1. CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins Sebastian J. Schultheiß Christoph Malisi

2. 2 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Overview  Motivation  Goals  Software Architecture and Design  Implementation

3. 3 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Motivation  Many proteins are involved in diseases like cancer and mad cow disease  A large number of biological sequences are available online due to sequencing projects  Scientific interest in characterisation and annotation of the proteins

4. 4 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Protein Annotation MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ CPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLK… Subcellular localisation prediction: MultiLoc Epitope prediction Protein sequence: Bioinformatics methods Many more … Database search

5. 5 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Existing Annotation Services  Existing web services are isolated  No common user interface/data format  Mostly counterintuitive presentation of results, not immediately reusable

6. 6 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Goals of Our Project  Workbench Application Integration of several different annotation services into one interface Faster Availability of results through parallel execution of several predictions Simplify and Combine the in- and output for more efficient work Intuitive and easily accessible user interface Graphical representation of results Save prediction projects and parameters to an xml file

7. 7 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Goals of Our Project  Targeting researchers in biology, biochemistry and medical science  User friendly due to extensive manual and tutorials with real world examples for getting started quickly  Immediate reuse of results for other services or for publication

8. 8 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi User Interface

9. 9 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Literature Annotation Architecture  Distributed Computing  Usage of CPU time on different servers  Require description of the services in WSDL  Communication over SOAP messages Internet Proteins! SOAP Prediction Server SOAP Database Server Distributed Computing Grid

10. 10 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Implementation  Client Programme in Java with Swing Toolkit for the user interface  SOAP server Apache AXIS 2 for Java Generates client and server java code automatically from a WSDL description of the service Runs inside Apache Tomcat web application server Provides classes for SOAP communication

11. 11 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Implementation  In addition to the Client, we provide SOAP frameworks for some prediction services Queen‘s University in Kingston, ON for literature based annotation Division for „Simulation of Biological Systems“ at the University of Tübingen

12. 12 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Integrative Bioinformatics  Existing Services can be integrated easily into out client by writing a WSDL and creating a SOAP web application from it (Tutorial)  Open Source under the GNU General Public License  Some effort has been made to standardise web services with WSDL, but there is no open-source stand- alone client HOBIT (Germany) Nat‘l Institute of Genetics (Japan) INCLUSive (Belgium)

13. 13 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi What we want to do here  Write a WSDL description for your literature-based service  Create a SOAP server application with AXIS 2 (Service Axis interface)  Client interface specification

14. 14 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi What we need from you  Which part of the service to integrate?  Service interface Command line Java classes  Input- and output specifications  GUI Parameter Input  Presentation of results Graphical represenation?

15. 15 CoMPAS Pro: Comprehensive Meta Prediction and Annotation Services for Proteins S.J. Schultheiß C. Malisi Acknowledgements  State of Baden-Württemberg for KSS Scholarship  Prof. Kohlbacher for advice and support  The people at the SBS Division