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

Welcome everyone to the end of year edition of the INCF newsletter! 2016 has been a productive year that saw the beginning of INCF’s third, more community-directed phase - including a new member-driven Council for Training, Science and Infrastructure, and our first ever round of seed funding for collaborative projects. We have unveiled a completely new website (as well as new websites for the NPRC and Neuroinformatics Congress), launched a pilot version of our CollaborationSpace on the AAAS-developed Trellis platform, presented a beta version of KnowledgeSpace community encyclopedia to the scientific community and began development of the TrainingSpace, a hub linking neuroinformatics educational materials. Many exciting developments are lined up for 2017!

This third phase of INCF began at a time where the field of neuroinformatics has emerged as a major and necessary enabler in modern data-intensive neuroscience. This is an exciting time of opportunity for the field and for our organisation. The recent INCF booth at SfN attracted more than 300 visitors and an INCF-linked social welcomed over 1000 people. The INCF Secretariat handles over 12 thousand incoming emails per month. We look forward to continuing to work with the community to develop and expand our activities further during 2017.  

During spring 2017, I will take parental leave to produce the newest member of the INCF team. While I will retain overall responsibility and strategic direction, two of our experienced Secretariat team members will handle day-to-day operations during this time: Helena Ledmyr will be Acting Executive Director managing the Secretariat, development of the INCF network and communications, Node and Congress events, and Mathew Abrams will be Acting Deputy Director with focus on science, training and infrastructure matters. Helena and Mathew will be pleased to help you during this time.  

We wish you a happy and peaceful festive season and much success in the coming new year.  
We thank you all for an intense and fruitful 2016!
Season's greetings from the INCF Secretariat 
INCF's 10th SfN exhibit in San Diego

INCF participated as an exhibitor at the the SfN meeting in San Diego in November, for the tenth year in a row. As usual, community demos were held in our booth during the three first exhibit days. We also co-hosted a very popular INCF US Node social with a reproducibility theme, together with NIF, SciCrunch, and GigaScience.

Booth visitors were asked to write down something they felt the field needs. We were encouraged to see that many want better reproducibility, more open data, and increased collaboration!

A summary of all our SfN booth activities can be found here:
KnowledgeSpace pilot community release

The 2016 SfN also marked the pilot release of KnowledgeSpace, a community encyclopedia developed by INCF, NIF, BBP and HBP. 
Call for Special Interest Group meetings at NI2017

INCF is calling for community proposals for Special Interest Group meetings to be held in Kuala Lumpur on August 22, the day after the 2017 Neuroinformatics Congress.

Please submit your proposals for themes and topics to Mathew Abrams, no later than February 15. Note that the submitter is assumed to also be the meeting leader, unless otherwise stated.
Save the date:
Community meeting in Oslo May 29-30

The INCF Secretariat and the INCF Node of Norway are pleased to invite you to the 2017 INCF Spring Nodes Workshop, which will be held in Oslo at the UiO campus on May 29-30.

The meeting is open to the community. All registered attendees are welcome to present a poster or demo. Registration will open in early January.

See the meeting website for more information.
Node event: BrainModes 2016

On December 1-2, the tenth edition of BrainModes took place in Brussels, in the beautiful and prestigious venue of the Royal Academy of Arts and Sciences.

The BrainModes meetings explore innovative means of understanding complex brain activity and multimodal neuroscience data sets, with the objective to foster informal discussion of brain modelling and multivariate data analysis (EEG,  MEG, fMRI,  etc). The central motif is that of "modes" –  that is, understanding how complex brain activity is organized around low dimensional manifolds.

Computational and modelling approaches to study the brain were discussed together with applications and new perspectives. The format promoted discussions with and among high-profile invited speakers, but gave also the opportunity to everyone to present their work during the poster reception and walking dinner.

The main conference was preceded by a workshop in Ghent, in which methodological aspects were discussed, and some tools were presented, such as Neuropower, meant to calculate the optimal sample size in experiments, PRoNTo, for pattern recognition in fMRI and The Virtual Brain, a neuroinformatics platform for large-scale personalized brain modelling.

The event was co-funded by INCF. 
Contributed by Daniele Marinazzo, INCF Belgian Node

Courses and Conferences

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

Computation Neurology 2017
Bridging computer science, neuroscience, imaging, modelling and neurology.
February 20-21, 2017
Newcastle, UK
Registration deadline: February 5

5th Neuro Inspired Computational Elements Workshop (NICE 2017)
March 6-8, 2017
San Jose, USA
Abstract submission deadline: December 16

CNS 2017
The Cognitive Neurosciense Society annual meeting
March 25-28
San Fransisco, USA
Early bird registration: January 5
Registration deadline: March 3

SAC 2017

The 32nd ACM SIGAPP Symposium On Applied Computing
April 3-7, 2017
Marrakesh, Marocco
Early bird registration: February 3

Spring Brain Conference 2017
Learning, memory and synaptic plasticity
April 23-26, 2017
Copenhagen, Denmark
Early bird registration: January 23
Registration deadline: February 14

ESANN 2017
April 26-28, 2017
Bruges, Belgium
Early bird registration: February 17

European neuroscience conference for doctoral students
May 4-6, 2017
Alicante, Spain
Registration deadline: February 15

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

2nd Nordic Neuroscience
June 7-9. 2017
Stockholm, Sweden
Abstract submission: April 1st
Early bird registration: February 15

