Nothing Special   »   [go: up one dir, main page]

Skip to main content

Overview of GeCo: A Project for Exploring and Integrating Signals from the Genome

  • Conference paper
  • First Online:
Data Analytics and Management in Data Intensive Domains (DAMDID/RCDL 2017)

Abstract

Next Generation Sequencing is a 10-year old technology for reading the DNA, capable of producing massive amounts of genomic data - in turn, reshaping genomic computing. In particular, tertiary data analysis is concerned with the integration of heterogeneous regions of the genome; this is an emerging and increasingly important problem of genomic computing, because regions carry important signals and the creation of new biological or clinical knowledge requires the integration of these signals into meaningful messages. We specifically focus on how the GeCo project is contributing to tertiary data analysis, by overviewing the main results of the project so far and by describing its future scenarios.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

Notes

  1. 1.

    http://www.bioinformatics.deib.polimi.it/geco.

References

  1. 1000 Genomes Consortium: An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56–65 (2012)

    Google Scholar 

  2. Albrecht, F., et al.: DeepBlue epigenomic data server: programmatic data retrieval and analysis of the epigenome. Nucleid Acids Res. 44(W1), W581–586 (2016)

    Article  Google Scholar 

  3. Accelerating bioinformatics research with new software for big data to knowledge (BD2K). Paradigm4 Inc. (2015). http://www.paradigm4.com/)

  4. Apache Flink. http://flink.apache.org/

  5. Apache Pig. http://pig.apache.org/

  6. Apache Spark. http://spark.apache.org/

  7. Bernasconi, A., et al.: Conceptual modeling for genomics: building an integrated repository of open data. In: Proceedings of the Entity-Relationship, Valencia, ES (2017)

    Chapter  Google Scholar 

  8. Bertoni, M., et al.: Evaluating cloud frameworks on genomic applications. In: Proceedings of the IEEE Conference on Big Data Management, Santa Clara, CA (2015)

    Google Scholar 

  9. Cattani, S., et al.: Evaluating genomic big data operations on SciDB and Spark. In: Cabot, J., De Virgilio, R., Torlone, R. (eds.) ICWE 2017. LNCS, vol. 10360, pp. 482–493. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-60131-1_34

    Google Scholar 

  10. Ceri, S., et al.: Data-Driven Genomic Computing (GeCo): Making sense of Signals from the Genome. In: Selected Papers of the XIX International Conference on Data Analytics and Management in Data Intensive Domains (DAMDID/RCDL 2017), CEUR Workshop Proceedings, vol. 2022, pp. 1–2 (2017)

    Google Scholar 

  11. Ceri, S., et al.: Data management for heterogeneous genomic datasets. IEEE/ACM Trans. Comput. Biol. Bioinf. 14(6), 1251–1264 (2016)

    Article  Google Scholar 

  12. Cumbo, F., et al.: TCGA2BED: extracting, extending, integrating, and querying the Cancer genome atlas. BMC Bioinf. 18(6), 1–9 (2017)

    Google Scholar 

  13. ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414), 57–74 (2012)

    Article  Google Scholar 

  14. FireCloud. https://software.broadinstitute.org/firecloud

  15. Jalili, V., et al.: Indexing next-generation sequencing data. Inf. Sci. 384, 90–109 (2016). https://doi.org/10.1016/j.ins.2016.08.085

    Article  Google Scholar 

  16. Jalili, V., et al.: Explorative visual analytics on interval-based genomic data and their metadata. BMC Bioinf. 18, 536 (2017)

    Article  Google Scholar 

  17. Kaitoua, A., et al.: Framework for supporting genomic operations, IEEE-TC (2016). https://doi.org/10.1109/TC.2016.2603980

  18. Masseroli, M., et al.: GenoMetric query language: a novel approach to large-scale genomic data management. Bioinformatics 31(12), 1881–1888 (2015)

    Article  Google Scholar 

  19. Masseroli, M., et al.: Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying. Methods 111, 3–11 (2016)

    Article  Google Scholar 

  20. Nanni, L., et al.: Exploring genomic datasets: from batch to interactive and back. In: Proceedings of the ExploreDB 2018, Co-Located with ACM-Sigmod, June 2018

    Google Scholar 

  21. Olston, C., et al.: Pig Latin: a not-so-foreign language for data processing. In: ACM-SIGMOD, pp. 1099–1110 (2008)

    Google Scholar 

  22. Romanoski, C.E., et al.: Epigenomics: roadmap for regulation. Nature 518, 314–316 (2015)

    Article  Google Scholar 

  23. SciDB. http://www.scidb.org/

  24. Schuster, S.C.: Next-generation sequencing transforms today’s biology. Nat. Methods 5(1), 16–18 (2008)

    Article  Google Scholar 

  25. Stephens, Z.D., et al.: Big data: astronomical or genomical? PLoS Biol. 13(7), e1002195 (2015)

    Article  Google Scholar 

  26. Weinstein, J.N., et al.: The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45(10), 1113–1120 (2013)

    Article  Google Scholar 

  27. Zaharia, M., et al.: Resilient distributed datasets: a fault-tolerant abstraction for in-memory cluster computing. In: Proceedings of the USENIX, pp. 15–28 (2012)

    Google Scholar 

Download references

Acknowledgment

This research is funded by the ERC Advanced Grant project GeCo (Data-Driven Genomic Computing), No. 693174, 2016-2021.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefano Ceri .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Ceri, S. et al. (2018). Overview of GeCo: A Project for Exploring and Integrating Signals from the Genome. In: Kalinichenko, L., Manolopoulos, Y., Malkov, O., Skvortsov, N., Stupnikov, S., Sukhomlin, V. (eds) Data Analytics and Management in Data Intensive Domains. DAMDID/RCDL 2017. Communications in Computer and Information Science, vol 822. Springer, Cham. https://doi.org/10.1007/978-3-319-96553-6_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-96553-6_4

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-96552-9

  • Online ISBN: 978-3-319-96553-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics