Neurodatabase


Neurodatabase.org Data Server {related:}

Resources:

BrainML Model Repository


Neurodatabase. org: networking the microelectrode D Gardner – Nature neuroscience, 2004 – nature.com Electrophysiological signals report activity of single neurons, neuronal arrays and networks.  Our understanding of neural coding, information transmission and brain processes would be  aided if such data could be made available for further analyses that could integrate and … Cited by 18 – Related articles – BL Direct – All 3 versions

[CITATION] Open neurodatabase access by Java-mediated controlled-vocabulary neuron terms and experimental protocols D Gardner, M Abato… – Soc Neurosci Abstr, 1998 Cited by 2 – Related articles

[PDF] BrainML and GENIE: Neuroinformatics schemas for neuroscience data sharing [PDF] from neurodatabase.org D Gardner, Y Xiao, M Abato… – Society for …, 2002 – neurodatabase.org … informational and other algorithms. URLS : • BrainML, GENIE & BrainMetaL: brainml.org • Our cortical database: neurodatabase.org • Human Brain Project: www.nimh.nih.gov /neuroinformatics/index.cfm 4. BrainML Describes … Cited by 4 – Related articles – View as HTML

NeuroDatabase: multimedia exploration of the nervous system. [PDF] from nih.gov SL Wertheim – Proceedings of the Annual Symposium on …, 1991 – ncbi.nlm.nih.gov The primary contents of the database are research results in neuroanatomy and regional  biochemistry. We support collaborative work among laboratories using a combination of localand  shared components. Each laboratory can have its own, private copy of the database to … Cited by 1 – Related articles – BL Direct – All 3 versions

A neurodatabase system for mammographic screening J Sklansky, EY Tao, C Ornes… – … -Based Medical Systems …, 1998 – ieeexplore.ieee.org Abstract A novel integration of a neural network and a mammographic database provides a  promising means of amplifying the radiologist’s power to screen mammograms. The  principal novelty of this system is a neural network that produces both a classifier and a … Related articles – All 5 versions

Visualization in the neurosciences: utility in research, teaching, and clinical practice SA Tobet, JC King, SL Wertheim… – … , 1992. Visualization’92, …, 1992 – ieeexplore.ieee.org … card. Steven L. Wertheim – NeuroDatabase: Managing images and graphics from anatomical experiments. NeuroDatabase is an information tool for neuroscience that is being developed to aid research and teaching. It focuses … All 5 versions

Issues and expectations for EMG decomposition KC McGill – Supplements to Clinical Neurophysiology, 2009 – Elsevier … These include PhysioNet (http://www.physionet.org) a research resource for complex physiologic signals including ECG, EEG, and gait; Neurodatabase (http://www.neurodatabase.org), a public basic neuroscience database; the Brain Resource International Database, which … Related articles – All 2 versions

Presenting Interactive Image Databases on the Web Using Java SL Wertheim – Proceedings of the AMIA Symposium, 1998 – ncbi.nlm.nih.gov … [PubMed]; Wertheim SL. NeuroDatabase: multimedia exploration of the nervous system. Proc Annu Symp Comput Appl Med Care. 1991:985-986. [PMC free article] [PubMed]; Wertheim SL. NeuroDatabase: multimedia exploration of the nervous system. … Related articles – All 2 versions

Visual mining of neuro-metaspaces [PDF] from liu.se SH Joshi, I Bowman, R Jennings… – ACM SIGGRAPH 2010 …, 2010 – dl.acm.org … Instead of pro- viding a restricted, unidimensional view of the data, we seek to place a multi-dimensional view of the entire neurodatabase at the user’s disposal. With the aim of visual navigation of complete neuro-repositories, we introduce the concept of brain meta-spaces. … Related articles – All 2 versions

[CITATION] Neuroinformatics for D Gardner, M Abato, KH Knuth… – Databasing the brain: from data to …, 2005 – Wiley Related articles

