The Helmholtz Network for Bioinformatics The Helmholtz Network for ...

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29 Σεπ 2013 (πριν από 3 χρόνια και 10 μήνες)

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helmholtz network
for bioinformatics
TheHelmholtzNetwork for Bioinformatics
Tour through the HNB web pages
TheHelmholtzNetwork for Bioinformatics
Tour through the HNB web pages
HNB Workshop
Agnes Hotz-Wagenblatt
helmholtz network
for bioinformatics
helmholtz network
for bioinformatics
EMBL
EMBL
MAX DELBRUECK CENTER
FOR MOLECULAR MEDICINE
MDC
DKFZDeutsches Krebsforschungszentrum, Heidelberg, Abteilung Molekulare Biophysik.
EMBLEuropean Molecular BiologyLaboratory, Heidelberg, Computational BiologyUnit.
GBFGesellschaft für Biotechnologische Forschung mbH, Braunschweig, AG Bioinformatik.
GSFForschungszentrum für Umwelt und Gesundheit, München, AGBIODV,R. Schneider, MIPS R.
Schneider.
MDCMax-Delbrück-Centrumfür molekulare Medizin, Berlin, Bioinformatics, J. Reich, Theoretical
Biophysics, H. Sklenar
MPIMGMax-Planck Institut für molekulare Genetik, Berlin, Computational Molecular Biology.
MPI InformatikMax-Planck Institut für Informatik, Saarbrücken, Computational Biology and Applied
Algorithmics.
RZPD Deutsches Ressourcen-zentrumfür Genomforschung GmbH, Berlin.
Universität zu KölnInstitut für Biochemie, Köln, AG Bioinformatics.
SCAIFraunhofer Institute for Algorithmsand Scientific Computing, St. Augustin, Target Area
Bioinformatics.
Universität Göttingen, Klinikum, Bereich Humanmedizin, Abteilung Bioinformatik, E.Wingender
Helmholtz Network for Bioinformatics
A joint effortof research groups of the ’Hermann von Helmholz-Gemeinschaft
Deutscher Forschungszentren'and other German research groups
helmholtz network
for bioinformatics
HNB Homepage, http://www.hnbioinfo.de
•About
•Forum
•Help FAQ
•Education
•Publications
•User registration
•Contact
•Registered user log in
helmholtz network
for bioinformatics
HNB Forum
•Possibility to discuss
•Exchange experience
•Contact other users
helmholtz network
for bioinformatics
Education
Introductory courses
-Aimed at novice users
-To get the user acquainted with the programs
offered on the HNB-webpage.
-Include extensive practical training.
Topics-The HNB-Webpage
-Guided Tool Finder
-One-click Analyses
-Themes
-Program details
-Examples
Locations-MDC (Berlin 20.10.03)
-DKFZ (once every month)
Duration-2 hours -1 day
Frequency-5-10 times per year
Advanced Workshops
-Character of a seminar-series.
-Programs and algorithms discussed in detail.
-Lecturers from HNB as well as invited speakers.
Topics-Pairwisesequence alignment
-Multiple sequence alignment
-Database searching (Blast, FastA)
-etc.
Locations-DKFZ (Heidelberg 19.-21.11.03)
Duration-3 days
Frequency-1-2 times per year
HNB Online Exercises
helmholtz network
for bioinformatics
HNB User Registration
User specific access:
-master password
-personal certificate
helmholtz network
for bioinformatics
helmholtz network
for bioinformatics
HNB FAQ
helmholtz network
for bioinformatics
HNB Publications
helmholtz network
for bioinformatics
HNB One-click: regulatoryregion
•Promoter prediction
•TF sites
helmholtz network
for bioinformatics
HNB One-click: protein analysis
•Family analysis
•Function prediction
•Interacting genes/proteins
helmholtz network
for bioinformatics
EasyAccess
EasyAccess:My UserSpace
Virtual userspacewhere analysis results
are saved.
Guided Solution Finder
Problem-oriented tool navigation.
Alphabetical RecourceIndex
A quick way to find analysis software.
For the experienced user.
helmholtz network
for bioinformatics
My UserSpace
Virtual user space where analysis results are saved.
