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

Welcome to the first INCF newsletter of 2017! We are delighted to welcome Canada as a new Governing Node of INCF this year and look forward to many highly productive collaborations with all our Canadian colleagues! Canada becomes the 18th Node in the current INCF Network spanning 4 continents.

The first round of INCF’s seed funding concluded recently, with many high quality applications from around the world. Congratulations to those who were successful! Details of projects awarded funding are on our website. We encourage submissions to the new call open until mid-March.

Preparations are underway for the series of events to be hosted by the Norwegian Node in Oslo in May-June. Everyone is invited to the 16th INCF Nodes workshop being held on May 29-30. The INCF Council for Training, Science & Infrastructure will meet May 31 - June 1, followed by meetings of the INCF Governing Board and Infrastructure Committee on June 1. We look forward to welcoming you to Olso this spring!

We are also very much looking forward to the 10th annual INCF Neuroinformatics Congress being hosted by the Malaysian Node in Kuala Lumpur on August 20-21. Abstract submission is open! Don’t forget to send your proposals for Special Interest Group meetings that you would like to host there: contact Mathew Abrams (

Another busy year of INCF events ahead! On behalf of the INCF Governing Board and Secretariat, I wish you all a very productive, collaborative and happy 2017!

Canada becomes a Governing Node

We’re happy to announce that Canada has joined INCF this month, through the efforts of long-time community member Prof. Alan Evans, McGill U, who comments on Canada’s membership here:

"Neuroscience has changed beyond all recognition in the last 20 years, integrating new ideas from the information revolution with technological advances in neurobiology. Canada is delighted to join its international partners within INCF in addressing the challenges of integrating complex data across different spatial scales and global data-sharing. The future of neuroscience is computational and multinational. Canada intends to be a leader in this transformation of brain research and INCF provides an ideal forum for building a global brain network."

The INCF community and the Secretariat are delighted to welcome our new Canadian Node to the INCF Network, and we’re looking forward to many fruitful collaborations!

Alan Evans at the INCF Neuroinformatics congress, 2016

Minister for Higher Education & Research visits the INCF Secretariat

The Swedish minister for Higher Education and Research, Helene Hellmark Knutsson, visited the INCF Secretariat on February 15 for presentations about INCF's current collaborative projects regarding infrastructure, standards, and datasharing for neuroscience, and a presentation of the Swedish Node by Node Head Prof Jeanette Hellgren Kotaleski. INCF's efforts in training were also highlighted, with a presentation of community encyclopedia KnowledgeSpace.

Call for seed funding

Submission is now open for the INCF's second round of seed funding. Applications for support for projects, workshops and travels are invited until March 16.

Funding will either drive forward delivery of a product that addresses a neuroscience use case or enable a project to develop to the stage of attracting larger-scale external funding. Suitably aligned projects are those that will deliver tools, data, research, education, training or community development. 

Find out more about our seed funding scheme here.

Training and Education Committee meeting

The INCF Training and Education Committee (TEC), joined by representatives from its strategic partners from BD2K, FENS, IBRO, iNeuro, and OHBM, held its inaugural meeting in Stockholm, 2-3 February 2017 to devise a strategy for INCF’s training and education activities. The major discussion points were on TrainingSpace, INCF’s role in certification, potential partnerships with Software Carpentry/Data Carpentry, and potential course offerings (either independently or in collaboration with partners).

TEC members:
Jean-Baptiste Polinec (Chair), Stephanie de La Rochefoucauld (Deputy Chair), Gaute Einevoll, 
William Grisham, Ariel Rokem, Aloise Saria, Ausra Saudargiene, John Van Horn, Thomas Wachtler, Menno Witter, and Daniel Wojcik

INCF Nodes Workshop in Oslo, May 29-30

The INCF Nodes Workshop, held each spring in collaboration with one of the INCF Nodes, is the main event bringing the wider community and representatives from each Node together.

This year the workshop will be held at the University of Oslo in collaboration with the Norwegian Node. Session themes include Tools for teaching & training neuroinformatics and Brain atlasing workflows and analytics.

The workshop is open to all interested participants with an interest in neuroscience tools, data management and collaboration. Representatives from INCF's Nodes and governing bodies will also be present. 

Learn more and register here
Georg Sverdrups hus, Oslo University

INCF Special Interest Groups

INCF is looking to broaden community engagement through the creation of Special Interest Groups (SIGs) which will be suggested and led by the community.