[PDF] Neuroanalysis. Org: Information-Theoretic and Extended Analyses of Neural Coding [PDF] from neuroanalysis.org MA Repucci, DH Goldberg, E Chan… – Biophysical …, 2010 – neuroanalysis.org … We thank the consultant-collaborators listed at left who have graciously provided algorithms, code, and insight, and the many labs who have provided datasets to neurodatabase.org, as well as the members of our Neuroanalysis Advisory Group: • Patricia M. Di Lorenzo • Esther … View as HTML – All 3 versions

A database system for electrophysiological data P Rautenberg, A Sobolev, A Herz… – Transactions on large- …, 2011 – Springer … One of the first attempts to build a database of neurophysiological data was the neurodatabase.org project [5], which was established 2004, funded by the NIMH Human Brain Project and created by the Laboratory of Neuroinformatics at Weill Medical College of Cornell … Cited by 1 – Related articles – All 3 versions

Mind your data with Neurodatabase. org E Hitt – The Scientist, 2004 – cat.inist.fr … Titre du document / Document title. Mind your data with Neurodatabase.org. Auteur(s) / Author(s). HITT Emma ; Résumé / Abstract. New database makes sense of neurophysiological information Revue / Journal Title. The Scientist ISSN 0890-3670 Source / Source. 2004, vol. … BL Direct

A dendrogram approach to the structure of spike trains [PDF] from biomedcentral.com C Houghton – BMC Neuroscience, 2011 – biomedcentral.com … This quantification is applied to an example spike- train data set described in [2] and made available on http://neurodatabase.org. The data consist of single cell recordings from the nucleus of the solitary tract in rat during presentation of taste stimuli. … Related articles – All 6 versions

[PDF] Deliverable D8-6 Towards generic tools for computational neuroscience: a perspective [PDF] from andrewdavison.info KTH Stockholm – andrewdavison.info … the CRCNS (Collaborative Research in Computational Neuroscoemce) data sharing website. http://www. crcns.org • the Neurodatabase.org Data Server. http://neurodatabase.org • the Cell Centered Database. http://ccdb.ucsd.edu • the INCF Japan Node. http://www.neuroinf.jp … Related articles – View as HTML

Spike train analysis toolkit: enabling wider application of information-theoretic techniques to neurophysiology [HTML] from nih.gov DH Goldberg, JD Victor, EP Gardner… – Neuroinformatics, 2009 – Springer … This resource integrates the neurophysiology data repository at Neurodatabase.org (Gardner et al. … One of these is illustrated in some detail; two others are briefly noted below. Many of the datasets used in these analyses are available via neurodatabase.org. … Cited by 18 – Related articles – All 10 versions

[PDF] Bibliography on neuroinformatics [PDF] from dtu.dk FÅ Nielsen – Rigshospitalet and Technicial University of …, 2004 – hendrix.imm.dtu.dk … (Gardner et al., 2001b; Gardner et al., 2001a), http://neurodatabase.org/, http://brainml.org/ … APLYSIA (“APLYSIA Proficienty Lets You Scan Indentifying Attributes”) once available from http://mollusc.med.cornell.edu/ seems to have been superseded http://neurodatabase.org/. … Cited by 3 – Related articles – View as HTML – All 13 versions

[PDF] Neurowissenschaftliche Datenbanken – eine Herausforderung [PDF] from uni-luebeck.de KML Menne… – Datenbank-Spektrum, 2004 – isip.uni-luebeck.de … von Säugetieren beschäftigt. Die Datenbank heißt wie die Webadresse, unter der sie zu finden ist: Neurodatabase.org. Im navEgate Projekt schließlich [Menne et al. 2004], in … 3.2 Neurodatabase.org Das, was das FMRI Data … Related articles – View as HTML – All 4 versions

Spatial knowledge representation for visualization of human anatomy and function R Schubert, K Höhne, A Pommert, M Riemer… – … Processing in Medical …, 1993 – Springer … Typical representatives are Page 3. 170 ADAM [16], BrainStorm [6], the Anatom-Tutor [19] or the NeuroDatabase [28]. These systems offer a convenient access to different anatomical information, but the related images are always precomputed views. … Cited by 29 – Related articles – BL Direct – All 4 versions

