News and Highlights
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.