News and Highlights
Coinciding with the 7th Neuroinformatics Congress (Leiden, the Netherlands), the INCF latest newsletter is now available! Take a look at updates on INCF and neuroinformatics activities, a message from the Executive Director, recent publications by our dedicated task force members and other interesting news.
Members of the INCF Standards for Data Sharing Electrophysiology Task Force take lead roles in new initiative to drive forward standards to enable sharing of electrophysiology data. INCF is co-sponsoring the the first Neurodata Without Borders Hackathon. The hackathon will be held at Janelia Farm, in Ashburn, Virginia, from November 20 – 22, 2014. Developers who would like to participate should contact: Fritz Sommer, email@example.com
In Frontiers in Cellular Neuroscience, members of the INCF community explore the predicted variance of dendritic calcium concentrations due to local changes in dendrite diameter and how this is affected by the modeling approach used, and investigate this in a model of dendritic calcium spiking in different reconstructions of cerebellar Purkinje cells and in morphological analysis of neocortical and hippocampal pyramidal neurons.
In Frontiers in Genetics, researchers highlight some points for best practices in the development of bioinformatics software and raise important issues to be discussed by the community.
The goal of the Alzheimer's Disease Big Data DREAM Challenge #1 (AD#1) is to apply an open science approach to rapidly identify accurate predictive AD biomarkers that can be used by the scientific, industrial and regulatory communities to improve AD diagnosis and treatment. AD#1 will be the first in a series of AD Data Challenges to leverage genetics and brain imaging in combination with cognitive assessments, biomarkers and demographic information from cohorts ranging from cognitively normal to mild cognitively impaired to individuals with AD.
In Frontiers in Neuroinformatics, researchers present Optimizer, a software that implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios.
In PNAS, researchers demonstrate that brain activity between multiple pairs of spatially distributed regions spontaneously fluctuates in and out of correlation over time in a globally coordinated manner, giving rise to sporadic intervals during which information can be efficiently exchanged between neuronal populations.
In Nature Neuroscience Reviews, members of the INCF community use grid cells in the medial entorhinal cortex as a gateway to understand network computation at a stage of cortical processing in which firing patterns are shaped not primarily by incoming sensory signals but to a large extent by the intrinsic properties of the local circuit.
In Frontiers in Neuroinformatics, task force members of the INCF DASH Program have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website.
In Frontiers in Integrative Neuroscience, members of the INCF community develop the ARTSCAN Search neural model to clarify how brain mechanisms across the What and Where cortical streams are coordinated to solve the Where’s Waldo problem, that is, how individuals can rapidly learn to search a scene to detect, attend, recognize, and look at a valued target object in it.
In Frontiers in Human Neuroscience, members of the INCF community study how segmentation of spontaneous real-world speech in linguistically-motivated units is a promising strategy for elucidating the neuronal basis of mental processing during non-experimental communication.
Members of the INCF German and Japanese Node report a novel approach to data sharing between collaborating scientists that brings together file system tools and cloud technologies, a service implementing this approach, called NeuronDepot, and an example application of the service to a complex use case in the neurosciences.
In a special focus issue on Neurogenomics, Nature Neuroscience highlights findings and insights into the genetics of neurodevelopmental, neurological and psychiatric disorders. The focus includes Perspectives and Reviews on the success of genome-wide association and whole-exome sequencing studies in identifying genetic variants associated with disorders such as schizophrenia and autism.
The INCF Leiden Hackathon will take place August 25-26. It is a great opportunity for open source neuroinformatics developers to meet and work collaboratively.
On July 7th, you are welcome to attend an informal social event for neuroscientists interested in finding new collaborators and resources, organized by the International Neuroinformatics Coordinating Facility. Speakers will include Sean Hill, Jan Bjaalie, Gordon Shepherd and Evelyne Sernagor.
In Frontiers in Human Neuroscience, member of the MSM Program provide a computational explanation for how MEC cells can emerge through learning with grid cell properties in modular structures.
In Frontiers in Neuroinformatics, members of the INCF Program DASH develop an automated collection of neuroimaging and clinical assessment data within: COINS (Collaborative Informatics and Neuroimaging Suite). COINS is an end-to-end data management system. It provides a comprehensive platform for data collection, management, secure storage, and flexible data retrieval
On 30 May, the version 5.7 of NeuroMorpho.Org was released.The release included 29 new data sets (1341 reconstructions), including from three new animal species (dragonfly, moth, and sheep). The database now contains 11,335 reconstructions from 144 contributing labs. More than 3.2 million reconstructions were downloaded in over 130,000 unique visits from 146 countries.
Members of the INCF Neuroimaging DASH task force publish the most comprehensive raw data set of natural language processing in the brain. It is freely accessible for interested researchers and the public (Source: Bernstein Network Computational Neuroscience)
In Nature Neuroscience Reviews, research shows not only that our brain is optimized for natural hearing tasks but also that using natural sounds to probe the auditory system is the best way to understand the neural computations that enable us to comprehend speech or appreciate music.
In PNAS, to investigate the organizational principles of human brain development, researchers analyze cerebral structural connectivity in the period leading up to the time of normal birth.
The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures.
In Frontiers in Neuroinformatics, members of the INCF DASH and DBA programs present a system for sharing neuroimaging data, designed to be simple to use and to provide benefit to the data provider.
Nine pioneer scientists have been named this year’s recipients of the Kavli Prizes – prizes that recognize scientists for their seminal advances in astrophysics, nanoscience and neuroscience, and include a cash award of one million dollars in each field. This year’s laureates were selected for pioneering the theory of cosmic inflation, making transformative contributions to the field of nano-optics and for the discovery of specialized brain networks for memory and cognition.
May 19 is the official 'coding start' date for the 2014 Google Summer of Code. This year, 13 students are working on neuroinformatics tools that will be open to the scientific community. Their mentors are volunteers from several large community projects and from the INCF National Nodes.
INCF has just published the latest issue of INCF newsletter, with updates on INCF and neuroinformatics activities, recent publications by our dedicated task force members and other interesting news.
In Frontiers of Neuroinformatics, members of the INCF DBA Program examine how certain algorithm and parameter choices influence the reproducibility of proposed graph metrics on a publicly available test-retest dataset consisting of 21 healthy adults.
In Frontiers in Neuroinformatics, members of the INCF DBA and DASH programs present a child-psychiatry oriented portal as an effort to deliver a knowledge environment wrapper that provides organization and integration of multiple information and data sources.
In Frontiers in Neuroinformatics, members of the DASH Neuroimaging Task Force combine a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library), and design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data.
In Frontiers in Computational Neuroscience, members of the INCF DASH and PONS programs present a full implementation of an olfactory bulb microcircuit using realistic three-dimensional (3D) inputs, cell morphologies, and network connectivity. The results provide new insights into the relations between the functional properties of individual cells and the networks in which they are embedded.
In Frontiers in Neuroinformatics, members of the INCF German Node describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API).
In Frontiers in Neuroinformatics, members of the DASH and MSM INCF programs describe two Application Programming Interfaces (APIs) written in Python, which simplify the process of developing and modifying models expressed in NeuroML and LEMS.
In Frontiers in Neuroinformatics, members of the Swedish, French and German INCF Nodes have developed a generic connection generator interface that provides a standard way to connect a connectivity-generating library to a simulator, such that one library can easily be replaced by another, according to the modeller's needs.
In December 2013, Professor Colin Ingram, Director of the Institute of Neuroscience at Newcastle University and Oversight Chair of the INCF Program on Standards for Data Sharing, suddenly passed away. To celebrate his scientific legacy there will be a one-day symposium on Thursday 24th July 2014 at Newcastle University, Newcastle Upon Tyne, UK. A memorial service will be held on the evening of Wednesday, 23rd of July.