[HTML] Neuroinformatics: from bioinformatics to databasing the brain [HTML] from nih.gov TM Morse – Bioinformatics and biology insights, 2008 – ncbi.nlm.nih.gov … 3). Figure 3. Figure 3 Searching for entries at Neurodatabase.org. This is a pilot project to explore ways in which electrophysiological data can be stored and then retrieved. … 2007a. [Accessed 21 March 2008]. LNI neurodatabase.org [online] URL: http://neurodatabase.org. … Cited by 5 – Related articles – All 14 versions

[CITATION] Medical Volume Visualization Based on” Intelligent Volumes K Hohne, A Pommert, M Riemer, T Schiemann… – … : Advances and Challenges, 1994 Cited by 6 – Related articles

Trial-by-trial estimation of amplitude and latency variability in neuronal spike trains [PDF] from upf.edu A Bollimunta, KH Knuth… – Journal of neuroscience methods, 2007 – Elsevier Cited by 6 – Related articles – All 6 versions

Experimental database system for the vascular brain diseases research P Vcelak, J Polivka, P Maule, P Kratochvil… – … Abstract: 2nd INCF …, 2009 – frontiersin.org … Created database of imaging examinations will allow studying of crucial values and dependencies of particular parameters in high amount of examinations with clinical data correlations.<br> Suggested project is not intended to be another imaging neurodatabase. … Cited by 3 – Related articles – Cached – All 2 versions

Terminology for neuroscience data discovery: multi-tree syntax and investigator-derived semantics [HTML] from nih.gov D Gardner, DH Goldberg, B Grafstein, A Robert… – Neuroinformatics, 2008 – Springer … or institution: Figure 2 shows a sample search for Neurodatabase.org resources relevant to a specific disease type. Selector Terms Allow General or Specific Searches for Relevant Datasets or Other Resource Contents A major … Cited by 8 – Related articles – All 18 versions

[BOOK] The synaptic organization of the brain GM Shepherd – 2004 – books.google.com … and Description of Dendritic Morphology (http://www.krasnow.gmu.edu/ L-Neuron/index.html), Development of a 3D Cell-Centered Neuronal Database (http://ncmir.ucsd.edu/NCDB), and Databases and Data Models Enabling Neuroinformatics (http://neurodatabase.org and http … Cited by 1444 – Related articles – Library Search – All 9 versions

Informatics in neuroscience [HTML] from oxfordjournals.org L French… – Briefings in bioinformatics, 2007 – Oxford Univ Press … The largest structured database we are aware of is Neurodatabase.org, which contains data from eleven experiments [82]. … The Neurodatabase data sets are well annotated and structured according to the BrainML standard [14]. … Cited by 8 – Related articles – BL Direct – All 14 versions

[CITATION] Biology workbenches A Maer, B Saunders, R Unwin… – 2005 – Wiley, Hoboken, NJ Cited by 1 – Related articles

Dynamic publication model for neurophysiology databases [PDF] from royalsocietypublishing.org D Gardner, M Abato… – … of the Royal …, 2001 – rstb.royalsocietypublishing.org Page 1. Dynamic publication model for neurophysiology databases Daniel Gardner*, Michael Abato, Kevin H. Knuth, Robert DeBellis and Steven M. Erde Department of Physiology,Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021- 4805, USA … Cited by 21 – Related articles – BL Direct – All 9 versions

Issues in the design of a pilot concept-based query interface for the Neuroinformatics Information Framework [HTML] from nih.gov L Marenco, Y Li, ME Martone, PW Sternberg… – Neuroinformatics, 2008 – Springer … Other mismatches may reflect the fact that different data- bases collect data at different levels of detail or in different ways (for example, NeuronDB has neuronal properties assigned to specific neuronal canonical compartments, while Neurodatabase.org (Gardner 2004) uses the … Cited by 5 – Related articles – All 19 versions

1st INCF Workshop on Global Portal Services for Neuroscience [PDF] from nature.com J van Pelt… – 2008 – precedings.nature.com … Integration of data and services, complexity hidden for users Neurodatabase.org http://neurodatabase.org Neurophysiology database + tools anatomical visualization NeuroMorpho.Org http://neuromorpho.org/ Inventory of digitally reconstructed neurons … All 2 versions

