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BIRDS SIGNED

Bioinformatics and Information Retrieval Data Structures Analysis and Design

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

BIRDS project word cloud

Explore the words cloud of the BIRDS project. It provides you a very rough idea of what is the project "BIRDS" about.

risk cpus amount nowadays age network company birds new processor computer searching time relative sequence disks class schools strengthen thousands repetitive algorithms structures synergies workshops transistors slower widening efficient cycles members computers personalized word amounts storing moore technologies searches navigating thanks indexing conferences designing market resilient software architectures law expertise search sme continents dna takes huge engine clock summer tens medicine biological community slowest partnership genome architecture gpus international representation cooperation tackled compressing networks bioinformatics exchange faster sharing staff innovative sequencing data retrieval size

Project "BIRDS" data sheet

The following table provides information about the project.

Coordinator	UNIVERSIDADE DA CORUNA Organization address address: CALLE DE LA MAESTRANZA 9 city: LA CORUNA postcode: 15001 website: http://www.udc.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Spain [ES]
Project website	http://birdsproject.eu/
Total cost	648˙000 €
EC max contribution	648˙000 € (100%)
Programme	1. H2020-EU.1.3.3. (Stimulating innovation by means of cross-fertilisation of knowledge)
Code Call	H2020-MSCA-RISE-2015
Funding Scheme	MSCA-RISE
Starting year	2016
Duration (year-month-day)	from 2016-01-01 to 2019-12-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	UNIVERSIDADE DA CORUNA UNIVERSIDADE DA CORUNA Organization address address: CALLE DE LA MAESTRANZA 9 city: LA CORUNA postcode: 15001 website: http://www.udc.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (LA CORUNA)	coordinator	265˙500.00
2	HELSINGIN YLIOPISTO HELSINGIN YLIOPISTO Organization address address: YLIOPISTONKATU 3 city: HELSINGIN YLIOPISTO postcode: 14 website: www.helsinki.fi contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FI (HELSINGIN YLIOPISTO)	participant	189˙000.00
3	INESC ID - INSTITUTO DE ENGENHARIADE SISTEMAS E COMPUTADORES, INVESTIGACAO E DESENVOLVIMENTO EM LISBOA INESC ID - INSTITUTO DE ENGENHARIADE SISTEMAS E COMPUTADORES, INVESTIGACAO E DESENVOLVIMENTO EM LISBOA Organization address address: RUA ALVES REDOL 9 city: LISBOA postcode: 1000 029 website: www.inesc-id.pt contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	PT (LISBOA)	participant	135˙000.00
4	ENXENIO SL ENXENIO SL Organization address address: ESTRADA BANOS DE ARTEIXO EDIFICIO SAN CRISTOBAL PORTAL B 2 IZQUIERDA A CORUNA 15 city: A CORUNA postcode: 15008 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (A CORUNA)	participant	58˙500.00
5	NATIONAL UNIVERSITY CORPORATION KYUSHU UNIVERSITY NATIONAL UNIVERSITY CORPORATION KYUSHU UNIVERSITY Organization address address: 744 MOTOOKA, NISHI-KU city: FUKUOKA postcode: 819 0395 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	JP (FUKUOKA)	partner	0.00
6	UNIVERSIDAD DE CHILE UNIVERSIDAD DE CHILE Organization address address: Av. Libertador Bernardo O'Higgins 1058 city: SANTIAGO postcode: 10 website: www.uchile.cl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CL (SANTIAGO)	partner	0.00
7	UNIVERSIDAD DE CONCEPCION UNIVERSIDAD DE CONCEPCION Organization address address: VICTOR LAMAS 1290 city: CONCEPCION postcode: 4070386 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CL (CONCEPCION)	partner	0.00
8	UNIVERSITY OF MELBOURNE UNIVERSITY OF MELBOURNE Organization address address: PARKVILLEOFFICE OF THE VICE CHANCELLOR city: MELBOURNE postcode: 3010 website: www.unimelb.edu.au contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	AU (MELBOURNE)	partner	0.00

