuroinformatics community. Similar to StackOverflow, this site uses contributor 'reputation', commentor up-voting, and other UI enhancements to present a next-generation internet formus experience. Built using Discourse, it is managed by the INCF Secretariat and open to the entire neuroinformatics community.

Funding oportunities

STINT Initiation Grants
Deadline May 9th   

Initiation grants are given for the implementation of short-term projects targeting the building of new and strategically interesting international relationships. Supports short stays abroad (outside EU) to start new collaborative research projects.

National Health and Medical Research Council Australia - Program Grants
Deadline May 17th
The aim of the Program Grants scheme is to provide support for teams of high calibre researchers to pursue broad based, multi-disciplinary and collaborative research activities.
 5-year funding programs for teams to perform multi-disciplinary, collaborative research in any field relevant for improving health.

CIFRA Azrieli Global Scholars Program (Canada)
Deadline May 23rd  
Supports young investigators (5 years from PhD defence) with $100000 CDN for their research plus mentorship. Grant also includes a two-year appointment to a CIFAR research program and specialized leadership and communication skills training.

Fulbright Center Distinguished Chairs Finland
Deadline August 1st
The Fulbright Center awards grants to enable Finnish institutions of higher education to invite American scholars to hold temporary lecturing or lecturing/research positions.
 Neuroinformatics relevant for University of Eastern Finland, the University of Tampere and the Nokia Foundation.

Fulbright Traditional Scholars Program Norway
Deadline August 1st
The U.S.-Norway Fulbright Foundation offers eight to twelve awards for lecturing, lecturing/research, or research for US scholars who hold a Ph.D. coming to Norway.
All topics are eligible.

Courses and Conferences

The Virtual Brain Node 5 Workshop
Simulated brains. Real memories. 2 day training workshop
May 15-16
Marseille, France
Application deadline: April 20

New Directions in Motor Control Workshop
May 18-19
Atlanta, USA
Registration deadline: May 4
Room reservations: April 25

INCF Nodes Workshop 2017
May 29-30
Oslo, Norway
Registration deadline: May 15

The 3rd workshop on cognitive neuroscience of auditory and cross-modal perception
May 29-31
Košice, Slovakia
Abstract submission deadline: May 1st
Registration is free but required

International Conferenc on Mathematical Neuroscience 2017
May 30 - June 2
Colorado, USA

Eighth International Workshop
Statistical Analysis of Neuronal Data (SAND8)

May 31-June 2nd
Pittsburgh, USA
Registration deadline: May 19
Hotel registration deadline: May 8

2017 NEURON Summer Course
June 5-10
Ohio, USA
Application deadline: May 15

2nd Nordic Neuroscience
June 7-9
Stockholm, Sweden

RLDM 2017
June 11-14
Michigan, USA
Early registration deadline: April 28

TEX 2017
Trieste Encounters on Cognitive Science:
Timing and temporal cognitation
June 12-16
Trieste, Italy
Registration deadline: April 30

7th Neuron Technology Summer School
June 26-July 7
Trieste, Italy
Application deadline: May 11

SNL 2017
First international workshop on Symbolic-Neural learning
July 7-8
Nagoya, Japan
Early bird registration: June 9

SciPy 2017
Scientific computing with Python
July 10-16
Texas, USA
Early bird registration: May 22

Berkeley summer course in mining and modeling of neuroscience data
July 10-21
California, USA
Application deadline: April 30

CNS 2017
26th annual computational neuroscience meeting
July 15-20
Antwerp, Belgium
Early bird registration: May 8

First HBP Curriculum Workshop Series
Intellectual property rights, translation & exploitation of research
July 17-19
Leimen, Germany
Application deadline: June 1

ESI- Systems Neuroscience Conference 2017
Principles of structural and functional brain connectivity

July 24-25
Frankfurt, Germany
Registration deadline: July 7

ICON 2017
International conference on cognitive neuroscience
August 5-8
Amsterdam, Netherlands
Early bird registration: May 15

MIND 2017
Methods in Neuroscience at Dartmouth
Computational Summer School
August 13-20
Hanover, USA
Application deadline: April 15

EANN 2017
The 18th international Conference on Engineering Applications of Neural Networks
August 25-27
Athens, Greece
Paper submission deadline: April 20
Early bird registration: May 27

The 1st International Neural Dynamics Summer School 2017
Experience experimental & computational neuroscience research

August 30-September 1
Bristol, UK
Application deadline: May 15

ISN Workshop 2017
The second Integrated Systems Neuroscience Workshop
September 7-8
Manchester, UK
Abstract submission deadline: June 30
Registration deadline: August 11

EBBS 2017
European brain and behaviour society meeting
September 8-11
Bilbao, Spain
Abstract submission deadline: April 20
Early bird registration: July 31

ICMI 2017
The 19th International Conference on Multimodal Interaction

November 13-17
Glasgow, Scotland

Paper submission deadline: May 12

Publications in brief

Applying an Archetype-Based Approach to Electroencephalo-graphy/Event-Related Potential Experiments in the EEGBase Resource 
This study study evaluates re-usage of existing openEHR (open electronic health record) archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories.