INCF will give support with group communications, coordination between groups, and assistance with logistics and outreach. All community members are welcome to be SIG members, regardless of their location in the world.

With SIGs, we aim to expand our core community, to be more responsive to new projects and changes in the domain, and to help community products have stronger impact in the neuroscience field. We look forward to offering our services and resources to neuroscientists worldwide.

Any questions can be directed to Mathew Abrams

Brain Function CoE meeting attendees

Australia Node meeting report

INCF has been well represented at Australian neuroscience conferences during the summer. First was the Australian Cognitive Neuroscience Society Meeting, where a number of the Australian INCF Node members contributed to a symposium entitled, ‘Neuroethics: where neuroscience meets society’click full details.
Next was the annual meeting of the ARC Centre of Excellence for Integrative Brain Function (Brain Function CoE), led by Prof. Gary Egan. Here, brain researchers from various disciplines and career stages converged to discuss their research on brain function.
Finally, INCF and the Brain Function CoE co-supported a symposium, ‘Connecting the dots: understanding brain function’ at Australia’s biggest neuroscience conference, the Australian Neuroscience Society’s annual meeting. Symposium speakers included Prof. Gary Egan and Dr Allan Jones, CEO of the Allen Institute for Brain Science – click for full details.

INCF awarded seed funding applications, 2016

Connectivity-based brain parcellation kit, Leonard Cerliani

International Brain Laboratory, Michael Hausser

Linking descriptions of experiment metadata in NIDM-Experiment with BIDS supported workflow, David B. Keator

Enabling cellular-resolution connectomic anlaysis of the primate cortex, Piotr Majka
Implementation of a Neuroimaging DOI system across major leading public neuroimaging data archives, Daniel Marcus

A first implementation of NIDM-Workflows, JB Poline

Standardized workflow of human EKG in NIX and odML, Hiroaki Wagatsuma

Roselyne Chauvin
Caroline Froehlich
Rafael Neto Henriques
Robin Ince
Camille Maumet
Annalisa Pascarella
You can read more about our funded grants here

Courses and Conferences

CNS 2017
The Cognitive Neurosciense Society annual meeting
March 25-28
San Fransisco, USA
Registration deadline: March 3

Connectomics Workshop
Advanced course in connectomics
April 22-29
Siena, Italy

ESANN 2017
April 26-28
Bruges, Belgium

European Neuroscience Conference by Doctoral Students
May 4-6
Alicante, Spain
Registration deadline: April 1

IJCNN 2017
The international joint conference on Neural Networks
May 14-19
Alaska, USA
Early bird registration deadline: March 20

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
Early bird registration: March 31

2nd Nordic Neuroscience
June 7-9
Stockholm, Sweden
Abstract submission: April 1st

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

Workshop on Brain Dynamics on Multiple Scales - Paradigms, their relations, and integrated approaches
June 19-23
Dresden, Germany
Application deadline: February 28

Interdisciplinary Training in Computational Neuroscience

Free two-week NIH funded Summer Short Course
June 19-30
Missouri, USA
Application deadline: March 1
Open to U.S citizens and permanent residents only

ISNN 2017
14th International symposium on Neural Networks
June 21-23, Hokkaido, Japan
June 24-26, Muroran, Japan

Interacting with neural circuits
July 2-22
Lisbon, Portugal
Registration deadline: March 20

SNL 2017
First international workshop on Symbolic-Neural learning
July 7-8
Nagoya, Japan
Paper submission deadline: March 15
Early bird registration: June 9

CCNSS 2017
Computational and Cognitive Neuroscience
Summer School
July 9-27
Shanghai, China
Application deadline: March 15

CNS 2017
26th annual computational neuroscience meeting
July 15-20
Antwerp, Belgium
Abstract submission deadline: March 5
Early bird registration: May 8

CAJAL Course in Computational Neuroscience
August 6-26
Lisbon, Portugal
Registration deadline: March 20

BMM Summer School 2017
Brain, minds and machines
August 13 - September 3

Massachusetts, USA
Application deadline: March 14

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

Abstract submission is now open!

Publications in brief

Is the statistic value all we should care about in neuroimaging? 
The authors address the absence of effect estimates in results reporting in the neuroimaging literature, and provide several easily adaptable recommendations for facilitating the reporting of effect estimates together with their corresponding statistic values.

