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Fast and efficient searching of biological data resources--using EB-eye

F. Valentin, S. Squizzato, M. Goujon, H. McWilliam, J. Paern, R. Lopez
2010 Briefings in Bioinformatics  
The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI.  ...  This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines.  ...  EB-eye is a catalogue of biological entities, similar to a library catalogue that describes publications, and contains enough information to allow for efficient searching.  ... 
doi:10.1093/bib/bbp065 pmid:20150321 pmcid:PMC2905521 fatcat:qebowfm43fauvno5ncgtxe5dom

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Silvano Squizzato, Young Mi Park, Nicola Buso, Tamer Gur, Andrew Cowley, Weizhong Li, Mahmut Uludag, Sangya Pundir, Jennifer A. Cham, Hamish McWilliam, Rodrigo Lopez
2015 Nucleic Acids Research  
We present the EBI Search engine, referred to here as 'EBI Search', an easy-to-use fast text search and indexing system with powerful data navigation and retrieval capabilities.  ...  The interconnectivity that exists between data resources at EMBL-EBI provides easy, quick and precise navigation and a better understanding of the relationship between different data types including sequences  ...  ACKNOWLEDGEMENTS We would like to thank the following staff and collaborators for their support: Anton Petrov, Dietmar Sturmayr, Francis Rowland, Philip Lewis, Andrea Cristofori and Simone Badoer.  ... 
doi:10.1093/nar/gkv316 pmid:25855807 pmcid:PMC4489232 fatcat:m6wp7w7c4zdbrpsunzxlzqy4mi

Autonomous Flying With Neuromorphic Sensing

Patricia P. Parlevliet, Andrey Kanaev, Chou P. Hung, Andreas Schweiger, Frederick D. Gregory, Ryad Benosman, Guido C. H. E. de Croon, Yoram Gutfreund, Chung-Chuan Lo, Cynthia F. Moss
2021 Frontiers in Neuroscience  
In this paper, we argue for a bio-inspired approach to solve autonomous flying challenges, outline the frontier of sensing, data processing, and flight control within a neuromorphic paradigm, and chart  ...  This results in both energy and computational resource savings being an inspiration for autonomous systems.  ...  data fusion inherent to biological sensing.  ... 
doi:10.3389/fnins.2021.672161 pmid:34054420 pmcid:PMC8160287 fatcat:nw6twkp3abeonlkqmtvc3nutsi

LAILAPS: The Plant Science Search Engine

Maria Esch, Jinbo Chen, Christian Colmsee, Matthias Klapperstück, Eva Grafahrend-Belau, Uwe Scholz, Matthias Lange
2014 Plant and Cell Physiology  
The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases.  ...  We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case  ...  Furthermore, we thank all transPLANT partners for fruitful discussions and providing mapping files to their plant genomic resources. Disclosures The authors declare no conflicts of interest.  ... 
doi:10.1093/pcp/pcu185 pmid:25480116 pmcid:PMC4301746 fatcat:7tlrxllcdzgsjgpmhxsnufelhu

What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins

James R. A. Hutchins, Doug Kellogg
2014 Molecular Biology of the Cell  
Such methods generate data sets of gene, transcript, or protein hits that researchers wish to explore to understand their properties and functions and thus their possible roles in biological systems of  ...  and proteins involved in biological processes.  ...  Both the NCBI's "GQuery" Global Cross-Database Search and the EBI Search (also known as EB-eye) allow the user to query all of their hosted databases in one operation; these multisearches can be initiated  ... 
doi:10.1091/mbc.e13-10-0602 pmid:24723265 pmcid:PMC3982986 fatcat:53kmvwius5dm5lekojvblip7ga

Performance Evaluation Of Structured And Semi-Structured Bioinformatics Tools: A Comparative Study

Abdelsalam M. Maatuk Raja A. Moftah
2018 Zenodo  
We used Sequence Retrieval System (SRS) and Entrez search tools for structured data, while Perl and BioPerl search programs were used for semi-structured data to retrieve complex queries including a combination  ...  In this paper, we investigate and evaluate the performance of some of these methods in terms of their ability to efficiently access bioinformatics databases using webbased interfaces.  ...  In a restricted sense, this requires a fast and efficient search engine that provides easy to use and uniform access to the biological data resources hosted on public free bioinformatics databases [11  ... 
doi:10.5281/zenodo.1453755 fatcat:h2uyatbi4jaqpeotn7atfsk4cu

Energy-based scheme for reconstruction of piecewise constant signals observed in the movement of molecular machines

Joachim Rosskopf, Korbinian Paul-Yuan, Martin B. Plenio, Jens Michaelis
2016 Physical review. E  
First, an efficient convex denoising scheme is applied which allows compression to tupels of amplitudes and plateau lengths.  ...  Comparison to existing step-finding methods shows that EBS is superior both in speed and precision.  ...  Such an approach is already in common use in the computer vision community [27] and is both computationally efficient and fast.  ... 
doi:10.1103/physreve.94.022421 pmid:27627346 fatcat:pus3hqsexnec5nves7uj4rop5y

A guide to the Proteomics Identifications Database proteomics data repository

Juan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Joseph M. Foster, Michael Mueller, Jonathan Rameseder, Henning Hermjakob, Lennart Martens
2009 Proteomics  
Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data.  ...  The Proteomics Identifications Database (PRIDE, is one of the main repositories of MS derived proteomics data.  ...  Finally, PRIDE data has also been incorporated into the EBI's new meta search tool (''EB-eye''), accessible at the top from every single EBI page.  ... 
doi:10.1002/pmic.200900402 pmid:19662629 pmcid:PMC2970915 fatcat:ppnagxm4bvb4nkjkevsmm3u5bq

