An Introduction to SyMBA
This page summarizes the current status of the SyMBA. SyMBA is available for viewing and testing
via the sandbox installation we have set up,
and is also available for download via SourceForge's Subversion repository. We welcome any comments or queries on
the system, which should be sent to
symba-devel@lists.sourceforge.net
.
The Integrative Bioinformatics Group, headed by
Neil Wipat and part of The Centre for
Integrated Systems Biology of Ageing and Nutrition (CISBAN), has developed a data archive and
integrator (SyMBA) based on Version 1 of the
Functional Genomics Experiment (FuGE)
Object Model (FuGE-OM), and which archives, stores, and retrieves raw high-throughput data. Until now,
few published systems have successfully integrated multiple omics data types and information about
experiments in a single database. SyMBA is the first published implementation of FuGE that includes a
database back-end, expert and standard interfaces, and a Life Science Identifier (LSID) Resolution and
Assigning service to identify objects and provide programmatic access to the database. Having a central
data repository prevents deletion, loss, or accidental modification of primary data, while giving
convenient access to the data for publication and analysis. It also provides a central location for
storage of metadata for the high-throughput data sets, and will facilitate subsequent data integration
strategies.
We encourage the use, installation and development of SyMBA by other groups. Please let us know if
you are interested in using or evaluating SyMBA for use at your own Centre.
SyMBA has been presented at or mentioned in:
-
September 1-4, 2008 MGED Society Meeting. SyMBA
was represented with a poster during this meeting. The SyMBA poster won 3rd place in the MGED
poster competition! You can download this poster as a pdf.
-
Summer 2008 OBI Workshop. At this workshop a short
presentation was given showing how pieces of OBI could be automatically retrieved from the OWL file
and translated into FuGE-ML structures. From there, it can be loaded and used within SyMBA.
Screencast avaialble soon.
-
Susanna-Assunta Sansone, Philippe Rocca-Serra, Marco Brandizi, Alvis Brazma, Dawn Field, Jennifer
Fostel, Andrew G. Garrow, Jack Gilbert, Federico Goodsaid, Nigel Hardy, Phil Jones, Allyson Lister,
Michael Miller, Norman Morrison, Tim Rayner, Nataliya Sklyar, Chris Taylor, Weida Tong, Guy Warner,
Stefan Wiemann.
The First RSBI (ISA-TAB)
Workshop: ?Can a Simple Format Work for Complex Studies??,
OMICS: A Journal of Integrative Biology. ahead of print. doi:10.1089/omi.2008.0019.
-
Kirkwood, T., A systematic look at an old problem, Nature. 2008 Feb 7;451(7179):644-7.
(Full Text,
Editor's Summary)
-
LifeSpan Network Annual Meeting, Leiden,
11-12 January 2008.
-
FuGE Users Workshop,
Manchester University, 13-14 December 2007.
-
1st RSBI Meeting, held at the
EBI, 6-8 December 2007.
-
CISB07 Meeting,
Centre For Life, Newcastle, 19-20 November 2007. Hosted by
CISBAN, Newcastle University.
-
CISBAN /
Centre for Systems Biology at Edinburgh (CSBE) Technology
Meeting, 22 August 2007.
- An
NEBC
-
EBI
Developer's Workshop,
19-20th February 2007, which included presentations and discussions of SyMBA,
omixed
,
MIBBI
,
OBI
,
MSI
,
PSI
, and
BioMAP
,
among others. Participants were from NEBC, EBI,
University of Manchester
, and
Newcastle University
.
-
North East Regional e-Science Centre
/
Digital
Curation Centre
Collaborative Workshop - 5th February 2007
- The 3rd
OBI
Workshop
, held
from 29 January - 2 February 2007 at the
La Jolla Institute for Allergy and
Immunology
in San Diego, California.
- The
2nd BioModels.net
Training
Camp
,
held from 13-15 January 2007 at the
Manchester Conference
Centre
.
Status: June 2011: 11.06
We now use Google Web Toolkit and hyperjaxb3. This has resulted in a much cleaner, simpler
application to use and to develop with. Please play with the sandbox installation of SyMBA 2, and see
what you think of the new user interface.