Constructing neuronal network models in massively parallel environments 
The authors investigate how to best use the computing power of petascale supercomputers for the creation of neuronal networks. They show that with thread-optimized memory allocators, thread-parallel network creation scales excellently. In addition, more complex tests on the locality of operations significantly improve scaling and reduce runtime by allowing construction algorithms to step through large networks more efficiently. The combination of these techniques increases performance by an order of magnitude. 

A framework for collaborative curation of neuroscientific literature
This paper presents a literature curation framework comprised of an annotation format, a Python API (NeuroAnnotation Toolbox; NAT), and a user-friendly graphical interface (NeuroCurator). The context of the annotated content is made explicit in a standard way by associating it with ontological terms (e.g., species, cell types, brain regions).

The Open Anatomy Browser: A collaborative web-based viewer for interoperable anatomy atlases
This technology report describes the Open Anatomy Browser (OABrowser); an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The atlas source data, processing tools, and the source for OABrowser are freely available through GitHub and are distributed under a liberal open source license.

Reproducible large-scale neuroimaging studies with the OpenMOLE Workflow Management System
This paper present OpenMOLE, a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL), and are re-executable across various Linux platforms thanks to a containerization solution based on CARE.

Neuronify: An educational simulator for neural circuits
This paper describes an educational app, Neuronify, which allows the user to easily create and explore neural networks in a plug-and-play simulation environment - aiming to provide a low entry point to simulation-based neuroscience by allowing students with no programming experience to create and simulate neural networks. The app runs on smart phones and tablet computers as well personal computers.

Pypes: workflows for processing multimodal neuroimaging data
This paper presents a high level software framework, Pypes, for robust processing and visualization of multimodal neuroimaging data, easing the composition of open source tools into  workflows. Pypes offers pre-processing pipelines for positron emission tomography,12 structural, functional, and diffusion-tensor MRI.

Neuroimaging, genetics, and clinical data sharing in Python using the CubicWeb Framework
The authors present present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories, and solutions that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities.

The Italian Neuroimaging Network Initiative (INNI): enabling the use of advanced MRI techniques in patients with MS
This paper describes the Italian Neuroimaging Network Initiative (INNI), involving centers and investigators with an International recognized expertise, with the major goal to determine and validate novel MRI biomarkers to be utilized as predictors and/or outcomes in future MS studies. The INNI initiative supported the creation of a centralized repository, where advanced structural and functional MRI scans available at the participating sites, with the related clinical and neuropsychological data, are collected.

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
The authors introduce 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). The portability of these applications (BIDS Apps) is achieved by using container technologies. BIDS Apps run on all three major operating systems with no need for complex setup and configuration.

Mapping the function of neuronal ion channels in model and experiment
The authors present a framework for the automated large-scale classification of ion channel models, the IonChannelGenealogy (ICGenealogy). It allows filtered search of individual ion channel models by metadata and relational information, and the comparison of channel model kinetics.

Best practices in data analysis and sharing in neuroimaging using MRI
The authors describe insights from developing a set of recommendations on behalf of the Organization for Human Brain Mapping and identify barriers that impede these practices, including how the discipline must change to fully exploit the potential of the world's neuroimaging data.

Computational approaches to fMRI analysis 
In this paper, the authors review the cutting edge of computational analyses of noisy and increasingly large fMRI datasets, and discuss future opportunities and challenges.

Mindboggling morphometry of human brains
This paper documents Mindboggle (, an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis.

Improving data availability for brain image biobanking in healthy subjects: Practice-based suggestions from an international multidisciplinary working group
This report documents a meeting of international experts from multiple disciplines, all interested in brain image biobanking. It summarises the lessons learned from the experiences of a wide range of individual image banks, and provides practical recommendations to enhance creation, use and reuse of neuroimaging data.

Open Ephys: An open-source, plugin-based platform for multichannel electrophysiology
This paper describes the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. The GUI includes modules for delivering feedback in response to events detected in the incoming data stream, and can be extended via plugins  through a simple API.

Join the Spikefinder competition to identify spike rates from 2p calcium imaging recordings. Submit your algoritm by April 30th to have a chance to win the 1200€ reward!
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