-Results from tasks
-Results from various other applications
-Data are ordered in different classes
-Data have an expiry date
My UserSpace –My task runs
helmholtz network
for bioinformatics
My UserSpace –My data
helmholtz network
for bioinformatics
ResourceIndex
RecourceIndex
Listing of all tools available on the HNB
web-page
-Tools sorted by name
-A short tool description is provided
Direct help access
Results in My UserSpace
Mail contact-person of resource
helmholtz network
for bioinformatics
Example using the resource index
helmholtz network
for bioinformatics
HNB Guided solution finder
•Questions lead to
programs
helmholtz network
for bioinformatics
HNB cathegories
•Sequence Analysis and Retrieval
•Gene Regulation
•Protein Families
•Protein Function
•Protein Structure
•Protein Interaction
•Enzymes and Metabolism
helmholtz network
for bioinformatics
Sequence Analysis and Retrieval
HUSAR4HNB
MiniPedant
SRS
BioRS
SequenceAnalysis and Retrieval
helmholtz network
for bioinformatics
HNB HUSAR
helmholtz network
for bioinformatics
HNB Minipedant
•Statistical evaluation of protein
properties
•Best Blast Hits, alignment of
homologous sequences
•Domain patterns
•Secondary structure and trans-
membrane domains
•3D structure when possible
helmholtz network
for bioinformatics
HNB Search for biological materials
•GO Annotation
•Clones, Genes, Unigene
helmholtz network
for bioinformatics
Genome Annotation
Genome annotation
Resources
•TRANSFAC
•SMARtDB
•EPD
•ElegansNet
•Gene Cards
Programs
•Genomic mapping
•Promoter Scan
•GO Annotation
•Dialign
•Blast
helmholtz network
for bioinformatics
Gene Regulation
Gene regulation
Resources •TRANSFAC public/professional
•SMARtDB
•EPD
•Cytomer
Programs
•Match
•Patch
•Dialign
•Bibliosphere
helmholtz network
for bioinformatics
Protein Families
Protein families
•SYSTERS
•SMART
helmholtz network
for bioinformatics
Protein function
•SMART
•STRING
•miniPEDANT
ProteinFunction
helmholtz network
for bioinformatics
Protein Structure
•Fully Automated Prediction
•Expert mode prediction
Fold recognition
Multiple alignment generator
Profile generation
Homology modeling/alignment
Structure model generation
ProteinStructure
helmholtz network
for bioinformatics
Protein Interaction
helmholtz network
for bioinformatics
EnzymesandMetabolism
Enzymes and Metabolism •BRENDA Enzyme database
helmholtz network
for bioinformatics
HOBIT
Requirements
Forthe interconnectionofvarious heterogeneous
bioinformatic resources we identified several demands:
•Openaccessof databases andapplications
•Independance
•Platform independence
•Programming language independance forat least
Perl, Java, C/C++, Python
•Maintaining investmentinlegacy applications/databases
•Location transparency
•Scalability
•Interconnectionandcomposite services
•Openstandards for Data formats(preferablyXMLbased)
•Protocols
•Datatransfer via theWWW
•.. andfinallyOpenSource based
•Web Services
Web Services
.
They offer everything one needs:
•OpenSourcesoftwarefor development...
•...even language independant
•TransportviaHTTP, FTPorSMTPprotocolandthe
corresponding standard ports
•Transport ofstandardXMLbased data formats
•They allow location transparencyand highpervasiveness
•Web Servicesare highly scalableandallowa
huge numberofnodes
•The technical requirements are very low. Even an
Apachewebserver withPerlCGIswill fit
the first needs
Web Services TechnologyStack
HTTP, SMTP, FTPService Transport
Web ServiceDescription Language(WSDL)ServiceDescription
UniversalDescription, Discovery and Integration
(UDDI),ebXML Registries
ServiceRegistry
BusinessProcess Execution Language forWeb
Services (BPEL4WS)
ServiceComposition
ebXMLStandardMessaging
Implementations
Layer Description
"IndustryStandard"
Is it difficult?
No!!!
•DefineWHATyouwilldeliver
–Describe your"classes" and "methods"
–WSDLstandard helps you
–Wrap your legacy codeinyour language
•DefineHOWyouwilldeliver
–Datamodel<->Messages
–Extend theSOAPprotocol
–Simply useXML
Analysis units for building blocks
from HOBIT partners
Analysis units for building blocks
from HOBIT partners
ANALYSIS UNITS
MODULES
DCA
Dialign
MSF-Generator
SYSTERS
BRENDA
STRING
Match
Patch
Transfac
Protein annotation
Protein-protein interaction
DNA annotation
Condalis: proposed EU-Project
Cooordinationby LION BioScience
with 19 partners
Coordinator: Clemens Suter-
Crazzolara, October 2004
SRS Server and Clients
WS server
WS client
Site
CONDALIS
Location X
Location
Z
Location Y
EBI
Biotech
LHS WS
Company
or Institute X
WS servers
WS clients
Federation creates single
“information bus” with tight
integration and failsafe
mechanisms
Current
CONDALIS
SRS as Backbone
•Database Ontology as collaborative effort
–will provide effective map for scientists to locate databanks of
interest and SRS servers that server them
–Support integration
•Mechanism to create a resource for SRS integration files for databanks
and tools
–check list to ensure quality
–central repository
–Quality control and testing against new SRS versions
•Mechanism for creating ‘predefined queries’ and workflows
•Coordinated exchange of indices andflatfiles
CONDALIS
•Current Situation
–A strong community of public SRS servers with large potential to
grow, but no structured access and quality check
–Web services industry standard for client server and SRS8
provides a well functioning interface for that
•Future activities
–Help establish virtual organisation of all public SRS servers with
clear guidelines, quality checking, coordination
–Documentation of all resources available through virtual
organisation, including database ontology, meta information about
databases, schemas
–Create “client only product” for SRS WS Objects and SRS
Gateway
–Applications e.g. in system biology and viewers created to be
included
End