News and Highlights
Neurodata Without Borders (NWB; www.nwb.org) is a broad initiative to standardize neuroscience data and to remove barriers to data sharing among neuroscientists. A paper describing their first collaborative project, finding a common data format for neurophysiology, has just been published in Neuron. The chosen format was strongly influenced by other existing systems, such as LBNL Brain and the German INCF Node's NIX, and informed by the INCF requirements document.
On October 9, the new INCF Malaysia Node hosted their annual workshop on Intelligent Signal and Imaging for Biomedical Applications, attended by just over 100 people. The workshop included the official launch of the Node, attended by the Deputy Minister for Higher Education. INCF's Executive Director Linda Lanyon made a presentation and took part in the press conference and discussions with the Deputy Minister. INCF Japan Node’s Yoko Yamaguchi and INCF Victoria Node’s David Abbott gave presentations about work in their Nodes.
We would like to thank everyone who who gave demonstrations, presented posters with INCF work, visited our booth, or came to one of our socials at SfN in Chicago last week! We had a great time meeting old and new community members, and hope to see everyone in San Diego next year.
Wellcome Trust, NIH and HHMI have announced the Open Science Prize, a prize for services, tools or platforms that enable open content – including publications, datasets, codes and other research outputs – to be discovered, accessed and re-used. Each competing team must include one person based in the US, and one based outside of the US. Up to six prizes of $80,000 each will be awarded to successful teams to develop their innovation over an eight to nine-month period. In the second phase, the phase I prize recipient judged to have the prototype with the greatest potential to advance open science will receive a prize of $230,000. The deadline is February 29, 2016.
Meet INCF at Neuroscience 2015 in Chicago, October 17-21! You are very welcome to visit us in booth #2114. Are you working on an interesting project, or looking for new collaborators? Come by and talk to us! For the 9th year running, we are hosting community tool demos in our booth, Sunday - Tuesday. Schedule and demo abstracts available via link below.
On Sunday October 18, you can meet us at the SfN-sponsored neuroinformatics social (room N229, 18:45-20:45), with presentations by Tom Insel and Sean Hill, chaired by David Kennedy from NITRC and with representation from NIF and INCF; or get an introduction to the Neurodata Without Borders data format at the Fairmont Chicago (Ambassador room, 18:30-->).
Coordination of the world's multiple brain projects is "necessary and feasible", states a Perspective article in the October 2 issue of Science, summarizing outcomes of representatives of the big brain projects meeting in Suzhou in June earlier this year. The Suzhou discussions pointed out several areas where the needs for international coordination are particularly acute, such as standardization, infrastructures for sharing, better multidisciplinary training, and funding mechanisms able to support international collaboration. The article concludes that INCF and other similar organizations may be best positioned to support community efforts and draw the necessary partnerships.
The INCF autumn Newsletter, with updates on our summer activities and autumn plans, is now out. Read about the INCF-OECD workshop on dementia in datasharing, our recent Neuroinformatics Congress in Cairns, and the results of or latest round of Google Summer of Code. As usual, we also offer an overview of upcoming events and recent papers.
In recent years, open science has become an active area of policy development. This OECD report aims to provide an analytical overview of recent open science policy trends, focusing in particular on initiatives to promote broad access to publicly funded research results, including both scientific publications and research data. The report discusses and presents evidence on the impacts of policies to promote open science and open data, and explores the legal barriers and solutions to greater access to research data.
INCF's yearly conference, Neuroinformatics 2015, took place in Cairns on August 20-22. A selection of the recorded talks can now be viewed on our YouTube channel, and photos from the meeting days can be found here on Flickr. We have also put together a Storify timeline of the event, with collected social media posts, videos and photos.
Efficient sharing of data in the experimental and clinical neurosciences would be of huge benefit to the field. Previous workshops hosted by the OECD and by INCF have identified a major obstacle to the advancement of data sharing as being the lack of incentives and support for producing, organizing and sharing reusable data. On September 21-22, INCF and OECD are hosting a workshop in Stockholm to bring together policy-makers, funders, and leading scientists to consider these issues in relation to dementia research and to begin to identify practical steps that can be taken to advance data sharing in this field.
