1. EMBOSS, MyGrid and EMBRACE
European Molecular Biology Open Software Suite
Taverna workbench and workflows
Web Services
Peter Rice

2. Who do we serve? Expert software developers Expert users
Bioinformaticians
Computer scientists
Expert users
Biology research community
Industry
Scientific users
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3. What do we serve? Sequence analysis tools Data resources Workflows
Open source
Comprehensive package
Data resources
Public sequence database resources
Locally installed data
Users’ own datasets
Workflows
Taverna workbench
Web services
Standard SOAP web services
Web service registry
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4. EMBOSS: A quick introduction
European Molecular Biology Open Software Suite
Open source package for sequence analysis
ANSI C source code
GPL licensed applications, LGPL libraries
200+ applications
100+ third party applications in 15 associated packages
Project started 1996 at Sanger Centre and HGMP
Now based at EBI
Release th July 2009
Funded by UK-BBSRC and EMBL-EBI
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5. EMBOSS World Wide
We have users in every continent - and a picture to prove it. This is British Antarctica. We are promised another photo from the frozen North
The first EMBOSS course was in Beijing, April 1999.
The wEMBOSS interface is from Canada, Argentina and Belgium
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6. EMBOSS command line interface
EMBOSS applications run from the command line
This is not the only interface
There are over 100 interfaces and packaged systems available
Web interfaces
Graphical user interfaces (GUIs)
Web services
All applications have a command definition file (.acd)
Defines all inputs, outputs, and other options
Read at startup
Contains all command line options with descriptions
Template for any other interface
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7. EMBOSS command line example
% antigenic
Input protein sequence(s): uniprot:actb1_fugru
Minimum length of antigenic region [6]:
Output report [actb1_fugru.antigenic]:
% antigenic uniprot:actb1_fugru -auto
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8. EMBOSS ACD File integer: minlen [ standard: "Y"
minimum: "1"
maximum: "50"
default: "6"
information: "Minimum length of antigenic region" ]
endsection: required
section: output [
information: "Output section"
type: "page"
report: outfile [
parameter: "Y"
rformat: "motif"
multiple: "Y"
taglist: "int:pos=Max_score_pos"
endsection: output
application: antigenic [
documentation: "Finds antigenic sites in proteins"
groups: "Protein:Motifs" ]
section: input [
information: "Input section"
type: "page"
seqall: sequence [
parameter: "Y"
type: "PureProtein"
endsection: input
section: required [
information: "Required section"
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9. EMBOSS makes things easy
ACD files define sequence input
Sequence type for DNA/protein, possible ambiguity codes, gaps
Sequences in files
40+ formats supported - auto detection
Sequence databases
Remote servers - SRS, Entrez, MRS, URL
Locally indexed - using the original data files
Local script utilities
Sequence output
40+ formats supported : sequence and features
DAS support (Distributed Annotation Servers)
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10. Example Dasty screen: Protein annotation
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11. Example Ensembl: DNA annotation
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12. EMBOSS Future plans Three open source books: users, developers, admin
Cambridge University Press
Original text can be freely reused
New areas of interest
Metadata and ontologies (EDAM, taxonomy, GO, SO, …)
(all) public data resources
Coordinate systems (ensembl, gene/protein input/results)
Project-based working
Next-generation sequence data – used by ordinary biologists
100+ new applications
Database index updates
Scientific advisory board
Developer / User courses courses: anywhere, any time
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13. Taverna workbench
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14. Taverna Workbench MyGrid UK e-Science project Taverna 2.0
Workbench for bioinformatics data and tools services
Open source
Integrates SOAP web services
Workflows can be saved, and exchanged by
Data passed to service, results returned
Complete record available
Taverna 2.0
Designed for scalability
New workflow model
Multiple servers
Data passed by reference
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15. EMBRACE Web Services EMBRACE EC Network of Excellence 18 partners
Application interface standards for data content:
DNA and protein sequence data
Structure and image data
Gene and protein expression
Literature and text mining
Analysis tools using data content standards
Sequence analysis tools (EMBOSS etc.)
Structure analysis tools
... and tools for other data types
Taverna as an example user interface
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16. EMBRACE Registry
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17. EMBRACE Registry Registry of EMBRACE Web Services BioCatalogue
Requires standard web service definitions
Test suites defined by service providers
Simple report of service availability
Standard annotation
Requires an ontology of terms for datatypes and methods
BioCatalogue
Manchester/EBI joint project
EMBRACE Registry is a prototype
Sharing a common schema
BioCatalogue will take over when EMBRACE ends in 2010.
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18. What do we serve? Sequence analysis tools Data resources Workflows
Open source
Comprehensive package
Data resources
Public sequence database resources
Locally installed data
Users’ own datasets
Workflows
Taverna workbench
Web services
Standard SOAP web services
Web service registry
China-UK Data Transmission

19. Acknowledgements
EBI: Peter Rice, Alan Bleasby, Jon Ison, Martin Senger, Tom Oinn, Jaina Mistry, Rodrigo Lopez, Sharmilla Pillai, Hamish McWilliam
RFCGR/HGMP: Alan Bleasby, Jon Ison, Tim Carver, Hugh Morgan, Claude Beazley, Lisa Mullan, Damian Counsell, Gary Williams, Val Curwen, Mark Faller, Sinead O’Leary, Thon deBoer, Martin Bishop
LION: Thomas Laurent, Bijay Jassal, Bren Vaughan, Thure Etzold
Sanger Institute: Ian Longden, Richard Bruskiewich, Simon Kelley
National bioinformatics service providers in: Norway, Spain, Italy, Netherlands, Germany, Belgium, Russia, China, Canada, Australia, Argentina
Others: Catherine Letondal, Don Gilbert, Rodger Staden, Bill Pearson, Webb Miller, Marie-Laetitia Denayer, Amandine Schurmann, Gabriele Weiler, Luke McCarthy, David Mathog, David Bauer, Henrikki Almusa, Thomas Siegmund, Scott Markel, Darryl Leon, Bastien Chevreux...
IBM, Hewlett-Packard, (Compaq), Apple, SGI, Sun, LION bioscience, SciTegic, Accelrys, Cambridge University Press
Open-Bio Foundation, Sourceforge
... And the British Antarctic Survey
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