In Frontiers in Neuroinformatics, researchers at the Computational Neuroscience Unit, Okinawa Institute of Science and Technology (Okinawa, Japan) introduce two new supporting toolkits that support geometry preparation and visualization for STEPS simulations.
In Nature, researchers discuss how in mouse, an axonal connectivity map showing the wiring patterns across the entire brain has been created using an EGFP-expressing adeno-associated virus tracing technique, providing the first such whole-brain map for a vertebrate species.
In Frontiers in Neuroinformatics, members of the INCF Program on Standards for Data Sharing, design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data, by combining a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library),
In Frontiers in Synaptic Neuroscience, members of the INCF Sweden and UK Node propose a Hebbian learning rule for spiking neurons inspired by Bayesian statistics, in which synaptic weights and intrinsic currents are adapted on-line upon arrival of single spikes, which initiate a cascade of temporally interacting memory traces that locally estimate probabilities associated with relative neuronal activation levels.
Members of the INCF DASH Neuroimaging Task Force, review in Frontiers in Neuroinformatics the relevant literature on differential privacy, a framework for measuring and tracking privacy loss in these settings, and demonstrate the feasibility of using this framework to calculate statistics on data distributed at many sites while still providing privacy.
In PLOS Computational Biology, members of the INCF UK Node discuss how unconstrained randomisation markedly diminishes all investigated architectural properties of cortical connectivity. By contrast, spatial and reduced surrogates largely preserve most properties and, interestingly, often more so in the reduced surrogates. Specifically, their results suggest that the cortical network is less tightly integrated than its spatial constraints would allow, but more strongly segregated than its spatial constraints would necessitate.
In Frontiers in Neuroinformatics, researchers present the software architecture of the gala library, and discuss several designs that they consider would be generally useful for other segmentation packages. They also discuss the current limitations of the gala library and how they intend to address them.
In Neuroinformatics, researchers introduce and release MANIA - Machine learning Application for NeuroImaging Analyses. MANIA is a Matlab based software toolbox enabling easy pattern classification of neuroimaging data and offering a broad assortment of machine learning algorithms and feature selection methods.
In Frontiers in Neuroinformatics, the INCF Victoria Node presents the Multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE), a national imaging and visualisation facility that provides hardware, software, and expertise to drive research in the biomedical sciences, particularly advanced brain imaging research using synchrotron x-ray and infrared imaging, functional and structural magnetic resonance imaging (MRI), x-ray computer tomography (CT), electron microscopy and optical microscopy.
In Nature Neuroscience Reviews, researchers discuss how at many physiological and anatomical levels in the brain, the distribution of numerous parameters is in fact strongly skewed with a heavy tail, suggesting that skewed (typically lognormal) distributions are fundamental to structural and functional brain organisation
In Neuroinformatics, Erik De Schutter discusses the dangers of plug-and-play simulation using shared models: one pulls a few models out of a database, ‘plugs’ them together into a new model and is ready to ‘play.
In Frontiers in Neuroinformatics, members of the INCF Belgian Node present an in-house cloud-computing system, named QSpike Tools, where CPU-intensive operations, required for preprocessing of each recorded channel (e.g., filtering, multi-unit activity detection, spike-sorting, etc.), are decomposed and batch-queued to a multi-core architecture or to a computers cluster.
Registration is now open for the 2nd Annual OHBM Hackathon, that will take place at c-base, a hacker/artists space, in Berlin, Germany from June 5-7, 2014. The Hackathon is sponsored by the Allen Institute for Brain Science, Amazon Web Services, INCF, NITRC, IBIC, BIRN, NDAR, LONI, HCP, Frontiers in Brain Imaging Methods, NIPY, GitHub and NeuroDebian.
In Frontiers in Neuroinformatics, members of the INCF Program on Multiscale Modeling present CyNEST, a maintainable Cython-based interface for the NEST simulator.