The 8th INCF Congress in Neuroinformatics is currently underway in Cairns, Australia. The three-day meeting features keynotes, workshops, posters and demos, and is held at the Pullman Cairns International. Follow the hashtag #NI2015 for live Twitter updates during August 20-22!
INCF is announcing a new partnership with F1000Research to create a dedicated, digital, open publishing solution for INCF’s members and the expanding neuroinformatics community. The new INCF Community Channel will provide an affordable, open publishing channel to capture research from our ctivities and research articles from the neuroinformatics field. The channel for INCF conferences and workshops is now open, and will enable presenters to share and publish academic posters and slides in one searchable domain.
INCF is exhibiting at the Organization of Human Brain Mapping (OHBM) conference at the Hawaii Convention Center on Oahu, June 14-18. Tools developed by the INCF Task Force on Neuroimaging Data Sharing - NeuroVault, NIDM and One Click Tool - will be demonstrated in the INCF exhibit booth #215 during during poster sessions Monday to Wednesday, 12:45-14:45. INCF also sponsored the OHBM hackathon on June 12-14, just before the main conference. Project ideas can be seen on www.brainhack.org.
The Resource Identification Initiative have just published a paper on their pilot project the to improve the reporting standards for research resources. In the pilot, authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication. Since the start of the pilot in February 2014, over 300 papers have appeared that report RRIDs, and more than 40 journals have joined. Identifiability of the resources pre- and post-pilot showed a dramatic improvement for all resource types, suggesting that the project has had a significant impact on reproducibility.
Registration is open for the Neuroimaging (NIDM) Data Model hackathon to be held in Cairns, August 17-18 at the Pullman Cairns hotel. The objective of the workshop is to introduce NIDM to developers and provide instruction on how to develop in NIDM, while the hackathon will focus on two topics: i. integration of NIDM with existing tools and ii. a common Neuroimaging Atlasing format.
INCF's recent workshop in Warsaw, April 16-17, was the first of our Nodes Workshops open to the wider community. Arranged by the INCF Polish Node at their home institution Nencki Institute in Warsaw, the workshop attracted 100 participants, with 17 talks, 30 posters and 9 demos. Slides and photos are now available on the meeting webpage.
Our latest Annual Report has just been published - we've collected a comprehensive view of INCF's Nodes, Programs and outreach activities and achievements during 2014.
INCF participates in the Google Summer of Code for the fifth time. This year, 15 students have been accepted and will be working over the summer together with mentors from the worldwide INCF community.
We would like to welcome our newest member country, Malaysia, to INCF! The Malaysian Node is based at the Centre for Intelligent Signal and Imaging Research (CISIR), Universiti Teknologi Petronas (UTP), and activities will initially focus on community building and starting collaborations within clinical neuroscience.
The NeuroElectro project aims to extract information about the electrophysiological properties of neurons reported in research papers and place them into a publicly available database that links specific neuron types to measurements of their biophysical properties, with associated metadata, across the literature. The project leads have now published a paper in the Journal of Neurophysiology where they use NeuroElectro data to compare brain-wide neurophysiological diversity of mammalian neurons, including corrections for variability caused by different experimental conditions.
BigNeuron is a community effort to define and advance the state of the art of single neuron reconstruction and analysis and create a common platform for analyzing 3D neuronal structure, led by Allen Institute for Brain Science and uniting some of the leading research and computing centers around the world, including INCF. The results will include a large set of open-source, community-based tools for neuroscience studies, standardized protocols, and a rich library of morphological feature definitions and algorithms.
We will have a booth at the 2015 Brain Forum in Lausanne, March 30 - April 1, where you can meet representatives from the INCF Swiss Node and the Secretariat in the exhibitions area. Are you working on an interesting project, or maybe looking for new collaborators? Come by and talk to us!
Registration is now open for the INCF-supported OHBM hackathon, which will be held June 12-14 at the Hawaii Convention Center, just before the Organization for Human Brain Mapping conference on July 14-18. More information on the event is available at brainhack.org, where it is also possible to view and submit ideas for projects to be worked on during the hackathon days.
