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

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

19. Metagenomic Workflows
FUNCTIONAL TRAI-BASED ANALYSIS OF
AQUATIC MICROBIAL COMMUNITIES

20. 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).

21. 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

22. Metagenomic Trait Database
http://mb3is.megx.net/mg-traits/sampleDetails?id=656

23. Ecological Analysis Tools for Microbial Ecology (EATME)
http://mb3is.megx.net/eatme

24. Interfaces

25. Web Services are interfaces
• Secured
• Versioned
• Interoperable

26. 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

27. Data Access: Visualization of unknown networks

28. ProX
Master Thesis: Matthias Stock (Hochschule Bremen)
Efficient web-based and large-scale visualization of
networks
• Outperforms state of the art web tools

29. 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

30. Entering Data

31. Features
Allows to take
data in the field
• NO internet
connection
needed
• GSC standards
compliant

32. 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/

33. 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