BioinfoGRID Project Milanesi Luciano National Research Council Institute of Biomedical Technologies, Milan, Italy ...
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BioinfoGRID Project
Milanesi Luciano
National Research Council
I tit t off Biomedical
Institute Bi di l TTechnologies,
h l i
Milan, Italy
luciano.milanesi@itb.cnr.it
Milanesi Luciano EGEE User Forum, Clermont-Ferrand , France 11-14 February, 2008Networks of resources
• The potential of new biological and biomedical
technological platforms in connection with HPC and
GRID technologygy will be p
particularly
y useful to deal with the
increasing amount, complexity, and heterogeneity of
biological and biomedical data.
• Bioinformatics applications for eHealth have become an
ideal research area where computer scientists can apply
and further develop new intelligent computation methods,
in both experimental and theoretical cases
cases.
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 2BioinfoGRID Project
BioinfoGRID Project web site: www.bioinfogrid.eu
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 3Consortium Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 4
BioinfoGRID Objectives • Objective of the BioinfoGRID project Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 5
Interaction with related projects
At present the BioinfoGRID project has established
co-operations with the following projects initiative:
• EGEE
• BELIEF
• EMBRACE
• EUCHINAGRID
• EUMEDGRID
• EELA
• DILIGENT
• ICEAGE
• LITBIO
• LIBI
• HEALTHGRID
• WISDOM
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 6BioinfoGRID Work Packages
Work-package No Work Package title
WP1 Genomics Applications in GRID
WP2 Proteomics Applications in GRID
WP3 Transcriptomics Applications in GRID
WP4 Database and Functional Genomics Applications
WP5 Molecular Dynamics Applications
WP6 Coordination of technical aspects and relation with Grid
j , user training,
infrastructure Projects, g, application
pp support
pp
and resources integration.
WP7 Dissemination and Outreach.
WP8 Project Management Office
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 7WP1 – Genomics Applications
GCG In house
In-house
(~130 developments
programs) - own programms
- automated tasks
HUSAR
Program Package
EMBOSS
(~150 Third-party
Third party
programs) programs
DATABASES
- >300 SRS
- Prompt updates ((Sequence
q Retrieval
(daily, weekly) System)
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 8WP1 – Genomics Applications
• Integrating
I t ti W3H,
W3H SoapLab
S L b and
d th
the GRID
target setup preliminary setup HTML pages
W2H
WebService
Solaris (OS)
ScLinux (OS)
W3H
SoapL analysis
y
ab tasks
@dkfz-heidelberg.de
Grid any
Client more
toolkit software ScLinux (OS)
??
ssh
%
G
Grid API
submit_formatd
b … any
Grid
Interface %Client more
software
submit_blastal
toolkit ??
l …
@dkfz or anywhere else
Grid CE
Grid CE
% formatdb % formatdb
… …
% blastall % blastall
… …
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 9WP2 – Proteomics Applications
• Perform functional protein analysis in GRID by using
the functional protein domain annotations on large protein
families using GRID and related databases
databases.
• All 518 human protein kinases and 5129 proteins from
non-redundant chainset of Protein DataBank were
analyzed with InterProScan applications
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 10WP2 – Proteomics Applications
• Protein surface calculation in GRID. : the grid was used to
compute the volumetric description of the proteins obtaining a
precise representation of the corresponding surface. Then
protein interactions could be quickly screened by the mean of
surface analysis.
– The ProSite domains were analyzedy all-against-all
g
– ATP-E against its inhibitor
– Collagen against integrin
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 11WP3 – Transcriptomics applications
• Ph
Phylogenetics
l ti : Reconstructing
R t ti theth evolutionary
l ti hi
history
t off
a group of taxa is major research thrust in computational
biology
gy and a standard p
part of exploratory
p y sequence
q
analysis.
• An evolutionary history not only gives relationships among
taxa but also an important tool for inferring structural
taxa, structural,
physiological, and biochemical properties of sequences
from other similar sequences, and reconstruction of tissue
evolution.
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 12WP4 – Databases & Genomics Applications
• Work Package 4: Databases and Functional Genomics
Applications
– Testing the main biological databases in the Grid
environment
optimization
p on storageg space,
p , bandwidth,, download
time
– Testing performances and scalability of database-based
applications
performances/scalability testing according to various
g
use cases and submission algorithms
– 1 challenge: Gene Analogous Finder
55+ years of computation on a single CPU, not
f
feasible
ibl iin a llocall environment.
