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BIRDS SIGNED

Bioinformatics and Information Retrieval Data Structures Analysis and Design

Total Cost €

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EC-Contrib. €

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Partnership

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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 ES (LA CORUNA) coordinator 265˙500.00
2    HELSINGIN YLIOPISTO FI (HELSINGIN YLIOPISTO) participant 189˙000.00
3    INESC ID - INSTITUTO DE ENGENHARIADE SISTEMAS E COMPUTADORES, INVESTIGACAO E DESENVOLVIMENTO EM LISBOA PT (LISBOA) participant 135˙000.00
4    ENXENIO SL ES (A CORUNA) participant 58˙500.00
5    NATIONAL UNIVERSITY CORPORATION KYUSHU UNIVERSITY JP (FUKUOKA) partner 0.00
6    UNIVERSIDAD DE CHILE CL (SANTIAGO) partner 0.00
7    UNIVERSIDAD DE CONCEPCION CL (CONCEPCION) partner 0.00
8    UNIVERSITY OF MELBOURNE 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

year authors and title journal last update
List of publications.
2020 Luís 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 Díaz-Domínguez, Diego; Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Navarro, Gonzalo; Puglisi, Simon J.
Assembling Omnitigs using Hidden-Order de Bruijn Graphs
published pages: , ISSN: , DOI:
2020-03-05
2020 Adrián Gómez-Brandón
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, Luís 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 Fariña
Revisiting compact RDF stores based on k2-trees
published pages: , ISSN: , DOI:
2020 Data Compression Conference 2020-03-05
2020 Nieves R. Brisaboa, Antonio Fariña, 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, José R. Paramá, Susana Ladra, Juan R. López, Gilberto Gutiérrez
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 Fariña, 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 Luís 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 Álvarez-García, Borja Freire, Susana Ladra, Óscar 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, Adrián Gómez-Brandón, Gonzalo Navarro, José R. Paramá
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 Fariña, Miguel A. Martínez-Prieto, Francisco Claude, Gonzalo Navarro, Juan J. Lastra-Díaz, 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 Fariña, 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 Hernández, 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 Díaz-Domínguez, 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, Luís 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 Luís M. S.  Russo, Andreia Teixeira, Alexandre  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 Fariña, Miguel A. Martínez-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 Ordóñez, 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 Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
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 José Fuentes-Sepúlveda, 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 José Fuentes-Sepúlveda, Juha Kärkkäinen, 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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