Micro B3 Information System and Biovel: Resources, Services, Workflows and Interfaces

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A selected subset of what Micro B3 Information System and BioVeL products are available 2014-06-03

A selected subset of what Micro B3 Information System and BioVeL products are available 2014-06-03

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  • 1. Micro B3 Information System & BioVeL Resources, Services, Workflows and Interfaces Microbial Genomics and Bioinformatics Research Group Renzo Kottmann rkottman@mpi-bremen.de Bremen, 2014-06-03
  • 2. Resources Databases & Technology
  • 3. www.arb-silva.de/ngs
  • 4. Megx.net and Micro B3 Information System Micro B3 Information System Megx.net
  • 5. PostBIS: In Database Sequence Data Compression PostBIS (Hamburg University) • Efficient storage and retrieval of DNA sequence data • <2 bits per nucleotide base • 500x faster substring operation PostgreSQL extension • In-database sequence compression • Special Data Types • Special Functions
  • 6. PostBIS: Storage Size Genomic DNA Short Alignments Short again
  • 7. PostBIS: Encoding Performance
  • 8. Services RESTful, WMS/WFS and Co.
  • 9. Who is out there and where? (in terms of sequenced genomes, metagenomes and key genes) Kottmann et al. NAR 2010 http://mb3is.megx.net/gms
  • 10. Geographic-BLAST
  • 11. OSD App Server Map http://mb3is.megx.net/osd-app/samples
  • 12. OSD Registry
  • 13. Ecological Analysis Tools for Microbial Ecology (EATME) http://mb3is.megx.net/eatme
  • 14. Workflows
  • 15. Ship Sterivex / DNA OSD Core Team Sample / Environmental Data OSD Phone App Collect Samples DNA Extraction OSD Core Team GGI Barcodes Ship Filters For BioArchiving Micro B3 Information System Ship DNA for Sequencing Enter Micro B3 & GGI Metadata Submit Raw Sequences Raw Sequences & Metadata Analysis Ocean Sampling Day Workflows Sequencing Match Filter with Barcodes
  • 16. YOU ANALYSIS TOOLS/SERVICES CONTEXTUAL DATA & METADATA SEQUENCING DATA & METADATA Data Access TOOLS/SERVICES Accessing and Analyzing
  • 17. Collaboration with BioVeL
  • 18. Metagenomic Workflows FUNCTIONAL TRAI-BASED ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES
  • 19. Examples of Metagenomic Traits GC (Guanine-Cytosine) content (mean and variance): • Related to genome size, environmental complexity and community composition. Functional and phylogenetic diversity: • Related to metabolic potential, community composition and environmental biogeochemistry. Dinucleotide frequency: • Related to phylogenetic composition. Explore community traits as ecological markers in microbial metagenomes. (Barberan, Fernandez et al. 2012).
  • 20. The Metagenomic Trait Workflow(s) Upstream: • Calculating traits  (traits-analysis workflow) Downstream • Calculating statistics  (traits-statistics workflow)  R scripts perform multivariate statistic analyses using the vegan package and plot the results using ggplot2
  • 21. Metagenomic Trait Database http://mb3is.megx.net/mg-traits/sampleDetails?id=656
  • 22. Ecological Analysis Tools for Microbial Ecology (EATME) http://mb3is.megx.net/eatme
  • 23. Interfaces
  • 24. Web Services are interfaces • Secured • Versioned • Interoperable
  • 25. Pelagibacter ubique proteome centered subnetwork Antonio Fernandez, submitted Cluster1800572 Unknown unknown SAR11_0487 Tryptophan synthase SAR11_1266 hypothetical protein SAR11_0686 hypothetical protein SAR11_1277 aspartate racemase Discovery: knowns, known unknowns and unknown unknowns
  • 26. Data Access: Visualization of unknown networks
  • 27. ProX Master Thesis: Matthias Stock (Hochschule Bremen) Efficient web-based and large-scale visualization of networks • Outperforms state of the art web tools
  • 28. Ocean Sampling Day App https://itunes.apple.com/us/app/osd-citizen/id834353532?mt=8 https://play.google.com/store/apps/details?id=com.iw.esa Early, consistent, digital acquisition of environmental data
  • 29. Entering Data
  • 30. Features Allows to take data in the field • NO internet connection needed • GSC standards compliant
  • 31. Megx.net / Micro B3-IS is Open Source Subversion • https://projects.mpi-bremen.de/micro-b3/svn/ Source Code Browser • https://colab.mpi-bremen.de/source/ Wiki • https://colab.mpi-bremen.de/wiki Issue Tracker • https://colab.mpi-bremen.de/its/
  • 32. Thanks for your attention 1st Marine Board Forum: Marine data Challenges: from Observation to Information http://www.microb3.eu http://twitter.com/Micro_B3http://www.oceansamplingday.org