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About BIRDS project (Bioinformatics and Information Retrieval Data Structures Analysis and Design)

Guillermo de Bernardo, Susana Ladra
2018 Proceedings of the 5th Spanish Conference on Information Retrieval - CERI '18  
BIRDS stands for "Bioinformatics and Information Retrieval Data Structures analysis and design" and is a 4-year project (2016--2019) that has received funding from the European Union's Horizon 2020 research  ...  The overall goal of BIRDS is to establish a long term international network involving leading researchers in the development of efficient data structures in the fields of Bioinformatics and Information  ...  Objectives The specific objectives for the project are: (1) To improve the scientific excellence of the participants in the design of advanced data structures and algorithms for the fields of bioinformatics  ... 
doi:10.1145/3230599.3230602 dblp:conf/ceri/BernardoL18 fatcat:q3svde6gizeefjofdz7s7ftd6m

Front Matter, Table of Contents, Preface, Conference Organization

Nadia Pisanti, Solon P. Pissis, Michael Wagner
2019 Annual Symposium on Combinatorial Pattern Matching  
Finally, we would like to thank the MSCA RISE 2015 BIRDS Project "Bioinformatics and Information Retrieval Data Structures Analysis & Design" (GA 690941) and the UniPi PRA2017-44 Project for providing  ...  and help in local arrangements.  ...  The problems this conference deals with include those in bioinformatics and computational biology, coding and data compression, combinatorics on words, data mining, information retrieval, natural language  ... 
doi:10.4230/lipics.cpm.2019.0 dblp:conf/cpm/X19 fatcat:pk4m4fdje5hzvncxblerji4vwe

Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course

J. Luo
2013 Briefings in Bioinformatics  
With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the 'How to teach' section.  ...  ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology.  ...  The author also thanks the critical comments from the anonymous reviewers and helpful suggestions from colleagues and students in the revision of the manuscript.  ... 
doi:10.1093/bib/bbt065 pmid:24008274 pmcid:PMC4239802 fatcat:6x7k5ib7ezccrkefqiv44mpf2e

Applied Bioinformatics Tools [chapter]

Jingchu Luo
2013 Basics of Bioinformatics  
We chose several samples as working projects to learn how to find the literature, how to obtain sequence and structure data, how to do the analysis step by step, and how to make a summary from the analysis  ...  List of Genome Databases • GOLD -Genomes Online Database, a comprehensive information resource for complete and ongoing genome sequencing projects with flowcharts and tables of statistical data.  ... 
doi:10.1007/978-3-642-38951-1_9 fatcat:ycrao5zo7baavjv3pxzzvljuye

Biological Data Resources at the EMBL-EBI

Rodrigo Lopez
2008 Revista Colombiana de Biotecnología  
These are Europe's flagships in bioinforma­tics and basic research in molecular biology.  ...  The web portal for the EBI can be found at http://www.ebi.ac.uk/ and represents a single entry point for all data resources and activities described below.  ...  genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.  ... 
doaj:1181789ff05043988701f7c984425c83 fatcat:aoqiuavzcreutlry6vbuzaoxhm

Database and Analytical Resources for Viral Research Community [chapter]

Sujal Phadke, Saichetana Macherla, Richard H. Scheuermann
2019 Reference Module in Life Sciences  
Databases allow storage and analysis of this information to fuel further wet-lab experimentation on the causative agents and comparative analyses of their genomes.  ...  For example, data and bioinformatics tools from ViPR and IRD have facilitated research into detection and diagnostics of viral pathogens, prediction of viral hosts and environmental reservoirs, viral evolution  ...  Analysis and Visualization Capabilities ViPR and IRD host a comprehensive suite of bioinformatics tools for data analysis and visualization, closely integrated with the supported data.  ... 
doi:10.1016/b978-0-12-809633-8.20995-3 fatcat:dbouvnr6hnebdio7fe6ydpjfn4

openBIS ELN-LIMS: an open-source database for academic laboratories

Caterina Barillari, Diana S. M. Ottoz, Juan Mariano Fuentes-Serna, Chandrasekhar Ramakrishnan, Bernd Rinn, Fabian Rudolf
2015 Bioinformatics  
The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic  ...  life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data.  ...  Acknowledgements We thank the yeast laboratory of the Stelling group for feedback during the implementation of the database and J. Stelling for his encouragement and support.  ... 
doi:10.1093/bioinformatics/btv606 pmid:26508761 pmcid:PMC4743625 fatcat:pr4h76dl2ngxjbsflvl5nczzni