Map

Project objective

Nowadays computers are used to process huge amounts of information, for example a major search engine processes tens of thousands of searches per second. Still the future of the information age is at risk. Computer architectures will not be resilient enough for the next information challenges. It is not only a matter of word size or clock cycles. New DNA sequencing technologies are evolving much faster than Moore's law, this means that they are evolving faster than the amount of transistors that go into CPUs and GPUs. Moreover computer disks are, by far, the slowest part of the architecture and are evolving even slower, therefore widening the relative time that information takes to reach the processor. Processing the amount of information, that will make personalized medicine a reality, requires a new approach. A new class of data structures has recently been developed to address the new challenges in storing, processing, indexing, searching and navigating biological data. Similar tasks have been also tackled by researchers in the information retrieval community: such as designing algorithms for sequence analysis, networks representation or compressing and indexing repetitive data. Synergies of researchers from both fields can lead to new efficient approaches to improve the technology used for analysis of genome-scale data. The overall goal of BIRDS is to establish a long term international network involving leading researchers in bioinformatics and information retrieval from four different continents, to strengthen the partnership through the exchange of knowledge and expertise, and to develop integrated approaches to improve current approaches in both fields. It will be implemented through staff exchanges, in addition to summer schools, workshops and conferences to facilitate knowledge sharing between members of the partnership. We will also bring research results to market, thanks to cooperation with an innovative SME software development company based in Europe.

Deliverables

List of deliverables.
Final report of WP3	Documents, reports	2020-03-06 15:47:15
Final report of WP6	Documents, reports	2020-03-06 15:47:20
Prototypes WP5	Demonstrators, pilots, prototypes	2020-03-06 15:47:19
Final report of WP4	Documents, reports	2020-03-06 15:47:33
Benchmark and test report	Documents, reports	2020-03-06 15:47:18
Final report of WP2	Documents, reports	2020-03-06 15:47:19
Integration report	Documents, reports	2019-08-30 15:45:59
Kick-Off Meeting documentation	Documents, reports	2019-08-30 15:45:59
Quality management plan	Documents, reports	2019-08-30 15:45:59

Take a look to the deliverables list in detail: detailed list of BIRDS deliverables.