Data sharing for computational neuroscience [PDF] from berkeley.edu JL Teeters, KD Harris, KJ Millman, BA Olshausen… – Neuroinformatics, 2008 – Springer … The workshop identified data from electrophysiology and from microscopic imaging of neural activity as resource types whose public availability is still vastly underrepresented- though at least one pioneer effort exists (NeuroDatabase. org; Gardner 2004). … Cited by 36 – Related articles – BL Direct – All 11 versions

Identifiable Neuro Ethics Challenges to the Banking of Neuro Data [PDF] from umn.edu J Illes… – Minn. JL Sci. & Tech., 2008 – HeinOnline … 23. See generally Marcia Baringa, Neuroimaging: Still Debated, Brain Image Archives Are Catching On, 300 SCIENCE 43 (2003); Daniel Gardner, Neurodatabase.org: Networking the Microelectrode, 7 NATURE NEUROSCIENCE 486 (2004); John D. Van Horn et al., The … Cited by 3 – Related articles – All 7 versions

The neuroscience information framework: a data and knowledge environment for neuroscience [HTML] from nih.gov D Gardner, H Akil, GA Ascoli, DM Bowden… – Neuroinformatics, 2008 – Springer … A representative set of projects that directly informed our work includes: Sense- Lab, Neurodatabase.org, the Internet Accessible Tool Registry (IATR), the Surface Management System Data- base (SumsDB), the Cell-Centered Database, GeneNet- work/WebQTL, and the … Cited by 52 – Related articles – All 29 versions

Time-resolved and time-scale adaptive measures of spike train synchrony [PDF] from arxiv.org T Kreuz, D Chicharro, M Greschner… – Journal of neuroscience …, 2010 – Elsevier … As a second application to real data we employ the spike train distances to discriminate single- unit responses to taste stimuli recorded in the nucleus of the solitary tract (NTS) in rats (Di Lorenzo and Victor, 2003; data available online at http://neurodatabase.org/, Gardner, 2004 … Cited by 7 – Related articles – All 10 versions

A multiscale approach for assessing the interactions of environmental and biological systems in a holistic health risk assessment framework [PDF] from twitdoc.com PG Georgopoulos – Water, Air, & Soil Pollution: Focus, 2008 – Springer Page 1. A Multiscale Approach for Assessing the Interactions of Environmental and Biological Systems in a Holistic Health Risk Assessment Framework Panos G. Georgopoulos Received: 15 November 2006 /Accepted: 22 February … Cited by 14 – Related articles – BL Direct – All 4 versions

NeuroExtract: facilitating neuroscience-oriented retrieval from broadly-focused bioscience databases using text-based query mediation [HTML] from 171.67.114.118 CJ Crasto, P Masiar… – Journal of the American Medical …, 2007 – jamia.bmj.com … VLDB 1996:203-214. ?: Gardner D. . Notes on neuroscience ontologies. In: Neurodatabase. org; 2004. ?: Marenco L,; Wang TY,; Shepherd G,; Miller PL,; Nadkarni P. . QIS: a framework for biomedical database federation. J Am Med Inform Assoc 2004;11(6):523-534. … Cited by 6 – Related articles – All 13 versions

Computational intelligence in electrophysiology: Trends and open problems C Günay, T Smolinski, W Lytton, T Morse… – … intelligence in biology, 2008 – Springer … 14.2.1 Introduction There are 176 neuroscience databases listed in the Neuroscience Database Gateway [7]. Only one of these, Neurodatabase [32], currently has electrical recordings available, indicating that electrophysiology datasets are currently rarely publicly available. … Cited by 2 – Related articles – All 5 versions

Cengiz Günay1, Tomasz G. Smolinski1, William W. Lytton2, Thomas M. Morse3 Padraig Gleeson4, Sharon Crook5, Volker Steuber4, 6, Angus Silver4, Horatiu Voicu7, … [PDF] from arizona.edu GA Mitra8… – … in biology: current trends and open …, 2008 – books.google.com … 1 Introduction There are 176 neuroscience databases listed in the Neuroscience Database Gateway [7]. Only one of these, Neurodatabase [32], currently has electrical recordings available, indicating that electrophysiology datasets are currently rarely publicly available. … Related articles – All 5 versions