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Jeremy G. Frey, Colin L. Bird
2013 Wiley Interdisciplinary Reviews. Computational Molecular Science  
sources of chemical, biochemical, biological, and medical information.  ...  Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data.  ...  ACKNOWLEDGMENTS The authors acknowledge the direct and indirect support for this review flowing from the grants from EPSRC (GR/R67729/, EP/C6008863/, EP/G026238/, EP/K003569/) and JISC (Data Management  ... 
doi:10.1002/wcms.1127 pmid:24432050 pmcid:PMC3884755 fatcat:vpqawnligbbyrgjepzznugq3vi

Conservation and modern information technologies: The global register of migratory species (GROMS)

Klaus Riede
2000 Journal of international wildlife law and policy  
As an initial example of the potential of GIS-analysis, GIS-maps of birds and mammals were intersected with administrative borders, and the number of species was calculated for each province.  ...  Consequences for conservation policies are discussed and future prospects for GIS analysis are outlined.  ...  , ICLARM Manila) for contributing data on migratory fish.  ... 
doi:10.1080/13880290009353953 fatcat:z5wkusawezfdhl6qxn4fxw5qcm

The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

John Deck, Michelle R. Gaither, Rodney Ewing, Christopher E. Bird, Neil Davies, Christopher Meyer, Cynthia Riginos, Robert J. Toonen, Eric D. Crandall
2017 PLoS Biology  
By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.  ...  GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients.  ...  Steve Karl, an early supporter and steering committee member for the Diversity in the Indo-Pacific Network, who helped to shape an early version of GeOMe and who passed away while this paper was in revision  ... 
doi:10.1371/journal.pbio.2002925 pmid:28771471 pmcid:PMC5542426 fatcat:cmiao4n6grasvb3cwa5unhn7ve

Colombia, an unknown genetic diversity in the era of Big Data

Alejandra Noreña – P, Andrea González Muñoz, Jeanneth Mosquera-Rendón, Kelly Botero, Marco A. Cristancho
2018 BMC Genomics  
We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions.  ...  Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches  ...  Acknowledgements The authors would like to acknowledge Simón Orozco Arias for providing help with the generation of scripts necessary to gather and process the data. Funding  ... 
doi:10.1186/s12864-018-5194-8 fatcat:vpaubbkz3nd3nmn5zrn22pdqsy

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard I. Kuo, Robert H. S. Kraus
2020 BMC Bioinformatics  
genome data which serve as a valuable foundation for Avimm.  ...  Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up.  ...  Acknowledgements The authors are grateful for the early access to 363 sequenced bird genomes and annotations through the B10K consortium, which sparked the idea for this project.  ... 
doi:10.1186/s12859-020-03764-3 pmid:33176685 pmcid:PMC7661159 fatcat:5ir2ivfpsrcghnuy3xbvjnhmrq

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
Marco Masseroli, and Dr. Fernando Palluzzi for numerous discussions regarding the data model. This work was supported by a PRIN awarded to Prof. Stefano Ceri.  ...  projects.  ...  Initially, we have designed a set of queries that retrieves non-redundant and repetitive information.  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

Isabl Platform, a digital biobank for processing multimodal patient data

Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung, Elli Papaemmanuil
2020 BMC Bioinformatics  
This presents an opportunity to consolidate data assets into digital biobanks—ecosystems of readily accessible, structured, and annotated datasets that can be dynamically queried and analysed.  ...  However, data processing in accordance with best practices remains challenging and the data capital often becomes siloed.  ...  members of the Papaemmanuil Laboratory, Computational Oncology, Center for Heme Malignancies and Department of Pediatrics for input on system design, functionality and system testing.  ... 
doi:10.1186/s12859-020-03879-7 pmid:33256603 fatcat:ehlgcmzqbvgz3cz5jhrij3dv7u

The Information Systems for DNA Barcode Data [chapter]

Di Liu, Juncai M
2011 Systems and Computational Biology - Bioinformatics and Computational Modeling  
chromatogram (trace files), geographic data and structured morphological information of each specimen.  ...  One of the major aims of bioinformatics is to finely store and manage the huge amount of biological data.  ...  The work in our centre is supported, in part, by the projects from the Bureau of Life Sciences and Biotechnology of CAS, the Project of Informatization of CAS, and the Project of Scientific Databases of  ... 
doi:10.5772/24474 fatcat:b7una4yowbh5zgxsvithhkioj4
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