Publications

List of publications.
year	authors and title	journal	last update
2020	LuÃs M. S. Russo, Ana D. Correia, Gonzalo Navarro, Alexandre P. Francisco Approximating Optimal Bidirectional Macro Schemes published pages: , ISSN: , DOI:	2020 Data Compression Conference	2020-03-05
2020	Daniil Galaktionov Compressed data structures for trajectory representation published pages: , ISSN: , DOI:		2020-03-05
2019	Valenzuela, Daniel; Kosolobov, Dmitry; Navarro, Gonzalo; Puglisi, Simon J. Lempel-Ziv-like Parsing in Small Space published pages: , ISSN: , DOI:		2020-03-05
2019	DÃaz-DomÃnguez, Diego; Belazzougui, Djamal; Gagie, Travis; MÃ¤kinen, Veli; Navarro, Gonzalo; Puglisi, Simon J. Assembling Omnitigs using Hidden-Order de Bruijn Graphs published pages: , ISSN: , DOI:		2020-03-05
2020	AdriÃ¡n GÃ³mez-BrandÃ³n Bitvectors with runs and the successor/predecessor problem published pages: , ISSN: , DOI:	2020 Data Compression Conference	2020-03-05
2020	Miguel E. Coimbra, Alexandre P. Francisco, LuÃs M. S. Russo, Guillermo de Bernardo, Susana Ladra, Gonzalo Navarro On dynamic succinct graph representations published pages: , ISSN: , DOI:	2020 Data Compression Conference	2020-03-05
2020	Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Antonio FariÃ±a Revisiting compact RDF stores based on k2-trees published pages: , ISSN: , DOI:	2020 Data Compression Conference	2020-03-05
2020	Nieves R. Brisaboa, Antonio FariÃ±a, Gonzalo Navarro, Tirso V. Rodeiro Semantrix: A Compressed Semantic Matrix published pages: , ISSN: , DOI:	2020 Data Compression Conference	2020-03-05
2020	Fernando Silva-Coira, JosÃ© R. ParamÃ¡, Susana Ladra, Juan R. LÃ³pez, Gilberto GutiÃ©rrez Efficient processing of raster and vector data published pages: e0226943, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0226943	PLOS ONE 15/1	2020-02-04
2018	Nieves R. Brisaboa, Antonio FariÃ±a, Daniil Galaktionov, M. Andrea Rodriguez A compact representation for trips over networks built on self-indexes published pages: 1-22, ISSN: 0306-4379, DOI: 10.1016/j.is.2018.06.010	Information Systems 78	2020-01-29
2019	LuÃs M.S. Russo A study on splay trees published pages: 1-18, ISSN: 0304-3975, DOI: 10.1016/j.tcs.2018.12.020	Theoretical Computer Science 776	2020-01-29
2019	Sandra Ãlvarez-GarcÃa, Borja Freire, Susana Ladra, Ã“scar Pedreira Compact and efficient representation of general graph databases published pages: 1479-1510, ISSN: 0219-1377, DOI: 10.1007/s10115-018-1275-x	Knowledge and Information Systems 60/3	2020-01-29
2019	Nieves R. Brisaboa, AdriÃ¡n GÃ³mez-BrandÃ³n, Gonzalo Navarro, JosÃ© R. ParamÃ¡ GraCT: A Grammar-based Compressed Index for Trajectory Data published pages: 106-135, ISSN: 0020-0255, DOI: 10.1016/j.ins.2019.01.035	Information Sciences 483	2020-01-29
2019	Suilen H. Alvarado Design of Mutation Operators for Testing Geographic Information Systems published pages: 43, ISSN: 2504-3900, DOI: 10.3390/proceedings2019021043	Proceedings 21/1	2020-01-29
2019	Antonio FariÃ±a, Miguel A. MartÃnez-Prieto, Francisco Claude, Gonzalo Navarro, Juan J. Lastra-DÃaz, Nicola Prezza, Diego Seco On the reproducibility of experiments of indexing repetitive document collections published pages: 181-194, ISSN: 0306-4379, DOI: 10.1016/j.is.2019.03.007	Information Systems 83	2020-01-29
2019	Jose Fuentes-Sepulveda, Susana Ladra Energy Consumption in Compact Integer Vectors: A Study Case published pages: 155625-155636, ISSN: 2169-3536, DOI: 10.1109/ACCESS.2019.2949655	IEEE Access 7	2020-01-29
2018	Nieves R. Brisaboa, Diego Caro, Antonio FariÃ±a, M. Andrea Rodriguez Using Compressed Suffix-Arrays for a compact representation of temporal-graphs published pages: 459-483, ISSN: 0020-0255, DOI: 10.1016/j.ins.2018.07.023	Information Sciences 465	2020-01-29
2019	Daniel Gibney, Sharma V. Thankachan On the Hardness and Inapproximability of Recognizing Wheeler Graphs published pages: 51:1--51:16, ISSN: , DOI: 10.4230/lipics.esa.2019.51	27th Annual European Symposium on Algorithms (ESA 2019)	2020-01-29