Join Orion Bionetworks April 4, 2014 for a complimentary all-day event to establish a forum for a dialogue between the Pharmaceutical, Academic, Patient & Technology community leaders, intended to address the progress and roadblocks in the Brain Disease Translational Roadmap and the role of systems biology and computational modeling as a strategy to address them.
In Frontiers in Neuroinformatics, members of the INCF Task Force in Data Sharing, discuss the central element of the software infrastructure, a web-based portal that enables community researchers to store, share, download and search data and metadata from electrophysiological experiments. They also describe the data model, domain ontology and usage of semantic web languages and technologies.
The Brain Health Registry — led by researchers at UCSF — is a groundbreaking, web-based project designed to speed up cures for Alzheimer’s, Parkinson’s and other brain disorders. It uses online questionnaires and online neuropsychological tests. It can make clinical trials — which are needed to develop cures — faster, better and less expensive.
In Frontiers in Neuroinformatics, the German INCF Node aims to provide open-source solutions for this domain that support the scientific data management and analysis workflow, and thus facilitate future data access and reproducible research. G-Node provides a data management system, accessible through an application interface, that is based on a combination of standardized data representation and flexible data annotation to account for the variety of experimental paradigms in electrophysiology.
In Frontiers in Neuroinformatics, members of the INCF US Node discuss the neuroinformatics challenges for TBI neuroimaging analysis in the context of structural, connectivity, and functional paradigms.
You are invited to attend the Orion Bionetworks Webinar series, the first of which will be held on March 11th at 12 noon ET. This webinar will feature Dave King, the CEO and co-founder of Exaptive. In this webinar, Dave King will discuss the power of applying data visualizations to big data in order to explore, manipulate and gain insight into complicated datasets. Dave will present a case study for Orion Bionetworks on how data visualization technologies can be applied to generate hypotheses and facilitate the discovery of new diagnostics, treatments and cures for multiple sclerosis.
Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. In Frontiers in Neuroinformatics, members of the INCF G-Node and French Node present a language-independent object model, Neo, for handling electrophysiology data in multiple formats.
One year more, INCF has been accepted as mentoring organization for Google Summer of Code 2014. The student applications open on 10 March at 19:00 UTC.
BioMed Central is pleased to announce its collaboration in the "Resource Identification Initiative". Sponsored by the Neuroscience Information Framework and the International Neuroinformatics Coordinating Facility, this initiative is aimed at promoting reproducible science by facilitating identification and tracking of research resourcesin the biomedical literature.
In Frontiers in Neuroinformatics, researchers discuss Diffusion Imaging in Python (Dipy), a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. Dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing. Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface.
In Science, researchers discuss how a newly discovered population of neurons called island cells may be important signaling hubs within neural microcircuits for memory.
INCF is entering an exciting new phase of growth and engagement with major international brain initiatives. To position itself for this new phase and prepare for increased collaboration and coordination of the global neuroscience community, the INCF is increasing the capacity of its leadership by the appointment of two directors: Dr Linda Lanyon is appointed as Executive Director and Dr Sean Hill, former Executive Director, is appointed to the role of Scientific Director.
In Frontiers in Neuroinformatics, members on the INCF Norwegian Node discusses how new opportunities for analyses have emerged with the recent release of an online resource of experimental data consisting of collections of high-resolution images from 6 experiments in which anterograde tracers were injected in S1 whisker or forelimb representations, and conduct a detailed analysis of the brain wide distribution of the efferent projections of the rat barrel cortex
In Frontiers in Neuroinformatics, researchers propose a multi-atlas segmentation scheme with a novel graph-based atlas selection technique that is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting.
In an editorial at Frontiers in Bioinformatics and Computational Biology John M Hancock discusses how as the amount of biological data and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it.
In Frontiers in Neuroinformatics, researchers explain how simulating biological neuronal networks is a core method of research in computational neuroscience. A full specification of such a network model includes a description of the dynamics and state changes of neurons and synapses, as well as the synaptic connectivity patterns and the initial values of all parameters.
In Frontiers in Neuroinformatics, researchers present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. They also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time.
