1. 15.02.2010 Sandra Gesing sandra.gesing@uni-tuebingen.de Division for Simulation of Biological Systems Eberhard-Karls-Universität Tübingen Portals for Life Sciences - Projects -

2. Sandra Gesing - Portals for Life Sciences - 15.02.2010 2 Outline Portals Grid and Cloud Computing MoSGrid Rapid TOPP Semantic Grid Portal for Bioinformatic Workflows IWPLS09 EuSGE

3. Sandra Gesing - Portals for Life Sciences - 15.02.2010 3 Life Sciences Sophisticated tools and algorithms available Scientists with different computational background Need of self-explanatory and intuitive user interfaces Portals

4. Sandra Gesing - Portals for Life Sciences - 15.02.2010 4 Portals Framework for integrating information and applications Single point of entry Provide each user with a repository of personal information Possibility to customize views and tools No installation of software on the end-user side No firewall issues

5. Sandra Gesing - Portals for Life Sciences - 15.02.2010 5 Unifying Diversity 12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa Slide copied from: Stuart Owen Workflows with Taverna

6. Sandra Gesing - Portals for Life Sciences - 15.02.2010 6 Aspects Users Tools and applications Security Authentication Authorisation Data access Monitoring Workflows Service discovery Ontologies Grid and Cloud Computing Grid Portal Developer Administrator Authentication User Cloud InternetServer

7. Sandra Gesing - Portals for Life Sciences - 15.02.2010 7 Grid and Cloud Computing Definition Grid Computing (Ian Foster, 1998) A computational grid is a hardware and software infrastructure that provides dependable, consistent, pervasive, and inexpensive access to high-end computational capabilities. Definition Cloud Computing (Sam Johnston, 2008) The Cloud is what The Grid could have been. Virtualisation Services

8. Sandra Gesing - Portals for Life Sciences - 15.02.2010 8 Buzzwords Portal Grid portal Workflows WS-BPEL Workflow engine Grid middleware Unicore 6 Grid computing Workflow language Cloud computing Hadoop Taverna Grid certificates x509 certificates Batch System Sun Grid Engine dCache

9. Sandra Gesing - Portals for Life Sciences - 15.02.2010 9 MoSGrid Molecular Simulation Grid Goal Providing users with Grid services for molecular simulation tools and docking via a portal Implementation of high-performance computing Workflows Annotations of results Data mining Use of the D-Grid-infrastructure

10. Sandra Gesing - Portals for Life Sciences - 15.02.2010 10 MoSGrid

11. Sandra Gesing - Portals for Life Sciences - 15.02.2010 11 Portal work package Evaluation of portal frameworks/Grid portals Design of user interfaces Workflow integration Security

12. Focus Sandra Gesing - Portals for Life Sciences - 15.02.2010 12 Evaluation User side Usability Performance Workflow Security Monitoring Administrator side JSR 168/268 Unicore 6 Time and effort on installation/implementation Support Security Monitoring Liferay, Pluto, Jboss, GateIn vs. P-Grade

13. Sandra Gesing - Portals for Life Sciences - 15.02.2010 13 User interface - Gaussian

14. Sandra Gesing - Portals for Life Sciences - 15.02.2010 14 User interface - Gromacs

15. Sandra Gesing - Portals for Life Sciences - 15.02.2010 15 Current work Evaluation Installation of portals Deployment of self-developed portlet Integration of Unicore 6 Portlet using UCC libraries (Unicore Commandline Client libraries) Dock tool box

16. Sandra Gesing - Portals for Life Sciences - 15.02.2010 16 Rapid

17. Sandra Gesing - Portals for Life Sciences - 15.02.2010 17 Rapid Job submission Fork Sun Grid Engine PBS Condor File transfer protocols Local file system HTTP SCP FTP/SFTP GSIFTP Data staging Jython plugin

18. Sandra Gesing - Portals for Life Sciences - 15.02.2010 18 Current / future work TOPP-Rapid portlet Pipelines Command line tool Sun Grid Engine PBS VirtualBox Integration of Unicore 6 Rapid extension using UCC libraries (Unicore Commandline Client libraries) Integration of Web services

19. Sandra Gesing - Portals for Life Sciences - 15.02.2010 19 TOPP HPLC-MS(-MS) raw data MS-MS peak data reliable protein/peptide identifications smoothed MS-MS raw data MS-MS raw data protein/peptide identifications FileFilter IDFilter PeakPicker InspectAdapter NoiseFilter mzData analysisXML

20. Sandra Gesing - Portals for Life Sciences - 15.02.2010 20 Workflow Engine Services Portal Internet/Server Administrator Grid/Cloud Developer User Portlets Authentication invokes TOPP TOPPAS TOPP tools based on call convert

21. Sandra Gesing - Portals for Life Sciences - 15.02.2010 21 Current / future work TOPP tools wrapped as Web services Providing infrastructure (workflow engine) Converter TOPPAS to WS-BPEL

22. Sandra Gesing - Portals for Life Sciences - 15.02.2010 22 Grid portal (GridSphere 3.1) Service Discovery Find Web services Interpret descriptions of services Support the invocation of services Ontologies Workflow engine (process WS-BPEL) Semantic Grid Portal for Bioinformatic Workflows

23. Sandra Gesing - Portals for Life Sciences - 15.02.2010 23 Semantic Grid Portal for Bioinformatic Workflows Workflow Engine Services Portal Internet/Server User Grid/Cloud Developer Administrator Portlets Service Discovery Engine Portlets Authentication finds invokes added

24. Sandra Gesing - Portals for Life Sciences - 15.02.2010 24 Future work TOPP tools wrapped as Web services Evaluation of ontologies Evaluation of service discovery engines Evaluation of editors for ontologies Providing infrastructure

25. Sandra Gesing - Portals for Life Sciences - 15.02.2010 25 IWPLS09 First International Workshop on Portals for Life Sciences 2-day workshop (September, 14 – 15, 2009) at the e-Science Institute at Edinburgh Target audience - Life scientists - Bioinformaticians - Computer scientists working on portals 9 papers resulted in talks (available in online proceedings) 9 abstracts resulted in lightning talks 36 attendees

26. Sandra Gesing - Portals for Life Sciences - 15.02.2010 26 Achievements of IWPLS09 Special Issue in Journal Concurrency and Computation: Practice and Experience IWPLS10 EU proposal EuSGE

27. Sandra Gesing - Portals for Life Sciences - 15.02.2010 27 EuSGE European Science Gateways for e-Science

28. Sandra Gesing - Portals for Life Sciences - 15.02.2010 28 Objectives of EuSGE Bringing together scientists from application domains, developers and providers for science gateways Creating an international platform to exchange experience, formulate ideas, and catch up on technological advances in the field of science gateways Offering a repository of existing solutions Promoting existing standards

29. Sandra Gesing - Portals for Life Sciences - 15.02.2010 29 Characteristics 13 partners from 7 countries in the EU Germany, Hungary, Italy, UK, Poland, France, Czech Republic 2 associated partners US, Malaysia 12 from academia, 3 companies WP1 – Management WP2 – Dissemination WP3 – Events and Workshops WP4 – Repository WP5 – Surveys and Standards

30. Sandra Gesing - Portals for Life Sciences - 15.02.2010 30 Impact Building science gateway provider community Building science gateway user community Improving knowledge of existing high-level science gateways frameworks Evaluating existing solutions Promoting standards International platform in Europe supported by associated partners from the US and Asia.

31. Sandra Gesing - Portals for Life Sciences - 15.02.2010 31 Thank you for your attention.