i
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007WP4 – Databases handling
• GridDBManager
– Automatic Updater
Timer based monitoring and update of Grid ported
databases
– Adaptive replica manager
Constantly adapts the number of replicas in relation
g of each database in the last 10 days
to the usage y
– Version Regression
Keeps patches on the Grid for allowing regression of
eachhddatabase
b to an earlier
li version
i
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007WP4 – Methods - GridDBManager Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 15
WP4 – Methods - DBApp Perf. Testing
• Testing performances and scalability of Database-Oriented
Bioinformatics Applications (DBApp) in the EGEE GRID
– Testing Performance and Scalability
Grid: too manyy variables (queue
(q time, database
download time, queue failures, execution failures)
Submission mode: too many variables (number of jobs,
rate-limiting settings, resubmission algorithm)
Application too many variables: (performance of
specific application, location of database)
Probing of Grid performances
Numeric simulation for all algorithms
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 16WP4 – Methods - DBApp Perf. Testing
• Probing Grid performances (Example)
– Grid queue times and reliability
Sent 150 jobs in 3 groups of 50 at different times
Grid queue times
(normal load)
30
25
20
% of jobs
15
10
5
0
1 2min
1-2min 4 10min
4-10min 30min 1h
30min-1h 4h 8h
4h-8h Time out
Time-out
8h
Queue times
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 17WP5 – Molecular docking The neuraminidase viruses is considered a valid target for antiviral drugs Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 18
WP5 – Molecular docking
Starting compound Starting target
database structure model Docking: predict how
small molecules bind
to a receptor of
DOCKING known 3D structure
Predicted
binding models There are successful examples
– rapid,
id
– cost effective…
Post-analysis
But there are limitations
– CPU and storage needed
Compounds
for assay
More specific
p talk by
y Ana Lucia Da Costa
Wednesday 13th 11:15 – Room: Bordeaux
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 19WP7 – Dissemination
• The following series of events were specifically associated to
or organized by the BioinfoGRID project:
– BioinfoGRID Symposium 2007: December 10th-13 13th 2007,
2007 Milan
– BioinfoGRID Session at EGEE '07: October 4th 2007, Budapest
– Biomed Grid School, Varenna, Italy, May 14th-19th 2007
– BioinfoGRID Workshop at Healthgrid 2007 Conference - Geneva,
Switzerland, 24th April 2007
– NETTAB 2006 Workshop: Distributed Applications, Web Services,
Tools and GRID Infrastructures for Bioinformatics - Santa
Margherita di Pula, Sardinia, Italy - July 10-13th, 2006
– BioinfoGRID Initial Training Course,
Course Bari Italy, March 8th-10th 2006
Bari, Italy
• In addition, the BioinfoGRID project has been represented at
58 national and international conferences and workshops.
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 20WP7 – Dissemination
• 24 Journal Articles written within the frame of the
BioinfoGRID project:
– 9 - BMC Bioinformatics
– 4 - IEEE Transactions on Nanobioscience
– 3 - Studies in Health Technology and Informatics
– 1 - Journal of Parallel and Distributed Computing
– 1 - Journal of Chemical Information and Modeling
– 1 - Parallel Computing
– 1 - Int. J. of Bioinformatics Research and Applications
– 1 - IEEE Transactions on Systems Science and Applications
– 1 - Nucleic Acids Research
– 1 - BMC Genetics
– 1 - Bioinformatics
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 21WP7 – Dissemination
• 19 Conferences proceedings achieved within BioinfoGRID
– 6 – NETTAB '06
– 2 – EGEE User Forum 06/07
– 2 – BITS '06
– 2 – HPDC '07
– 1 – EGEE 06/07
– 1 – CAPI 2006
– 1 – Bioinformatics of African Pathogens and Disease Vectors
Vectors.
Nairobi 2007
– 1 – MAS-BIOMED '06 Workshop
– 1 – CCGrid '07 Symposium
– 1 – EvoBIO '08
– 1 – CHEP '07
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 22People Acknowledgments
• Cristina Aiftimiei • David Fergusson • Alessandro Orro
• Roberta Alfieri • Geraldine Fettahi • Giovanni Paolella
• Claudio Arlandini • Sandro Fiore • Silvano Paoli
• Roberto Barbera • Riccardo Gervasoni • Antonio Pierro
• Endre Barta • Karl-Heinz Glatting • Giorgio Pietro Maggi
• F
Francesco Beltrame
B lt • J h H
John Hatton
tt • M
Marco Pi l
Pirola
• Attila Bende • Ally Hume • Raffaele Ponzini
• Chiara Bishop • Nicolas Jacq • Ivan Porro
• Chirstophe Blanchet • Atul Jain • Paolo Ramieri
• Ignacio Blanquer • Miklos Kozlovszky • Paolo Romano
• Vincent Bloch • Giuseppe La Rocca • Ermanna Rovida
• Gianpaolo Bottoni • Yannick Legré • Erika Salvi
• Vincent Breton • Pietro Liò • Jean Salzemann
• Andrea Calabria • Carles Loomis • Diego Sardaci
• Andrea Caprera • Mario Marchisio • Salvatore Scifo
• Tiziana Castrignanò
g • Hajnal
j Marton • Martin Senger
g
• Federidica Chiappori • Rafael Mayo Garcia • Giuliano Taffoni
• Dario Corrada • Mirco Mazzucato • Livia Torterolo
• Paolo Cozzi • Giovanni Meloni • Gabriele Trombetti
• Stefano Cozzini • Ivan Merelli • Angelica Tulipano
• Enza D’Alba • Emanuale Merelli • Vania Ugè
• Pasqualina D’Ursi
’ • L i
Luciano Mil
Milanesii • Eli b th van der
Elizabeth d Wath
W th
• Ana Da Costa • Elisa Molinari • Richard van der Wath
• Paride Dagna • Ettore Mosca • Kasam Vinod
• Guilia De Sario • Georgina Moulton • Federica Viti
• Davide Di Pasquale • Loukas Moutsianas • Guy Warner
• Giacinto Donvito • Tibor Nagy • Ted Wen
• Vihang Dudhalkar • Alessandro Negro • Pierfrancesco Zuccato
• Peter Ernst • Laszlo Oroszi
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 23Projects Acknowledgements
ISSeG EU
GRID
Diligent
A DIgital Library Infrastructure
on Grid ENabled Technology
Milanesi Luciano BioinfoGRID Symposium, Milan 10-13 December 2007 24You can also read