The first seminar in the 2014 INCF Seminar series: Karlheinz Meier, Professor at the Ruprecht Karl University of Heidelberg and Co-director of the Human Brain Project, will give a seminar entitled From Ions to Electrons - Physical Models of Brain Circuits, February 6th at 15:00 in the Lennart Nilsson lecture hall, at Karolinska Institutet (Stockholm, Sweden)
In Brain and Behavior, Maryann Martone encourages all who publish in Brain and Behavior to make their data available. For example, Brain and Behavior will now allow researchers to publish data papers. Data papers will allow researchers to publish a paper describing a data set that will be deposited within a certified data repository.
In Frontiers in Neuroinformatics, members of the INCF UK Node describe morphforge, a toolbox for simulating small networks of biologically detailed neurons in Python that will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development.
Co-hosted by the Allen Institute for Brain Science and the Computational Neuroscience Program at the University of Washington and directed by Drs. Christof Koch and Adrienne Fairhall, this intensive two-week, interdisciplinary course aims to give advanced students in neuroscience, biology, physics, engineering and computer science a rapid introduction to the current state of understanding of the neurobiology of sensory processing, including anatomy, physiology and neural coding.
In PLOS Computational Biology, members of the INCF Swiss and UK Node suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.
Comparing local neural structures across large sets of examples is crucial when studying gene functions, and their effect in the Drosophila brain. In this paper, researchers propose and evaluate an image-based retrieval method for neurons, relying on local appearance, which can cope with spatial variability across the population.
In Frontiers in Neuroinformatics, members of the Polish, Norwegian and Swedish INCF Node describe LFPy, an open source Python package for numerical simulations of extracellular potentials.
Patterns of distributed brain activity are thought to underlie virtually all aspects of cognition and behavior. In this paper, researchers explore the degree to which it is possible to predict such functional patterns from the network of anatomical connections that link brain regions and shed light on the important role of anatomical networks and communication processes in shaping the brain’s functional activity.
This Frontiers in Neurogenomics Research Topic aims to be an online extension of the INCF Short Course on Neuroinformatics, Neurogenomics and Brain Disease. In this workshop, six groups of "next-gen" neuroscientists evaluated how key online data resources can be exploited to address important topics at the interface of neuroscience, genetics, and genomics. Inspired by the concept of a “speed coding jamboree”, the groups took part in a “speed neuroinformatics analysis jamboree” over a one-week period and produced draft papers as an initial output.
The INCF Training Committee cordially invites organizers of neuroinformatics-related courses to apply for co-funding for courses taking place in 2015. The aim is to support development of new courses as well as the re‐design of existing courses for improved neuroinformatics coverage. Eligible courses should be 2-7 days long. They must be held in English, with a target audience at the PhD student level and beyond. Interested applicants should submit a Letter of Intent outlining their course plans latest March 7.
Neuroscientists worldwide are invited to enroll in the 4th annual Art of Neuroscience competition. They are looking for spectacular images and videos that capture the beauty of the brain. Submissions can consist of raw data, processed data, or visualizations of concepts in neuroscience. A jury consisting of artists and scientists will judge the submissions on aesthetic and scientific value, but also originality and reproduction quality. Two winners and four honorable mentions will be selected and announced at our annual symposium in the Eye Film institute in Amsterdam on the 11th of March 2014.
In Frontiers in Computational Neuroscience, researchers examine the Laplacian spectra of the macroscopic anatomical neuronal networks of the macaque and cat, and the microscopic network of the Caenorhabditis elegans.
In Frontiers in Neuroinformatics, researchers present Nengo 2.0, a Python tool for building large-scale functional brain models, that uses simple and extendable syntax, simulates a benchmark model on the scale of Spaun 50 times faster than Nengo 1.4, and has a flexible mechanism for collecting simulation results.
In Frontiers in Computational Neuroscience, members of the INCF German and Norwegian Node discuss how pattern formation in ring networks of excitatory and inhibitory spiking neurons depends on the input current regime.