architectural constraints on current bioinformatics integration systems norman paton department of...
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Architectural Constraints on Current Bioinformatics Integration Systems
Norman PatonDepartment of Computer Science
University of ManchesterManchester, UK
<norm>@cs.man.ac.uk
Structure of Presentation Current integration proposals.
What they support. What they don’t support, and why.
Requirements for integration. What could be useful, and why.
Grid opportunities. Relevant Grid technologies. Absent Grid technologies.
Current Integration Proposals
Classification
Feature Values
Data Location In-situ, Replicated, Reorganised
Integration Model
None, Relational, Semi-Structured, Object-Oriented
Architecture Thin Client, Client-Server, Multi-Tier
Analysis Support
Function Call, Query, Workflow
SRS
Sequence Retrieval Systemhttp://srs.ebi.ac.uk/
SRS In Use
List of Database
s
Search Interface
s
Selected Database
s
SRS Results
Links to Result
Records
Classification of SRS
Feature Values
Data Location Replicated
Integration Model
None
Architecture Thin Client
Analysis Support
Function Call, Query
BioNavigator BioNavigator combines data
sources and the tools that act over them.
As tools act on specific kinds of data, the interface makes available only tools that are applicable to the data in hand.
Online trial from:https://www.bionavigator.com/
Initiating Navigation
Select database
Enter accession number
Viewing Selected Data
Relevant display options
Navigate to related programs
Chaining Analyses in Macros
Chained collections of navigations can be saved as macros and restored for later use.
Classification of BioNavigator
Feature Values
Data Location Replicated
Integration Model
None
Architecture Thin Client
Analysis Support
Function Call, Workflow
Current Public Integration Systems Location: data is replicated – under
control. Integration model: often minimal. Architecture: The architecture is often
two-tier. Analysis support: Query and analysis
access is carefully contained.
Only very careful instantiation of the classificationyields sufficiently predictable performance.
GIMS
GIMS – recent experience
Feature Values
Data Location Reorganised
Integration Model
Object-Oriented
Architecture Multi-tier
Analysis Support
Function Call
Example Analysis Data:
Yeast genome sequence. Protein-protein interaction data. 350 transcriptome experiments. Overall database ~350Mb.
Analysis: Correlate transcription of interacting
proteins.
Features of Experience Challenging to conduct single runs
of analyses – must break into bits. These are modest data sets
compared with what is coming. Environment has been designed
with analysis in mind. These analyses will never make it
into the public release!
Requirements for Integration
Requirements for Integration Location: replication is
transparent. Integration model: standards. Architecture: Flexible, multiple tier. Analysis support: Arbitrary
analyses over diverse data sets.True integration in bioinformatics should not just be data oriented, but involve integration of analyses.
Three Tier Architecture Clients handle
user interaction and presentation.
Application servers perform computation and analysis.
Data servers manage and query databases.
Client
ApplicationServer
DataServer
Three Tier Architecture Scaleability:
Replace/Upgrade components as needed.
Replace/Upgrade layers independently. Flexibility:
Application server layer protects clients from changes in database layer.
Classical three tier architectures are configured statically, and are adapted slowly as needs evolve.
Grid Opportunities
Necessary and Missing Necessary:
Directory services. Discovery
services. Co-allocation. Data replication. Workload
management. Accounting and
payment.
Missing: Databases. Data models. Heterogeneity
resolution. Personalisation. Web services. Standards.
Dynamic Multi-Tier
Client
ApplicationServer
DataServer
ApplicationServer
ApplicationServer
DataServer
Resources need to be identified,selected andscheduleddynamically.
Grid Classification
Feature Values
Data Location In-situ, Replicated
Integration Model
None
Architecture Multi-Tier
Analysis Support
Function Call, Workflow
The current Grid is not the answer, but the answersubsumes the current facilities of the Grid.
Summary Current integration facilities in biology:
Are cunningly restrictive. Make the most of limited distributed
computational architectures. The Grid is bringing to the table:
Resource description facilities. Resource scheduling and workflow
management facilities. The Grid does not directly address current
needs in biology, but its descendents may.