1 / 31

Portals for Life Sciences - Projects -

Portals for Life Sciences - Projects -. Sandra Gesing sandra.gesing@uni-tuebingen.de Division for Simulation of Biological Systems Eberhard-Karls-Universität Tübingen. 15.02.2010. Outline. Portals Grid and Cloud Computing MoSGrid Rapid TOPP

bianca-campbell
Download Presentation

Portals for Life Sciences - Projects -

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

  2. Outline • Portals • Grid and Cloud Computing • MoSGrid • Rapid • TOPP • Semantic Grid Portal for Bioinformatic Workflows • IWPLS‘09 • EuSGE 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 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 Sandra Gesing - Portals for Life Sciences - 15.02.2010

  5. 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 Unifying Diversity Slide copied from: Stuart Owen „Workflows with Taverna“ Sandra Gesing - Portals for Life Sciences - 15.02.2010

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

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

  10. MoSGrid 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 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 Focus Liferay, Pluto, Jboss, GateIn vs. P-Grade Sandra Gesing - Portals for Life Sciences - 15.02.2010

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

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

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

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

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

  22. Semantic Grid Portal for Bioinformatic Workflows • 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) Sandra Gesing - Portals for Life Sciences - 15.02.2010

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

  25. IWPLS‘09 • 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 Sandra Gesing - Portals for Life Sciences - 15.02.2010

  26. Achievements of IWPLS‘09 • Special Issue in Journal „Concurrency and Computation: Practice and Experience“ • IWPLS’10 • EU proposal EuSGE Sandra Gesing - Portals for Life Sciences - 15.02.2010

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

  29. Characteristics • 13 partners from 7 countries in the EUGermany, 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 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 standardsInternational platform in Europe supported by associated partners from the US and Asia. Sandra Gesing - Portals for Life Sciences - 15.02.2010

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

More Related