RLDM 2017
June 11-14, 2017
Michigan, USA
Paper submission deadline: February 19
Early registration deadline: April 28

FENS Summer School 2017
Chemical neuromodulation: neurobiological, neurocomputational, behavioural and clinical aspects
June 18-24, 2017
Bertinoro, Italy
Registration deadline: February 13

Workshop on Brain Dynamics on Multiple Scales - Paradigms, their Relations, and Integrated Approaches

June 19-23, 2017
Dresden, Germany
Application deadline: February 28, 2017

ISNN 2017
14th International symposium on Neural Networks
June 21-23
Hokkaido, Japan
Paper submission deadline: January 1
Registration opening soon

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

CNS 2017
26th annual computational neuroscience meeting
July 15-20, 2017
Antwerp, Belgium
Registration opens January 11
Abstract submission opens January 12

EPIA 2017
18th EPIA conference on Artificial Intelligence
September 5-8
Porto, Portugal
Paper submission deadline: April 1

Save the date!
The INCF Neuroinformatics Congress comes to Malaysia in 2017
Brainhack Global, March 2-5
A linked series of Brainhacks taking place all over the world during the same dates. Several INCF Nodes and community members will participate.

Email for more info.

Publications in brief

Sharing brain mapping statistical results with the neuroimaging data model [Dec 6]
In this paper, the members of the INCF NIDASH task force describe NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment.

SparseTracer: the Reconstruction of Discontinuous Neuronal Morphology in Noisy Images [Dec 7]
The authors describe a pipeline for tracing discontinuous neuronal morphology in a strong noise environment, using DIADEM and BigNeuron datasets for benchmarking.

A phenome-wide examination of neural and cognitive function [Dec 6]
This data descriptor is linked to a dataset from the UCLA Consortium for Neuropsychiatric Phenomics, which focused on understanding the dimensional structure of memory and cognitive control functions in both healthy individuals and individuals with neuropsychiatric disorders including schizophrenia, bipolar disorder, and attention deficit/hyperactivity disorder.

Cyberinfrastructure for Open Science at the Montreal Neurological Institute [Dec 1]
This paper describes the ethical and policy challenges, the technical infrastructure used for storage and curation of the various data types, and the workflows and processing environment for the implementation of Open Science at the MNI.

Detecting Mild Traumatic Brain Injury Using Resting State Magneto-encephalographic Connectivity [Dec 1]
The authors describe a method using MEG connectivity to detect mild TBI, in the form of concussion, which is typically not possible using established methods (MRI and CT scan). Confidence of classification correlated with symptom severity.

Memory-Efficient Analysis of Dense Functional Connectomes [Nov 29]
This paper discusses the challenge of memory-hungry analyses of dense connectome data, presents an object-based matrix representation with a very low memory footprint, and announces a software package implemeting this representation.

Collection of Simulated Data from a Thalamocortical Network Model [Nov 11]
This data article is linked to a rich simulation-derived dataset, intended for use as a proxy for experimental ground truth data and as benchmarks for validation and comparisons of different methods of neural data analysis.

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging [Nov 10]
This review provides a straightforward overview of each of the major stages of the fMRI analysis pipeline, listing the techniques and software tools involved.

Ten Simple Rules for Developing Public Biological Databases [Nov 10]
The authors suggest ten simple rules for anyone considering developing a new biological database.

Reproducibility and Bias in Healthy Brain Segmentation: Comparison of Two Popular Neuroimaging Platforms [Nov 9]
The authors evaluated and compared the performance of two popular neuroimaging processing platforms: Statistical Parametric Mapping (SPM) and FMRIB Software Library (FSL), and found large differences. They conclude that the reproducibility of neuroimaging studies depends both on the software-processing platform and tissue probability thresholds, and suggest that probability thresholds may not be comparable across platforms.

The real-time fMRI neurofeedback based stratification of Default Network Regulation Neuroimaging data repository [Nov 9]
This data paper describes a repository of openly shared data from an experiment to assess inter-individual differences in default mode network (DMN) activity.

Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions [Nov 9]
This review gives an overview of recently introduced methods for high-resolution connectomics, and an assessment of their qualities.

Graph Theoretic and Motif Analyses of the Hippocampal Neuron Type Potential Connectome [Nov 7]
The authors computed and analyzed the potential connectivity map of all known neuron types in the rodent hippocampal formation, using data from

Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience [Nov 4]
This paper introduces BRAINformat, an HDF5-based data format standardization framework and API for scientific data, and shows and implementation for electrophysiology data.

NEURON Special Issue on global neuroscience [Nov 2]
This special issue contains a collection of essays and perspectives on the future of global neuroscience, including a set of papers describing many of the major brain projects and initiatives.

2015 Brainhack Proceedings [Nov 1]
This first issue of Brainhack Proceedings includes 23 project papers — presenting an overview of the broad range of interests, content, and achievements that converged at Brainhack events during 2015.

How do we know what we know? Discovering neuroscience data sets through minimal metadata [Oct 13]
This paper argues for establishing a minimal metadata standard that allows the discovery of and access to similar or related data sets.

INCF gains a Community Engagement Fellow
INCF Community Engagement Officer Malin Sandström has been selected as one of 17 fellows in the pilot cohort of AAAS' Community Engagement Fellows training program
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