journal
MENU ▼
Read by QxMD icon Read
search

Frontiers in Neuroinformatics

journal
https://www.readbyqxmd.com/read/29765315/challenges-in-reproducibility-replicability-and-comparability-of-computational-models-and-tools-for-neuronal-and-glial-networks-cells-and-subcellular-structures
#1
Tiina Manninen, Jugoslava Aćimović, Riikka Havela, Heidi Teppola, Marja-Leena Linne
The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29755335/corrigendum-event-and-time-driven-techniques-using-parallel-cpu-gpu-co-processing-for-spiking-neural-networks
#2
Francisco Naveros, Jesus A Garrido, Richard R Carrillo, Eduardo Ros, Niceto R Luque
[This corrects the article on p. 7 in vol. 11, PMID: 28223930.].
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29755334/deep-learning-methods-to-process-fmri-data-and-their-application-in-the-diagnosis-of-cognitive-impairment-a-brief-overview-and-our-opinion
#3
Dong Wen, Zhenhao Wei, Yanhong Zhou, Guolin Li, Xu Zhang, Wei Han
No abstract text is available yet for this article.
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29743871/corrigendum-software-for-brain-network-simulations-a-comparative-study
#4
Ruben A Tikidji-Hamburyan, Vikram Narayana, Zeki Bozkus, Tarek A El-Ghazawi
[This corrects the article on p. 46 in vol. 11, PMID: 28775687.].
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29713272/credibility-replicability-and-reproducibility-in-simulation-for-biomedicine-and-clinical-applications-in-neuroscience
#5
REVIEW
Lealem Mulugeta, Andrew Drach, Ahmet Erdemir, C A Hunt, Marc Horner, Joy P Ku, Jerry G Myers, Rajanikanth Vadigepalli, William W Lytton
Modeling and simulation in computational neuroscience is currently a research enterprise to better understand neural systems. It is not yet directly applicable to the problems of patients with brain disease. To be used for clinical applications, there must not only be considerable progress in the field but also a concerted effort to use best practices in order to demonstrate model credibility to regulatory bodies, to clinics and hospitals, to doctors, and to patients. In doing this for neuroscience, we can learn lessons from long-standing practices in other areas of simulation (aircraft, computer chips), from software engineering, and from other biomedical disciplines...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29706880/a-dictionary-learning-approach-for-signal-sampling-in-task-based-fmri-for-reduction-of-big-data
#6
Bao Ge, Xiang Li, Xi Jiang, Yifei Sun, Tianming Liu
The exponential growth of fMRI big data offers researchers an unprecedented opportunity to explore functional brain networks. However, this opportunity has not been fully explored yet due to the lack of effective and efficient tools for handling such fMRI big data. One major challenge is that computing capabilities still lag behind the growth of large-scale fMRI databases, e.g., it takes many days to perform dictionary learning and sparse coding of whole-brain fMRI data for an fMRI database of average size...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29706879/experimental-directory-structure-exdir-an-alternative-to-hdf5-without-introducing-a-new-file-format
#7
Svenn-Arne Dragly, Milad Hobbi Mobarhan, Mikkel E Lepperød, Simen Tennøe, Marianne Fyhn, Torkel Hafting, Anders Malthe-Sørenssen
Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5) is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29695959/pymus-python-based-simulation-software-for-virtual-experiments-on-motor-unit-system
#8
Hojeong Kim, Minjung Kim
We constructed a physiologically plausible computationally efficient model of a motor unit and developed simulation software that allows for integrative investigations of the input-output processing in the motor unit system. The model motor unit was first built by coupling the motoneuron model and muscle unit model to a simplified axon model. To build the motoneuron model, we used a recently reported two-compartment modeling approach that accurately captures the key cell-type-related electrical properties under both passive conditions (somatic input resistance, membrane time constant, and signal attenuation properties between the soma and the dendrites) and active conditions (rheobase current and afterhyperpolarization duration at the soma and plateau behavior at the dendrites)...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29670519/neuromatic-an-integrated-open-source-software-toolkit-for-acquisition-analysis-and-simulation-of-electrophysiological-data
#9
Jason S Rothman, R Angus Silver
Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models)...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29628885/a-statistically-representative-atlas-for-mapping-neuronal-circuits-in-the-drosophila-adult-brain
#10
Ignacio Arganda-Carreras, Tudor Manoliu, Nicolas Mazuras, Florian Schulze, Juan E Iglesias, Katja Bühler, Arnim Jenett, François Rouyer, Philippe Andrey
Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila , one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29615887/a-density-driven-method-for-the-placement-of-biological-cells-over-two-dimensional-manifolds
#11
Nicolas P Rougier
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary placement of cells over a two-dimensional manifold. Using a bitmap image whose luminance provides cell density, this method guarantees a discrete distribution of the positions of the cells respecting the local density. This method scales to any number of cells, allows one to specify arbitrary enclosing shapes and provides a scalable and versatile alternative to the more classical assumption of a uniform spatial distribution...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29599715/dynasim-a-matlab-toolbox-for-neural-modeling-and-simulation
#12
Jason S Sherfey, Austin E Soplata, Salva Ardid, Erik A Roberts, David A Stanley, Benjamin R Pittman-Polletta, Nancy J Kopell
DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29599714/clustering-coefficients-for-correlation-networks
#13
Naoki Masuda, Michiko Sakaki, Takahiro Ezaki, Takamitsu Watanabe
