G09-Misc-EMBOSS

EMBOSS European Molecular Biology Open Software Suite Open-Bio Project Update 2011 Peter Rice pmr@ebi.ac.uk Alan Bleasby, Jon Ison, Mahmut Uludag, Michael Schuster

A quick introduction
Open source package for sequence analysis
ANSI C source code
GPL licensed applications, LGPL libraries
275+ applications
150+ third party applications in 15 associated packages
MIRA, MEME, HMMER, PHYLIP, VIENNA, etc.
Project started 1996 at Sanger and Daresbury/HGMP
Now based at EBI
Release 1.0.0 15th July 2000
Release 6.4.0 15th July 2011
Funded by UK-BBSRC and EMBL-EBI
Originally funded by the Wellcome Trust
Additional funds from UK-MRC
BOSC 2011: EMBOSS 17.07.11

Who do we serve?
Expert software developers
Bioinformaticians
Computer scientists
Expert users
Biology research community
Industry
Scientific users
Biology research community
Industry
BOSC 2011: EMBOSS 17.07.11

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: wEMBOSS, Mobyle
GUI: Jemboss
Web Services: SoapLab
Workflows: Galaxy, Taverna, Pipeline Pilot
Windows: mEMBOSS
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
BOSC 2011: EMBOSS 17.07.11

EMBOSS Update
Release 6.4.0 as usual on 15th July 2011
New Website emboss.open-bio.org
Three open source books: users, developers, admin
Cambridge University Press
BOSC 2011: EMBOSS 17.07.11

Data sources for EMBOSS
Server definitions
One server, 100+ databases
server:dbname as the database name
Data access methods
Ensembl, DAS, BioMart, CHADO,SRS, Entrez, MRS
EBI REST and SOAP services
Data resource Catalogue (DRCAT)
emboss.standard file for all installations
IF-ELSE-ENDIF to customize for SQL, AXIS2C, local setup
New applications
showserver, dbtell, servertell
BOSC 2011: EMBOSS 17.07.11

New data types: input and output
OBO ontology terms
NCBI Taxonomy
Data Resource Catalogue entries
Text
URL
Cross-references:
dbname and identifier
data content
BOSC 2011: EMBOSS 17.07.11

New query language
SRS-like syntax
id lists: dbname:{ida,idb,idc}
or operator: dbname-{id:h* | des:hemoglobin}
and operator: dbname-{id:h* & des:hemoglobin}
and operator: dbname-{id:h* & des:hemoglobin}
eor operator: dbname-{id:h* ^ des:hemoglobin}
Compressed (20-fold) b+tree indexes
New indexing applications (obo, taxon, drcat)
BOSC 2011: EMBOSS 17.07.11

EDAM ontology
EDAM defines topic, operation, data, format, identifier
ACD file application, inputs, outputs, parameters
DRCAT resources, queries, identifiers
SoapLab web services
Redefined EMBOSS program groups.
OBO format ontology
2835 terms
Available throughout EMBOSS as database EDAM:
New applications
EDAM namespace searches, relation queries
OBO ontology applications
GO, SO, and other OBO ontologies in release
BOSC 2011: EMBOSS 17.07.11

DRCAT Data Resource Catalogue
Public Data Resources
EDAM annotations
UniProt and EMBL/GenBank/DDBJ cross-references
Query prototypes
Example identifiers for testing
662 entries
Available in EMBOSS as database DRCAT:
Applications:
Search by EDAM annotation
Search by 18 indexed fields
BOSC 2011: EMBOSS 17.07.11

Ontologies: NCBI Taxonomy
Parsers for “.dmp” files
Indexed by dbxtax
Navigation up, down, siblings (the usual suspects)
Automatic cross references from sequence data
EMBL source line
UniProt OX lines
BioMart mart name (organism name)
etc.
New applications
Search and retrieve from taxon hierarchy
BOSC 2011: EMBOSS 17.07.11

Installation
Release size increased
EDAM, DRCAT, NCBI Taxonomy, GO, plus index files
Associated packages
AXIS2C (SOAP web service access)
MYSQL (Ensembl)
PostgresQL (FlyBase)
mEMBOSS for Windows
Enhanced QA testing
Standard test set adapted for use on Windows and Unix
BOSC 2011: EMBOSS 17.07.11

EMBOSS Interfaces and wrappers
Two releases in this year
Too many for other projects to keep up
So we are obliged to help, starting with:
SoapLab2
Jemboss
Galaxy
Mobyle
… and anyone else who asks
Interface generation should be automated
Tested during development
Changes highlighted before release
BOSC 2011: EMBOSS 17.07.11

EMBOSS Future Plans
Further development this year
Mapped short reads
Reference sequences
Sequence variation
Genome browser data format support
Leaving EBI in December
… into the unknown
… still supporting EMBOSS and planning new developments
BOSC 2011: EMBOSS 17.07.11

The Emboss Team BOSC 2011: EMBOSS 17.07.11 Peter Rice Alan Bleasby Jon Ison Mahmut Uludag Michael Schuster

Acknowledgements
EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Michael Schuster, Martin Senger, Tom Oinn, Jaina Mistry, Rodrigo Lopez, Sharmilla Pillai, Hamish McWilliam, Syed Haider
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, Ivo Hofacker, Kristoffer Rapacki, Matus Kalas
Cambridge University Press, LION bioscience, IBM, Hewlett-Packard, (Compaq), Apple, SGI, Sun, SciTegic, Microsoft Research
Open-Bio Foundation, Sourceforge, ... And the British Antarctic Survey
http://emboss.open-bio.org
http://emboss.open-bio.org/wiki
BOSC 2011: EMBOSS 17.07.11

G09-Misc-EMBOSS

by Bioinformatics Open Source Conference on Jul 17, 2011

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