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

Welcome to the second newsletter of 2016. We are recently back from Tokyo and filled with enthusiasm following one of the most successful Nodes Workshops in INCF history. Many thanks and congratulations to our Japan Node for hosting this event. I am pleased to announce that the Norwegian Node will host the next Nodes Workshop in spring 2017.

The INCF Network now consists of 5 Governing Nodes and 12 Associate Nodes - see The new INCF is very much a Node-driven organisation with the Council for Training, Science and Infrastructure (see below) focussing on strategy for science, infrastructure and training.

In April a new INCF web portal was launched. The INCF community can now also interact via a beta version of a platform for community collaboration, within AAAS’s Trellis. We hope this will prove useful for promoting communications and development of Special Interest Groups. Later this year it will be possible to apply for seed funding to help develop projects emerging from these collaborations.

A busy summer of events is soon here. Please stop by the INCF booth this week if you are attending OHBM. On July 4th we are co-hosting a social-symposium on the theme ‘The era of sharing in neuroscience’ at FENS in Copenhagen (program), arranged with the UK Node. We also look forward to the annual Neuroinformatics Congress, and all associated events, in September in Reading, UK.

The Secretariat is here to help the INCF community. Please let us know your thoughts at any time. We wish all our Northern Hemisphere colleagues a happy and successful summer, and wish an equally happy and successful winter to our community in the Southern Hemisphere.

New INCF portal

After a year of intense preparation, the new INCF website was unveiled on April 25. It is completely rebuilt and works across a range of platforms, from computers to mobile phones.

There are some major changes especially relevant to our core community:  
  • The new website has a stronger focus on collaboration, and will be paired with the more community-directed INCF CollaborationSpace, based on the AAAS Trellis platform.
  • The structure is new, so many URLs are changed. Please check your links to any pages!
  • Workshop reports are collected on a new page
  • We removed the Event calendar and Job Board, which required a lot of manual work and presented a high threshold for new users. Instead, please send announcements of events and job openings to the neuroinformatics community list

Join us in Reading for NI2016!

INCF is holding its 9th Neuroinformatics Congress in Reading, UK on September 3-4 September, in collaboration with the INCF UK Node. An exciting program featuring themes of neuroimaging, computational neuroscience, brain disorders and normal development, has been developed by the Program Committee chaired by Prof. Alan Evans, McGill. 

Early registration rates end on June 30. Don't miss the deadline, register now

Call for papers: INCF Channel series

The INCF Neuroinformatics channel on F1000Research is now inviting contributions for an article series in the lead up to Neuroinformatics 2016. A diverse array of article types are welcome, including original research findings, study protocolsdataset/database descriptions and software tools
The deadline will be August 18th; submissions are welcome after that date but they might not be published in time for the congress.

Successful Nodes Workshop in Japan

This year's INCF Nodes workshop was organized together with our Japan Node (J-Node), back-to-back with their yearly Advances in neuroinformatics meeting, AINI 2016, at RIKEN, on May 28-29.

Under the main theme "Integration of multi-dimensional neuroscience", presentations and discussions were given from wide perspectives such as on theoretical neuroscience, brain imaging, data and knowledge, and possible international collaborations. Twenty five invited talks, 37 posters and 14 demonstrations were presented. There were 122 participants, from 11 countries. INCF thanks everyone for their contributions, especially Japan Node secretariat for their hard work in organizing this event. 

More info, including abstracts:
Meeting summary, including photos:

New INCF Council for Training,
Science and Infrastructure (CTSI)

As part of INCF's new phase, representatives from the INCF Nodes are forming the Council for Training, Science, and Infrastructure (CTSI). The CTSI is responsible for recommending INCF’s direction in these areas and overseeing INCF scientific and infrastructure projects. It will also be involved in the review process for INCF's upcoming seed funding. Later this year, independent expertise will also be appointed to the CTSI, ensuring broad global and domain representation. The CTSI will have a permanent sub-committee on Training and Education.

The first CTSI meeting will be held in Reading, UK on September 5-6, in conjunction with the INCF Neuroinformatics Congress.

OHBM June 26-30
Booth 21 (w. NITRC)
FENS social July 4
coorganized with
UK Node

Publications in brief

Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
This paper describes a a new functionality of a fully searchable, curated catalog of human and machine-readable definitions, each linked to the corresponding neuron and property terms.

Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space
This paper describes a a highly accurate segmentation method for densely packed cells based on the curvatures of the iso-intensity surfaces, implemented as a graphical user interface program that allows visualization and correction of the results.

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig
This paper introduces a new toolkit called NeuroPigPen that was developed using Apache Hadoop and Pig data flow language to address the challenges posed by large-scale electrophysiological signal data.

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template
This paper describes a computational pipeline for coregistration of retrograde tracing data on connections of cortical areas into a 3D marmoset brain template, generated from Nissl-stained sections. The procedure enables comparison and visualization of large datasets, which in turn opens the way for integration and analysis of results from many animals.

On the Data-Driven Road from Neurology to Neuronomy
This editorial looks back on 15 years of neuroinformatics, and notes much progress has been made - and much work remains ahead.

Ten Simple Rules for Taking Advantage of git and GitHub
This preprint describes how to use git and GitHub to track collaborative development projects, as users, teams and organizations.

Building the Ferretome
This paper describes the development of the Ferretome, a database of anatomical connections and architectonic features of the ferret brain. The database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model, simplified and extended in order to accommodate new data modalities.

Neuron-Miner: An Advanced Tool for Morphological Search and Retrieval in Neuroscientific Image Databases
This paper presents the Neuron-Miner tool for fast and accurate reference-based retrieval within neuron image databases. The results are quantified using 31266 neuron reconstructions from the dataset.

CATI: A Large Distributed Infrastructure for the Neuroimaging of Cohorts
This paper provides an overview of CATI, a platform dedicated to multicenter neuroimaging initiated by the French Alzheimer’s plan. Its core mission is to support the neuroimaging of large populations by bringing together a service infrastructure, the know-how of its expert academic teams and a large-scale, harmonized network of imaging facilities. CATI aims to make data sharing across studies easier and promotes sharing as much as possible.

Brainhack: a collaborative workshop for the open neuroscience community
This paper describes the Brainhack events series, a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees.

Towards standard practices for sharing computer code and programs in neuroscience
How can we maximize the chances that other scientists can reproduce our computations or reuse our methods on their data? asks this preprint report based on discussions from a workshop supported by INCF and the Software Sustainability Institute.
Submit your paper to the new INCF Community Channel on F1000 Research!

Courses and Conferences

OHBM 2016
June 26-30, 2016
Geneva, Switzerland

Cells, Circuits and Computation
Expanding the Horizons of Big Data Analysis
July 1
Copenhagen, Denmark

10th FENS Forum of Neuroscience
July 2-6, 2016
Copenhagen, Denmark

3rd International Synthetic and Systems Biology Summer School
Biology meets Computer Science and Engineering
July 9-13, 2016
Tuscany, Italy
Early Registration: by June 30

Neuroinformatics 2016
September 3-4, 2016
Reading, UK
Submission deadline: April 30

Bernstein Conference
Computational Neuroscience conference
September 21-23, 2016
Berlin, Germany
Early registration: July 24
Poster abstracts: August 1

2016 International Conference on Brain Informatics & Health
October 13-16, 2016
Omaha, Nebraska, USA
Tutorial proposal deadline: July 10

Neuroscientific Image Analysis at the Microscopic Scale (NIAMS'16)
October 17, 2016
Athens, Greece

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