A very simple, re-executable neuro-imaging publication 
In this paper, the authors document a set of procedures, which include supplemental additions to a manuscript, that unambiguously define the data, workflow, execution environment and results of a neuroimaging analysis, in order to generate a verifiable re-executable publication.

Ensemble Neuron Tracer for 3D Neuron Reconstruction 
This paper presents a fully automatic neuron tracer in an ensemble framework, with integration of data perturbation and model selection concepts. By regenerating multiple samples using data perturbation, it enables multiple tracing results, and then the ensemble framework combines and selects an optimal tracing result as the final output.

Using connectome-based predictive modeling to predict individual behavior from brain connectivity 
The authors present a data-driven protocol for developing predictive models of brain–behavior relationships from connectivity data, using cross-validation. The protocol is designed to serve as a framework illustrating how to construct and test predictive models, and to encourage investigators to perform these types of analyses.

Is software reproducibility possible and practical? 
This blog post discusses software reproducibility over time, among other things pointing out that there are several layers of software underneath 'research software', which all tend to stop working over time, and asks: how much effort should go into addressing this problem?

MRI and MRS of the Human Brain at Magnetic Fields of 14 T to 20 T: Technical Feasibility, Safety, and Neuroscience Horizons
This paper evaluates the improvements in technol-ogy for increasing magnetic flux density (magnetic field) to 14 T in the next few years; highlights neuroscience opportunities enabled by these advances; and evaluates the physio-logical and biophysical effects associated with MRI at very high performance levels.

Statistical power and prediction accuracy in multisite resting-state fMRI connectivity 
Multisite studies are becoming increasingly common, but also potentially introduce systematic biases in connectivity measures across sites. In this paper, the authors measure the inter-site effect in connectivity and its impact on ability to detect individual and group differences.

AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter
The authors present an open-source software package for simulating white matter microstructure, which can be used to study interplay between myelin/fiber density and restricted water fraction in MRI.

Win–win data sharing in neuroscience 
In this commentary, the authors -- with connections to the decade old open neuro-data repository NeuroMorpho -- outline the main benefits of individual and big science data sharing, and propose pragmatic recipes to ensure a win–win outcome for both researchers giving and receiving data.

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers 
This paper describes an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. It achieves supralinear scaling on computing clusters, making simulation of whole neurons in 3D

Neuroscience: Big brain, big data
This feature article gives some recent history and current status of data sharing in the neurosciences.

Scientific computing: Code alert 
Feature article about researchers learning to code, mostly focused on community resources for R.

SEGMA: An Automatic SEGMentation Approach for Human Brain MRI Using Sliding Window and Random Forests
The authors developed an automatic segmentation method for human brain MRI, using a sliding window approach and a multi-class random forest classifier. The method performed well on brain MRI data acquired from newborns, children, adolescents and adults.

Whole Brain Magnetic Resonance Image Atlases: A Systematic Review of Existing Atlases and Caveats for Use in Population Imaging 
This review of 66 whole brain structural MRI atlases finds several important lacks, and issues a set of recommendations for increased relevance and utility of atlases. These include: more subjects at the upper and lower extremes of age, additional structural sequences, a range of appropriate statistics, and detailed cognitive and clinical profiles of the included subjects.

Longitudinal multiple sclerosis lesion segmentation: Resource and challenge
This paper describes the results of the longitudinal lesion segmentation challenge held in 2015, using MR data acquired at multiple time points from MS patients. Algorithms were evaluated against manual segmentations from multiple raters. The training and test data are available.

A manifesto for reproducible science 
The authors argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives.

Scanning the horizon: towards transparent and reproducible neuroimaging research 
Problems such as low statistical power, flexi-bility in data analysis, software errors and a lack of direct replication apply to many fields, but perhaps particularly to functional MRI. The authors discuss these problems, and outline current and suggested best practices.

Time to Bring Single Neuron Modeling into 3D 
The authors of this editorial argue that as neuron reconstruction methods get better, computational modelling techniques must develop to keep up.

Unlocking the brain with open data
In this Roundtable transcript, two neuroscientists discuss the impact of open data with an astrophysicist.

2017 Google Summer of Code 

INCF is applying as a mentoring organization in the 2017 Google Summer of Code. Our initial Project Ideas list is now available here 
If you have questions about our participation in GSoC, please contact us.

Research Data Alliance (RDA/US) invites applications for its Early Career Data Share fellowship program. Stipend and travel to RDA plenaries included. Deadline March 7. More info here
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