Graph theory is a useful tool for deciphering structural and functional networks of the brain on various spatial and temporal scales. The clustering coefficient quantifies the abundance of connected triangles in a network and is a major descriptive statistics of networks. For example, it finds an application in the assessment of small-worldness of brain networks, which is affected by attentional and cognitive conditions, age, psychiatric disorders and so forth. However, it remains unclear how the clustering coefficient should be measured in a correlation-based network, which is among major representations of brain networks...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29593520/iclinfmri-software-for-integrating-functional-mri-techniques-in-presurgical-mapping-and-clinical-studies
#14
Ai-Ling Hsu, Ping Hou, Jason M Johnson, Changwei W Wu, Kyle R Noll, Sujit S Prabhu, Sherise D Ferguson, Vinodh A Kumar, Donald F Schomer, John D Hazle, Jyh-Horng Chen, Ho-Ling Liu
Task-evoked and resting-state (rs) functional magnetic resonance imaging (fMRI) techniques have been applied to the clinical management of neurological diseases, exemplified by presurgical localization of eloquent cortex, to assist neurosurgeons in maximizing resection while preserving brain functions. In addition, recent studies have recommended incorporating cerebrovascular reactivity (CVR) imaging into clinical fMRI to evaluate the risk of lesion-induced neurovascular uncoupling (NVU). Although each of these imaging techniques possesses its own advantage for presurgical mapping, a specialized clinical software that integrates the three complementary techniques and promptly outputs the analyzed results to radiology and surgical navigation systems in a clinical format is still lacking...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29593519/evolving-simple-models-of-diverse-intrinsic-dynamics-in-hippocampal-neuron-types
#15
Siva Venkadesh, Alexander O Komendantov, Stanislav Listopad, Eric O Scott, Kenneth De Jong, Jeffrey L Krichmar, Giorgio A Ascoli
The diversity of intrinsic dynamics observed in neurons may enhance the computations implemented in the circuit by enriching network-level emergent properties such as synchronization and phase locking. Large-scale spiking network models of entire brain regions offer a platform to test theories of neural computation and cognitive function, providing useful insights on information processing in the nervous system. However, a systematic in-depth investigation requires network simulations to capture the biological intrinsic diversity of individual neurons at a sufficient level of accuracy...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29563867/convis-a-toolbox-to-fit-and-simulate-filter-based-models-of-early-visual-processing
#16
Jacob Huth, Timothée Masquelier, Angelo Arleo
We developed Convis , a Python simulation toolbox for large scale neural populations which offers arbitrary receptive fields by 3D convolutions executed on a graphics card. The resulting software proves to be flexible and easily extensible in Python, while building on the PyTorch library (The Pytorch Project, 2017), which was previously used successfully in deep learning applications, for just-in-time optimization and compilation of the model onto CPU or GPU architectures. An alternative implementation based on Theano (Theano Development Team, 2016) is also available, although not fully supported...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29556187/arkheia-data-management-and-communication-for-open-computational-neuroscience
#17
Ján Antolík, Andrew P Davison
Two trends have been unfolding in computational neuroscience during the last decade. First, a shift of focus to increasingly complex and heterogeneous neural network models, with a concomitant increase in the level of collaboration within the field (whether direct or in the form of building on top of existing tools and results). Second, a general trend in science toward more open communication, both internally, with other potential scientific collaborators, and externally, with the wider public. This multi-faceted development toward more integrative approaches and more intense communication within and outside of the field poses major new challenges for modelers, as currently there is a severe lack of tools to help with automatic communication and sharing of all aspects of a simulation workflow to the rest of the community...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29551969/detecting-large-scale-brain-networks-using-eeg-impact-of-electrode-density-head-modeling-and-source-localization
#18
Quanying Liu, Marco Ganzetti, Nicole Wenderoth, Dante Mantini
Resting state networks (RSNs) in the human brain were recently detected using high-density electroencephalography (hdEEG). This was done by using an advanced analysis workflow to estimate neural signals in the cortex and to assess functional connectivity (FC) between distant cortical regions. FC analyses were conducted either using temporal (tICA) or spatial independent component analysis (sICA). Notably, EEG-RSNs obtained with sICA were very similar to RSNs retrieved with sICA from functional magnetic resonance imaging data...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29527160/a-ternary-hybrid-eeg-nirs-brain-computer-interface-for-the-classification-of-brain-activation-patterns-during-mental-arithmetic-motor-imagery-and-idle-state
#19
Jaeyoung Shin, Jinuk Kwon, Chang-Hwan Im
The performance of a brain-computer interface (BCI) can be enhanced by simultaneously using two or more modalities to record brain activity, which is generally referred to as a hybrid BCI. To date, many BCI researchers have tried to implement a hybrid BCI system by combining electroencephalography (EEG) and functional near-infrared spectroscopy (NIRS) to improve the overall accuracy of binary classification. However, since hybrid EEG-NIRS BCI, which will be denoted by hBCI in this paper, has not been applied to ternary classification problems, paradigms and classification strategies appropriate for ternary classification using hBCI are not well investigated...
2018: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/29503613/extremely-scalable-spiking-neuronal-network-simulation-code-from-laptops-to-exascale-computers
#20
Jakob Jordan, Tammo Ippen, Moritz Helias, Itaru Kitayama, Mitsuhisa Sato, Jun Igarashi, Markus Diesmann, Susanne Kunkel
State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity...
2018: Frontiers in Neuroinformatics
journal
journal
42054
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"