We just published our first newsletter for 2015, with updates on Google Summer of Code, the next INCF Nodes Workshop, the OHBM hackathon, and other community events and news. There is also a list of recent interesting publications in neuroscience and neuroinformatics. And we switched to a new platform, which also works on mobile phones! You can read the newsletter here:
Introducing the major open questions of neuroscience and teach state-of–the-art techniques for analyzing and modeling neuroscience data sets, this course is designed for students at the graduate level and researchers with background in a quantitative field such as engineering, mathematics, physics or computer science who may or may not have a specific neuroscience background. The course runs July 6-17, and is organized by members of the INCF US Node. Apply latest April 6th.
Python is quickly becoming a standard tool for the programming neuroscientist. The INCF German Node (G-Node) is organizing the summer school "Advanced Scientific Programming in Python" together with the BCCN Munich and the Graduate School of Systemic Neurosciences, for Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or Mathematica is absolutely required. The course will be held August 31 - September 5 in Munich, Germany. Apply latest March 31.
INCF has been accepted as a mentoring organization for Google Summer of Code, our fifth year running! Project ideas and mentors have been recruited from our community, mainly our Nodes and Programs, and range from simulators and computational modelling to tools for neuroimaging, EEG data management and connectivity analysis. Students can apply for projects from March 16th.
The Foundation for the National Institutes of Health (FNIH) has selected Karl Deisseroth (Stanford), as the 2015 winner of the Lurie Prize in Biomedical Sciences. Dr. Deisseroth is being recognized for leading the development of optogenetics, a technology for controlling cells with light to determine function, as well as for CLARITY, a method for transforming intact organs into transparent polymer gels to allow visualization of biological structures with high resolution and detail.
CAMP (Computational Approaches to Memory and Plasticity at NCBS, Bangalore) is a 16-day summer school on the theory and simulation of learning, memory and plasticity in the brain. It takes place June 27 - July 12, and is co-organized by Indian Node members at the NCBS in Bangalore. The curriculum combines lectures with hands-on exercises. International applicants from experimental and theoretical backgrounds are welcome. Two letters of reference needed. Applications are open until March 1.
Frontiers in Neuroinformatics | Efficient neuroimaging workflows and parallel processing using Matlab and XML
Frontiers in Neuroinformatics | A new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data
A recent study in humans analysed the effects of γ-band-specific entrainment of cortical areas and found that interhemispheric connectivity could be increased by artificially increasing interhemispheric coherence (that is, in-phase stimulation) and reduced by anti-phase stimulation.
Mirror neurons—brain cells that are activated when viewing the actions of another—have been implicated in everything from obesity to autism. While many of the claims made about these cells remain to be tested, they continue to persist in popular culture, much to the frustration of those working in the field. Christian Keysers considers an attempt to set the record straight in a review of The Myth of Mirror Neurons: The Real Neuroscience of Communication and Cognition.
In Nature, researchers explain a technique, called expansion microscopy, that involves physically inflating biological tissues using a material more commonly found in baby nappies (diapers).
The Bernstein Conference is the Bernstein Network's central forum that has developed over time into the largest annual Computational Neuroscience conference in Europe, attracting an international audience from across the world. It is organized by members of the Bernstein Network at annually changing locations and offers a broad overview over the topics of Computational Neuroscience and Neurotechnology. The next conference is organized by the Bernstein Center Heidelberg-Manheim and will take place in Heidelberg. The call for Satellite Workshop proposals will open in January 2015.
PyNN (pronounced 'pine' ) is a simulator-independent language for building neuronal network models.For a list of the main changes between PyNN 0.7 and 0.8, see the release notes for the 0.8 alpha 1 release.
In Frontiers in Neuroinformatics, researchers introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data.
In Nature Neuroscience, researchers have developed an organic material–based, ultraconformable, biocompatible and scalable neural interface array (the ‘NeuroGrid’) that can record both local field potentials(LFPs) and action potentials from superficial cortical neurons without penetrating the brain surface.
The INCF Secretariat is now looking for a friendly, positive and service-oriented individual to join our team as a systems/cloud engineer.