[HTML] Surrogate spike train generation through dithering in operational time [HTML] from nih.gov S Louis, GL Gerstein, S Grün… – Frontiers in …, 2010 – ncbi.nlm.nih.gov Cited by 8 – Related articles – All 6 versions

[PDF] What can spike train distances tell us about the neural code? [PDF] from upf.edu D Chicharro, T Kreuz… – J Neurosci Methods, 2011 – cns.upf.edu … Furthermore, apart from the simulated data, in Section 3.3 we also use exemplary experimental recordings. These data were delivered via http://neurodatabase.org, a neuroinformatics resource funded by the Human Brain Project (Gardner, 2004). … Cited by 3 – Related articles – View as HTML – All 3 versions

Geometrical interpretation of fMRI-guided MEG/EEG inverse estimates [PDF] from mit.edu SP Ahlfors… – NeuroImage, 2004 – Elsevier Cited by 51 – Related articles – All 11 versions

What time scale parametric spike train distances can tell us about the neural code? D Chicharro, T Kreuz… – Journal of Neuroscience Methods, 2011 – Elsevier … Furthermore, apart from the simulated data, in Section 3.3 we also use exem- plary experimental recordings. These data were delivered via http://neurodatabase.org, a neuroinformatics resource funded by the Human Brain Project (Gardner, 2004). …

Database-Aided Diagnosis in Digital Mammography [PDF] from dtic.mil J Sklansky – 2000 – DTIC Document … Task 6. Construct a mapped database system (originally called “neurodatabase system,”) consisting of a graphical user interface, a relational map, the visual neural classifier, and the proven mammographic database, (month 17) This Task was completed successfully, 5 months … Related articles – All 6 versions

The NIF DISCO framework: facilitating automated integration of neuroscience content on the web [PDF] from ucsd.edu L Marenco, R Wang, GM Shepherd… – Neuroinformatics, 2010 – Springer … Architecture Management System), Willy WaiHo Wong and Maryann Martone (Cell Centered Database), Rolf Kotter (CocoDat), David Kennedy (Internet Brain Volume Database), Maryam Halavi and Giorgio Ascoli (Neuromorpho.org), and Daniel Gardner (Neurodatabase.org). … Cited by 3 – Related articles – All 14 versions

DATA-MEAns: an open source tool for the classification and management of neural ensemble recordings MP Bonomini, JM Ferrandez, JA Bolea… – Journal of neuroscience …, 2005 – Elsevier Cited by 15 – Related articles – All 4 versions

[CITATION] Bioinformatic databases [PDF] from njit.edu S DATABASES – 2008 – Wiley Online Library Cited by 1 – Related articles – All 3 versions

SynapticDB, Effective Web-based Management and Sharing of Data from Serial Section Electron Microscopy [HTML] from nih.gov B Shi, J Bourne… – Neuroinformatics, 2010 – Springer … al. 2007; Martone et al. 2004; Marenco et al. 2010, http://ccdb.ucsd.edu/index.shtm; http://neuinfo.org/; http://neurodatabase.org/; http://neuromorpho.org/). Synap- ticDB is the first integrated system for ssEM studies. It promotes … Related articles – All 7 versions

Online variational inference for state-space models with point-process observations AZ Mangion, K Yuan, V Kadirkamanathan… – Neural …, 2011 – MIT Press Cited by 2 – Related articles – All 7 versions

[PDF] Section I Evaluation and Benefit [PDF] from nih.gov BC Benefit – ncbi.nlm.nih.gov Page 1. Contents AMIA Board of Directors, 1990-1991 1991 SCAMC Program Committee 1991 SCAMC Reviewer List Assessing Our Accomplishments Section I Evaluation and Benefit FieldTrialsofMedical Decision-Aids: Potential … View as HTML

[PDF] BrainFrame: a knowledge visualization system for the neurosciences [PDF] from psu.edu SJ Barnes… – … and Data Analysis 2009, Proccedings of SPIE, 2009 – Citeseer … In KOSLOW, SH AND SUBRAMANIAM, S. (eds.): Databasing the Brain. John Wiley & Sons Inc., Canada, 2005, 47-67. [Gar04] GARDNER, D.: Neurodatabase.org: networking the microelectrode. Nat. Neurosci., 7 (2004), 486-487. … Cited by 1 – Related articles – View as HTML – All 5 versions