Human neuroimaging as a "Big Data" science

John Darrell Van Horn, Arthur W. Toga
2013 Brain Imaging and Behavior  
As neuroimaging advances further, e.g. aging, genetics, and age-related disease, new vision is needed to manage and process this information while marshalling of these resources into novel results.  ...  In this article, we discuss how modern neuroimaging research represents a mutifactorial and broad ranging data challenge, involving the growing size of the data being acquired; sociologial and logistical  ...  We express our gratitude the faculty and staff of the Laboratory of Neuro Imaging (LONI) at the University of California Los Angeles.  ... 
doi:10.1007/s11682-013-9255-y pmid:24113873 pmcid:PMC3983169 fatcat:vrbn7rrx2zbsvah6c5hssu5upa

Development of a Machine Learning Model for Knowledge Acquisition, Relationship Extraction and Discovery in Domain Ontology Engineering using Jaccord Relationship Extraction and Neural Network

2019 International journal of recent technology and engineering  
A Jaccord Relationship extraction process and the Neural Network Approval for Automated Theory is used for retrieval of data, automated indexing, mapping and knowledge discovery and rule generation.  ...  various techniques of data extraction.  ...  Systems are evaluated using three measures of reliability, model precision, and system efficiency.  ... 
doi:10.35940/ijrte.c6362.098319 fatcat:whgnce4aa5aofalvusaypt6pje

2022 Roadmap on Neuromorphic Computing and Engineering [article]

Dennis V. Christensen, Regina Dittmann, Bernabé Linares-Barranco, Abu Sebastian, Manuel Le Gallo, Andrea Redaelli, Stefan Slesazeck, Thomas Mikolajick, Sabina Spiga, Stephan Menzel, Ilia Valov, Gianluca Milano (+47 others)
2022 arXiv   pre-print
We hope that this Roadmap will be a useful resource to readers outside this field, for those who are just entering the field, and for those who are well established in the neuromorphic community. https  ...  This new generation of computers has the potential to be used for the storage and processing of large amounts of digital information with much lower power consumption than conventional processors.  ...  concerns are increasingly pressuring our way of life, become an essential component of a sustainable society.  ... 
arXiv:2105.05956v3 fatcat:pqir5infojfpvdzdwgmwdhsdi4

Clinical-Grade Human Pluripotent Stem Cells for Cell Therapy: Characterization Strategy

Daniela Rehakova, Tereza Souralova, Irena Koutna
2020 International Journal of Molecular Sciences  
Quality and safety must be of the highest importance when humans' lives are at stake. With the rising number of clinical trials, there is a need for a consensus on hPSCs characterization.  ...  Here, we summarize mandatory and ′for information only′ characterization methods with release criteria for the establishment of clinical-grade hPSC lines.  ...  and pre-testing of the starting biological material can prevent wasting resources.  ... 
doi:10.3390/ijms21072435 pmid:32244538 pmcid:PMC7177280 fatcat:ygl4pmrtobgilnd2e5ja5bmkfm

Interactive and innovative technologies for smart education

Babatomiwa Omonayajo, Fadi Al-Turjman, Nadire Cavus
2022 Computer Science and Information Systems  
This concept is accomplished through the use of smart devices and technologies that are interconnected to access digital resources.  ...  It is with great hope that the use of modern technologies in smart education will improve educational quality while also making teaching and learning more convenient.  ...  Operation Efficiency Performance measures the intelligent allocation of educational resources between the increased efficiency of cloud technology, learning management systems, and applications.  ... 
doi:10.2298/csis210817027o fatcat:xyal7ovaybhf3lw4pev5hugxmq

The MicroRNA miR-277 Controls Physiology and Pathology of the Adult Drosophila Midgut by Regulating the Expression of Fatty Acid β-Oxidation-Related Genes in Intestinal Stem Cells

Lisa Zipper, Sai Batchu, Nida Hatice Kaya, Zeus Andrea Antonello, Tobias Reiff
2022 Metabolites  
Here, taking advantage of the genetically accessible adult Drosophilamelanogaster intestine and the availability of ex vivo single cell sequencing data, we tested that hypothesis and investigated the metabolism  ...  Our initial in silico analysis of single cell RNAseq data and functional experiments identify the microRNA miR277 as a posttranscriptional regulator of fatty acid β-oxidation (FAO) in the intestinal lineage  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo12040315 pmid:35448502 pmcid:PMC9028014 fatcat:xk7hlotaw5bx5phlcvsjkuepam

Insect-Inspired Robots: Bridging Biological and Artificial Systems

Poramate Manoonpong, Luca Patanè, Xiaofeng Xiong, Ilya Brodoline, Julien Dupeyroux, Stéphane Viollet, Paolo Arena, Julien R. Serres
2021 Sensors  
These interconnected and interdependent areas are all crucial to improving the level of performance of hexapod robotics in terms of energy efficiency, terrain adaptability, autonomy, and operational range  ...  How can we build intelligent autonomous hexapod robots that can exploit their biomechanics, morphology, and computational systems, to achieve autonomy, adaptability, and energy efficiency comparable to  ...  Acknowledgments: We thank Vincent Fourcassié and Pierre Moretto from CRCA UMR5163 (CNRS/ University of Toulouse 3), France, for their fruitful discussions concerning biological inputs in ants.  ... 
doi:10.3390/s21227609 pmid:34833685 pmcid:PMC8623770 fatcat:7gne3leewjhwhaqs4bcd5hmxjm
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