Implementation of CC Web Services for the HOBIT Platform

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Implementation of C/C Web Services for the
HOBIT Platform

• Eva Lange

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Overview

• Idea of the HOBIT initiative
• Oligo Selection for chip design
• Web Services
• gSOAP Development of C/C Web Services and
  Clients

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Helmholtz Open Bioinformatics Technology

• Idea open bioinformatic resources for research
• Organisational and technological platform for
  interconnection of bioinformatics activities
• Provide a comprehensive and integrating structure
  for exchange of information via the web
• Based on open source technologies it is dedicated
  to every interested institution or person

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• Freie Universität Berlin Algorithmic
  Bioinformatics Group  
• DKFZ Heidelberg Department of Molecular
  Biophysics 
• Bielefeld University Research Group in Practical
  Computer Science 
• GBF Braunschweig Department of Genome Analysis
• University of Cologne Cologne University
  Bioinformatics Center 
• GSF Munich MIPS / Institute for Bioinformatics 
• Georg-August University Göttingen Department of
  Bioinformatics 
• MDC Berlin Bioinformatics Department
• MDC/EMBL Heidelberg Comparative Sequence
  Analysis 
• Ludwig Maximilians Universität Munich Lehr- und
  Forschung-seinheit Bioinformatik  
• Universität Würzburg Institute of Bioinformatics

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Overview

• Idea of the HOBIT initiative
• Oligo Selection for chip design
• Web Services
• gSOAP Development of C/C Web Services and
  Clients

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• Oligo selection for chip design
• (Gunnar W. Klau, Sven Rahmann, Alexander Schliep,
  
• Martin Vingron und Knut Reinert)
• Ole Schulz-Trieglaf
• (Bachelor thesis)

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Motivation

• DNA-Microarrays can be used to test for the
  presence or absence of biological agents, the
  targets.
• Probes (oligonucleotides) sit on spots of the
  array.
• After experiment observe hybridization pattern
  (consider experimental errors!).
• Problems unique probes often difficult to find
  want to use only few probes
• Task find design (minimal set of probes) that
  allows to infer which targets are in the sample

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Motivation Example
Motivation Example
Hybridization matrix (Hij)
Assume only one target in the sample
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Motivation Example
Motivation Example
Hybridization matrix (Hij)
p1
p2
p3
p4
p5
p6
p7
p8
p9
t1
1
1
1
0
1
1
0
0
0
t2
1
0
1
1
0
0
1
1
0
t3
0
1
1
1
0
1
1
0
1
t4
0
1
0
0
1
0
1
1
1
Assume two targets in the sample, e.g., t2,t3
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Motivation Example
Motivation Example
Hybridization matrix (Hij)
Then take all probes ?
Those suffice !!!
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Oligo selection

• Old approach Greedy algorithm (Schliep et al)
• A design that guarantees d-separability for all
  pairs of targets
• ? Note! Due to the greedy nature of this
  algorithm the chosen design is not guaranteed to
  be minimal.
• New approach Integer Linear Programming based
  algorithm (Klau et al.)
• Do what greedy does optimally and also separate
  small groups

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Overview

• Idea of the HOBIT initiative
• Oligo Selection for chip design
• Web Services
• gSOAP Development of C/C Web Services and
  Clients

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Web Services
Internet
SOAP over HTTP (XML message)
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Web Service Definition

• A Web service is a software application
  identified by a URI, whose interfaces and
  bindings are capable of being defined, described,
  and discovered as XML artifacts.
• A Web service supports direct interactions with
  other software agents using XML based messages
  exchanged via Internet-based protocols.
• (by W3C web service architecture group)

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Remote Procedure Calls (RPC)
An automated Simple Object Access Protocol RPC
Stub generator for C by Saurabh Pant
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Web Service Technology Stack
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SOAP

• Light-weight protocol based on XML as the
  marshalling format for data in request and
  response messages
• Vendor- and platform-neutral
• Language-neutral
• Object-model-neutral
• Transport-neutral
• XML allows data transformation (XSLT)
• XML enables long-term data persistence

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RPC

• Remote Procedure Calls bestehen gewöhnlich aus
  zwei Nachrichten (Request-Response)
• Eine Nachricht für die Anfrage an die
  entfernte Prozedur
• Eine Nachricht für die Antwort
• (Die Antwortnachricht ist nicht zwingend.)