2019	Daniel Inostroza, Cecilia HernÃ¡ndez, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa Cell cycle and protein complex dynamics in discovering signaling pathways published pages: 1950011, ISSN: 0219-7200, DOI: 10.1142/s0219720019500112	Journal of Bioinformatics and Computational Biology 17/03	2020-01-29
2019	Diego DÃaz-DomÃnguez, Travis Gagie, Gonzalo Navarro Simulating the DNA Overlap Graph in Succinct Space published pages: 26:1--26:20, ISSN: , DOI: 10.4230/lipics.cpm.2019.26	30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)	2020-01-29
2018	Rui Henriques, Alexandre P. Francisco, LuÃs M. S. Russo, Hideo Bannai Order-Preserving Pattern Matching Indeterminate Strings published pages: , ISSN: , DOI: 10.4230/lipics.cpm.2018.2	Annual Symposium on Combinatorial Pattern Matching (CPM 2018) 2:1--2:15	2020-01-29
2019	P. Mirabal, J. Abreu, D. Seco Assessing the best edit in perturbation-based iterative refinement algorithms to compute the median string published pages: 104-111, ISSN: 0167-8655, DOI: 10.1016/j.patrec.2019.02.004	Pattern Recognition Letters 120	2020-01-29
2018	LuÃsÂ M.Â S.Â Russo, Andreia Teixeira, AlexandreÂ Francisco Linking and Cutting Spanning Trees published pages: 53, ISSN: 1999-4893, DOI: 10.3390/a11040053	Algorithms 11/4	2020-01-29
2017	Gagie, Travis; Kempa, Dominik; Salmela, Leena; Sverdlov, Sophie; Toivonen, Jarkko; Ukkonen, Esko; Francisco, Alexandre An Experiment in Learning the Language of Sequence Motifs: Sequence Logos vs. Finite-State Machines published pages: , ISSN: , DOI: 10.1101/143024	14	2020-01-29
2016	Francisco Claude, Antonio FariÃ±a, Miguel A. MartÃnez-Prieto, Gonzalo Navarro Universal indexes for highly repetitive document collections published pages: 1-23, ISSN: 0306-4379, DOI: 10.1016/j.is.2016.04.002	Information Systems 61	2019-08-30
2016	Nieves R. Brisaboa, Guillermo De Bernardo, Roberto Konow, Gonzalo Navarro, Diego Seco Aggregated 2D range queries on clustered points published pages: 34-49, ISSN: 0306-4379, DOI: 10.1016/j.is.2016.03.004	Information Systems 60	2019-08-30
2017	Alberto OrdÃ³Ã±ez, Gonzalo Navarro, Nieves R. Brisaboa Grammar compressed sequences with rank/select support published pages: 54-71, ISSN: 1570-8667, DOI: 10.1016/j.jda.2016.10.001	Journal of Discrete Algorithms 43	2019-08-30
2017	Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha KÃ¤rkkÃ¤inen, Gonzalo Navarro, Simon J. Puglisi, Jouni SirÃ©n Document retrieval on repetitive string collections published pages: 253-291, ISSN: 1386-4564, DOI: 10.1007/s10791-017-9297-7	Information Retrieval Journal 20/3	2019-08-30
2017	Fernando Silva-Coira Compact data structures for large and complex datasets published pages: , ISSN: , DOI:		2019-08-30
2018	Alexandre P. Francisco, Travis Gagie, Susana Ladra, Gonzalo Navarro Exploiting Computation-Friendly Graph Compression Methods published pages: , ISSN: , DOI:	Data Compression Conference DCC 2018	2019-08-30
2016	JosÃ© Fuentes-SepÃºlveda, Erick Elejalde, Leo Ferres, Diego Seco Parallel construction of wavelet trees on multicore architectures published pages: , ISSN: 0219-1377, DOI: 10.1007/s10115-016-1000-6	Knowledge and Information Systems	2019-08-30
2018	JosÃ© Fuentes-SepÃºlveda, Juha KÃ¤rkkÃ¤inen, Dmitry Kosolobov, Simon J. Puglisi Run Compressed Rank/Select for Large Alphabets published pages: , ISSN: , DOI:	Data Compression Conference DCC 2018	2019-08-30
2017	Sandra Alvarez-Garcia, Guillermo de Bernardo, Nieves R. Brisaboa, Gonzalo Navarro A succinct data structure for self-indexing ternary relations published pages: 38-53, ISSN: 1570-8667, DOI: 10.1016/j.jda.2016.10.002	Journal of Discrete Algorithms 43	2019-08-30
2017	Nieves R. Brisaboa, Ana Cerdeira-Pena, Guillermo de Bernardo, Gonzalo Navarro Compressed representation of dynamic binary relations with applications published pages: 106-123, ISSN: 0306-4379, DOI: 10.1016/j.is.2017.05.003	Information Systems 69	2019-08-30

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