[PDF] Stochastic generation of biologically accurate brain networks [PDF] from tamu.edu A Aluri – 2005 – research.cs.tamu.edu Page 1. STOCHASTIC GENERATION OF BIOLOGICALLY ACCURATE BRAIN NETWORKS A Thesis by ARAVIND ALURI Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE … Related articles – View as HTML – Library Search – All 15 versions

CARMEN [Code, Analysis, Repository & Modelling for e-Neuroscience] [PDF] from ed.ac.uk G Pryor – 2008 – era-test.lib.ed.ac.uk … within the discipline; ? the provision of use cases from the ongoing requirements gathering programme that will assist in the definition of terms; ? the Technical Moderator’s critical examination of existing systems in neuroscience and related fields (eg http://neurodatabase.org) to … Cited by 1 – Related articles – All 5 versions

Characterization of information and causality measures for the study of neuronal data [PDF] from tesisenred.net D Chicharro Raventós – 2011 – tesisenred.net Page 1. Characterization of information and causality measures for the study of neuronal data Daniel Chicharro Ravent´os Tesi Doctoral UPF / 2011 Supervised by Dr. Ralph Gregor Andrzejak Department of Information and Communication Technologies … Related articles – All 3 versions

Common data model for neuroscience data and data model exchange [HTML] from 171.67.114.118 D Gardner, KH Knuth, M Abato… – Journal of the …, 2001 – 171.67.114.118 Cited by 56 – Related articles – BL Direct – All 14 versions

MatOFF: A tool for analyzing behaviorally complex neurophysiological experiments [HTML] from nih.gov A Genovesio… – Journal of neuroscience methods, 2007 – Elsevier Cited by 1 – Related articles – All 5 versions

A novel framework for storage, analysis and integration through mediation of large-scale electrophysiological data B Ljungquist, P Petersson… – … (NER), 2011 5th …, 2011 – ieeexplore.ieee.org … Vol. 206. Addison- wesley Reading, MA, 1995. [7] Garcia, Samuel, and Nicolas Fourcaud-Trocmé. “OpenElectrophy: an electrophysiological data- and analysis-sharing framework.” Frontiers in Neuroinformatics 3 (2009)9. [8] Gardner, D. “Neurodatabase. … Cited by 2 – Related articles

Reusable architectural decision model for model and metadata repositories [PDF] from tuwien.ac.at C Mayr, U Zdun… – Formal Methods for Components and …, 2009 – Springer Page 1. Reusable Architectural Decision Model for Model and Metadata Repositories Christine Mayr, Uwe Zdun, and Schahram Dustdar Distributed Systems Group Information System Institute Vienna University of Technology … Cited by 2 – Related articles – All 11 versions

[HTML] A bottom-up approach to data annotation in neurophysiology [HTML] from nih.gov J Grewe, T Wachtler… – Frontiers in Neuroinformatics, 2011 – ncbi.nlm.nih.gov We are sorry, but NCBI web applications do not support your browser, and may not function properly. More information here… … Related articles – All 6 versions

View-based model-driven architecture for enhancing maintainability of data access services [PDF] from univie.ac.at C Mayr, U Zdun… – Data & Knowledge Engineering, 2011 – eprints.cs.univie.ac.at Page 1. View-based Model-Driven Architecture for Enhancing Maintainability of Data Access Services Christine Mayra, Uwe Zdunb, Schahram Dustdara aDistributed Systems Group, Information Systems Institute, Vienna University … Related articles – All 4 versions

LONI & Co: Die epistemische Spezifität digitaler Wissensräume in der kognitiven Neurowissenschaft L Huber – Berichte zur Wissenschaftsgeschichte, 2011 – Wiley Online Library Page 1. DOI: 10.1002/bewi.201101502 Lara Huber LONI & Co: Die epistemische Spezifität digitaler Wissensräume in der kognitiven Neurowissenschaft1 Summary: LONI & Co: About the Epistemic Specificity of Digital Spaces of Knowledge in Cognitive Neuroscience. … All 2 versions