Request
SOAP Client
SOAP Server
Response
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Benefits of Web Services

• Reusability
• Location transparency
• Composition
• Scalability
• Reduced vendor dependence

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Overview

• Idea of the HOBIT initiative
• Oligo Selection for chip design
• Web Services
• gSOAP Development of C/C Web Services and
  Clients

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The gSOAP Toolkit

• Open source (C, C, and Java)
• gt2000 registered users
• Automates the deployment of (legacy) C/C
  applications as Web Services
• Automates the development of clients
• Suitable for high-performance computing

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Server Development
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• Service description (WSDL)Method names
  ns1__greedySelection, ns1__ilpSelectionInput
  parameter min_cov of type xsdunsignedInt
• min_sep of type xsdunsignedInt
• target_in of type ns1TargetList
• Output parameter result of type ns1TargetList
• Remote procedure declaration
• int ns1__greedySelection(xsd__unsignedInt
  min_cov, xsd__unsignedInt min_sep,
  ns1__TargetList target_in,
• struct ns1__greedySelectionResponse result)
• Client code
• main()
• if (soap_call_ns1__greedySelection(soap,server,""
  ,mincov,minsep,
• t_list,result2))
• // Error
• else

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Client Development
Specification of Data Types and Remote
Procedures in C/C Header File
Client Application
gSOAP-generated Stub Routines
WSDL
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The gSOAP Stub Compiler

• Generates source code stubs for SOAP RPC
• Generates XML (de)marshalling routines for native
  and user-defined C/C data types
• The gSOAP runtime provides low-level HTTP, TCP,
  SOAP/XML handling and memory management
  capabilities

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SOAP Request

• lt?xml version"1.0" encoding"UTF-8" ?gt
• ltSOAP-ENVEnvelope xmlnsSOAP-ENVhttp//schemas.x
  mlsoap.org/soap/envelope/
• xmlnsns1"http//page.mi.fu-berlin.de/lange/Oli
  goSelection.wsdl"gt
• ltSOAP-ENVBody SOAP-ENVencodingStylehttp//schem
  as.xmlsoap.org/soap/encoding/
• id"_0"gt
• ltns1greedySelectiongt
• ltmin-cov xsitype"xsdunsignedInt"gt10lt/mincovgt
• ltmin-sep xsitype"xsdunsignedInt"gt5lt/minsepgt
• lttarget-in xsitype"ns1TargetList"gt
• lttarget-list xsitype"ns1Target"gt
• ltname xsitype"xsdstring"gtX75453lt/namegt
• ltoligo-list xsitype"ns1Oligo"gt
• ltsequence xsitype"xsdstring"gtTAAATGCGGCTAC
  GTGAAAAGCTAGlt/sequencegt
• ltbadness-value xsitype"xsdfloat"gt1lt/badnes
  s-valuegt
• lt/oligo-listgt
• lt/target-listgt
• lt/target-ingt
• lt/ns1greedySelectiongt
• lt/SOAP-ENVBodygt

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SOAP Response

• lt?xml version"1.0" encoding"UTF-8"?gt
• ltSOAP-ENVEnvelope xmlnsSOAP-ENVhttp//schemas.x
  mlsoap.org/soap/envelope/
• xmlnsns1"http//page.mi.fu-berlin.de/lange/Oli
  goSelection.wsdl"gt
• ltSOAP-ENVBody SOAP-ENVencodingStylehttp//schem
  as.xmlsoap.org/soap/encoding/
• id"_0"gt
• ltns1greedySelectionResponsegt
• ltresult-list xsitype"ns1TargetList"gt
• lttarget-list xsitype"ns1Target"gt
• ltname xsitype"xsdstring"gtX75453lt/namegt
• ltoligo-list xsitype"ns1Oligo"gt
• ltsequence xsitype"xsdstring"gtTAAATGCGGCTAC
  GTGAAAAGCTAGlt/sequencegt
• ltbadness-value xsitype"xsdfloat"gt1lt/badnes
  s-valuegt
• lt/oligo-listgt
• lt/target-listgt
• lt/result-listgt
• lt/ns1greedySelectionResponsegt
• lt/SOAP-ENVBodygt
• lt/SOAP-ENVEnvelopegt

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References

• An automated Simple Object Access Protocol RPC
  Stub generator for C by Saurabh Pant, MSc
  Report
• gSOAP paper in the proceedings of IEEE CCGrid
  Conference 2002
• Enterprise Applications, lecture of Prof.
  Fischer, TU Braunschweig
• (http//www.ibr.cs.tu-bs.de/lehre/ss04/ea/index.h
  tml)
• Java Web Services Architecture by J. Mc Govern
  et al, Morgan Kaufmann Publishers

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Thank you for your attention !!!