Micro B3 Information System & BioVeL
Resources, Services, Workflows and Interfaces
Microbial Genomics and
Bioinformatics R...
Resources
Databases & Technology
www.arb-silva.de/ngs
Megx.net and Micro B3 Information System
Micro B3 Information System
Megx.net
PostBIS: In Database Sequence Data Compression
PostBIS (Hamburg University)
• Efficient storage and retrieval of DNA seque...
PostBIS: Storage Size
Genomic DNA Short Alignments Short again
PostBIS: Encoding Performance
Services
RESTful, WMS/WFS and Co.
Who is out there and where?
(in terms of sequenced genomes, metagenomes and key genes)
Kottmann et al. NAR 2010
http://mb3...
Geographic-BLAST
OSD App Server Map
http://mb3is.megx.net/osd-app/samples
OSD Registry
Ecological Analysis Tools for Microbial Ecology (EATME)
http://mb3is.megx.net/eatme
Workflows
Ship
Sterivex / DNA
OSD Core Team
Sample /
Environmental
Data
OSD Phone App
Collect
Samples
DNA
Extraction
OSD Core Team
G...
YOU ANALYSIS
TOOLS/SERVICES
CONTEXTUAL
DATA & METADATA
SEQUENCING
DATA & METADATA
Data Access
TOOLS/SERVICES
Accessing and...
Collaboration with BioVeL
Metagenomic Workflows
FUNCTIONAL TRAI-BASED ANALYSIS OF
AQUATIC MICROBIAL COMMUNITIES
Examples of Metagenomic Traits
GC (Guanine-Cytosine) content (mean and variance):
• Related to genome size, environmental...
The Metagenomic Trait Workflow(s)
Upstream:
• Calculating traits
 (traits-analysis workflow)
Downstream
• Calculating s...
Metagenomic Trait Database
http://mb3is.megx.net/mg-traits/sampleDetails?id=656
Ecological Analysis Tools for Microbial Ecology (EATME)
http://mb3is.megx.net/eatme
Interfaces
Web Services are interfaces
• Secured
• Versioned
• Interoperable
Pelagibacter ubique proteome centered subnetwork
Antonio Fernandez, submitted
Cluster1800572 Unknown unknown
SAR11_0487 Tr...
Data Access: Visualization of unknown networks
ProX
Master Thesis: Matthias Stock (Hochschule Bremen)
Efficient web-based and large-scale visualization of
networks
• O...
Ocean Sampling Day App
https://itunes.apple.com/us/app/osd-citizen/id834353532?mt=8
https://play.google.com/store/apps/det...
Entering Data
Features
Allows to take
data in the field
• NO internet
connection
needed
• GSC standards
compliant
Megx.net / Micro B3-IS is Open Source
Subversion
• https://projects.mpi-bremen.de/micro-b3/svn/
Source Code Browser
• ht...
Thanks for your attention
1st Marine Board Forum: Marine data Challenges: from Observation to Information
http://www.micro...
Micro B3 Information System and Biovel: Resources, Services, Workflows and Interfaces
Upcoming SlideShare
Loading in …5
×

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

358 views

Published on

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

Published in: Technology, Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
358
On SlideShare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
2
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

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

  1. 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. 2. Resources Databases & Technology
  3. 3. www.arb-silva.de/ngs
  4. 4. Megx.net and Micro B3 Information System Micro B3 Information System Megx.net
  5. 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. 6. PostBIS: Storage Size Genomic DNA Short Alignments Short again
  7. 7. PostBIS: Encoding Performance
  8. 8. Services RESTful, WMS/WFS and Co.
  9. 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. 10. Geographic-BLAST
  11. 11. OSD App Server Map http://mb3is.megx.net/osd-app/samples
  12. 12. OSD Registry
  13. 13. Ecological Analysis Tools for Microbial Ecology (EATME) http://mb3is.megx.net/eatme
  14. 14. Workflows
  15. 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. 16. YOU ANALYSIS TOOLS/SERVICES CONTEXTUAL DATA & METADATA SEQUENCING DATA & METADATA Data Access TOOLS/SERVICES Accessing and Analyzing
  17. 17. Collaboration with BioVeL
  18. 18. Metagenomic Workflows FUNCTIONAL TRAI-BASED ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES
  19. 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. 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. 21. Metagenomic Trait Database http://mb3is.megx.net/mg-traits/sampleDetails?id=656
  22. 22. Ecological Analysis Tools for Microbial Ecology (EATME) http://mb3is.megx.net/eatme
  23. 23. Interfaces
  24. 24. Web Services are interfaces • Secured • Versioned • Interoperable
  25. 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. 26. Data Access: Visualization of unknown networks
  27. 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. 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. 29. Entering Data
  30. 30. Features Allows to take data in the field • NO internet connection needed • GSC standards compliant
  31. 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. 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

×