Microarray Informatics Team

coachkentuckyΤεχνίτη Νοημοσύνη και Ρομποτική

25 Νοε 2013 (πριν από 3 χρόνια και 4 μήνες)

91 εμφανίσεις

Funded by:

Misha Kapushesky

(
ostolop@ebi.ac.uk
)




September 27, 2006


Partner 6: EBI

Microarray Informatics Team

(Alvis Brazma)

DIAMONDS Mid
-
Term Review Meeting

Funded by:

Our participation


WP2


Data warehousing


WP3


Novel functional information from integrated
datasets


WP4


Cell cycle modelling and simulation


WP5


Cell cycle portal

Funded by:

Microarray Informatics @ EBI (Review)


Databases


ArrayExpress Repository


ArrayExpress Warehouse


Analytical Tools


Expression Profiler Platform


Research



Gene Network Reconstruction


Clustering Algorithms


Meta
-
analysis of Genomic Data

Funded by:

Progress Summary


ArrayExpress Repository


New website: easier to use, better functionality


New services: XML (REST) APIs for ease of integration


Data growth: from 12000 hybs in 2005 to ~50000 now


ArrayExpress Warehouse


From prototype to released product


First data release coming: 70+ experiments, 5000+ hybs


New analytics: gene + experiment relevance rankings


Expression Profiler Platform


Streamlined architecture, deployed on new hardware


Novel algorithms developed


Better integration with R/BioConductor


Web services (SOAP) API


Taverna Workflows in KAWA

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ArrayExpress Growth
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Hybridization
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Funded by:

Cell Cycle Data in ArrayExpress Repository


About 40 experiments match “cell cycle”


More than 1200 hybridizations


Only 2 with raw Affymetrix CEL files


most non
-
Affy


Turns out one of these is not a cell cycle experiment…


Organisms:


Homo sapiens


Mus musculus


Caenorhabditis elegans


Saccharomyces cerevisiae


Schizosaccharomyces cerevisiae


Arabidopsis thaliana


Drosophila melanogaster

http://www.ebi.ac.uk/arrayexpress

Funded by:

Expression Profiler Platform


Online Gene Expression Analysis Platform


Provides data visualization capabilities


Data normalizations


Basic data pre
-
processing


Analytical algorithms


clustering, ordination, GO annotation, etc.


Extensible with new components, look
-
and
-
feel
modifiable


Core functionality


User and dataset management


Data analysis history preserved


Integrated with ArrayExpress, easy to add additional sources

http://www.ebi.ac.uk/expressionprofiler

Funded by:

Expression Profiler Platform Developments



New architecture



two 64
-
bit 4
-
CPU servers with 32GB RAM each



large scale data processing (60 Affymetrix HG
-
U133 2.0 arrays normalized in under 3 mins)



Web services and workflows



EP components as SOAP services



Taverna workflows published



Integration with BioConductor



Close connection to R package



Sequence analysis + visualization modules



SPEX, Pattern Matching, Seq. Logos

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WP3


integrated datasets

WP4


modelling and simulation

Funded by:


New Algorithm Development


A new algorithm for comparing and visualizing relationships
between hierarchical and flat gene expression data clusterings
(Torrente, Kapushesky, Brazma,
Bioinformatics
, 2005)


ChroCoLoc: an application for calculating the probability of co
-
localization of microarray gene expression (Blake, Schwager,
Kapushesky, Brazma,
Bioinformatics,
2005)

Funded by:


Lead
-
up


Integrated Gene Expression Networks (Schlitt & Brazma, 2003, 2004)


Gene Network Reconstruction by Integrative Supervised
Classification: Wnt Signalling Pathway (Soinov & Kapushesky, 2004)


Maps of interactions


Finite State Linear Models (Brazma & Schlitt, 2006)


Made an attempt to integrate…


Decision tree as a linear model generator

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Funded by:

Further Work


Maintenance + updates to DIAMONDS platform beta at VIB


EP
-
KAWA


A DIAMONDS
-
funded Taverna workflow server for bioinformatics,
integrated with the DIAMONDS platform


ArrayExpress Warehouse


New meta
-
analysis method development


Tighter integration with the EP/DIAMONDS platform


Training/Dissemination


Dedicated EBI
-
based person for developing workflows, documenting
suggested analyses, building tutorials, conducting seminars, etc.

Funded by:

Funding, Collaborations


All
Expression Profiler development (core platform,
collaborations, teaching, …) is funded from two
sources


DIAMONDS (EU)


Contributed components from 2005 onwards


Internships and studentships


EMBL Internal Funding


Related projects


BioSapiens (EU)


ENFIN (EU)


FELICS (EU)


BioMap (Bloomsbury Transcriptiomics Consortium)


BioC
-
WebGUI (BBSRC)


Others…