Recent developments in

deadhorsecapableInternet και Εφαρμογές Web

8 Δεκ 2013 (πριν από 3 χρόνια και 8 μήνες)

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EBI is an Outstation of the European Molecular Biology Laboratory.

Recent developments in
the Ensembl Web inteface

M.
Ridwan Amode, Simon Brent,
Maurice Hendrix,
Anne
Parker,Bethan Pritchard, Harpreet Riat, Stephen
Trevanion


HSF (Hinxton), 28 October 2010


Recent web developments




Upcoming developments




Performance optimisation




Architectural improvements




Conclusion




Acknowlegements

Outline


T
ab for markers (e57) and regulation data (e56
)




'
Download as RTF
' and '
Blast this sequence
'





Multi species views (e56)





Functional genomics


'multi
-
wiggle' tracks: chip
-
seq data for cell lines, configured via multi
-
select
config panel.






Recent web
developments


Variation related:


o
Locus Reference Genomic (LRG)
displays

o
Variation (SNP) effect predictor tool

o
Colour gradient display for the phenotype



Recent web developments
(2)


Interface improvements

o
Slider navigation on location views





o
Sort and filter tables









o
Select/deselect all controls on image & view config



o
Masthead redesign, tabs depend on window width


Recent web developments (3)

e60 (8 November 2010):


Auto complete Gene searching on Location pages









History and Bookmarks in tabs with login












WIG and BEDgraph upload/URL support





Transcript xrefs on Gene page (External references)



Upcoming developments (e60)

Upcoming developments (e60)

e60 (8 November 2010) continued:


Transcription factor binding sites shown as part


of regulatory features tracks


Gene Ontology view

o
Image and Table displays

o
Uses Ensembl Ontology API

o
Can display term graphs for any OBO ontology

o
Display clearly separated by root term


(cellular_component, biological_process, molecular_function)


Saved user configurations




Custom pages




Rewrite BLAST interface




Pipeline for web tools (eg Variation Effect Predictor)

Upcoming developments
(e61+)


Use of caching (Memcached) and proxy (Nginx)



International mirror sites



Apache optimization

o
Reduce HTTP requests

o
Changes to 'Expires' headers

o
Gzipping of page components

o
Minifying JavaScript

o
Switching ETags off


Use of AJAX

(jQuery)



Images refresh individually if configuration changes


Views with large amounts of sequence have been split
into smaller chunks to avoid timeouts


Performance optimisations

Architectural improvements: Web
Code


Exalead:

o
Proprietry software

o
Used by Ensembl since 2006

o
Slow to build indexes and inflexible


Lucene:

o
Java, open source, used by EB
-
eye, www.sanger.ac.uk

o
Quick to build indexes, flexible, copied to EC2

o
Ensembl indexed on Lucene and presented on Sanger
homepage for the last two releases (e59 = ~150M
records)

o
e60 will use Lucene backend
-

hardware upto it ?

o
e61+ will see frontend redesign, extension to static
content/help

Architectural improvements:
Search


Ensembl website constantly improving


Amount of Data will continue to increase rapidly



Continue to improve interface to offer more
flexibility to users

Conclusion


Ensembl Web team


All of Ensembl


Systems


Web team (search): Mark Wilson,
Stephen Keenen

Acknowledgments