15.02.2010 Sandra Gesing [email protected] Division for Simulation of Biological Systems Eberhard-Karls-Universität Tübingen Portals for Life

15.02.2010

Sandra [email protected]

Division for Simulation of Biological SystemsEberhard-Karls-Universität Tübingen

Portals for Life Sciences- Projects -

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• IWPLS‘09• EuSGE


Life Sciences• Sophisticated tools and algorithms available• Scientists with different computational background• Need of self-explanatory and intuitive user

interfaces⇒ Portals


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


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“


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

Internet

Server


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


Buzzwords

Portal

Grid portal

Workflows

WS-BPEL

Workflow engine

Grid middleware

Unicore 6Grid computing

Workflow language

Cloud computingHadoop

Taverna

Grid certificates

x509 certificates

Batch System

Sun Grid Engine dCache


MoSGridMolecular Simulation GridGoal • 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


MoSGrid


Portal work package• Evaluation of portal frameworks/Grid portals• Design of user interfaces• Workflow integration• Security

Focus


EvaluationUser 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, GateInvs.

P-Grade


User interface - Gaussian


User interface - Gromacs


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


Rapid


Rapid• Job submission

• Fork• Sun Grid Engine • PBS• Condor

• File transfer protocols • Local file system• HTTP• SCP• FTP/SFTP• GSIFTP

• Data staging• Jython plugin


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


TOPPHPLC-MS(-MS)raw data

MS-MSpeak data

reliableprotein/peptideidentifications

smoothed MS-MSraw data

MS-MSraw data

protein/peptideidentifications

FileFilter

IDFilter

PeakPicker

InspectAdapter

NoiseFilter

mzData mzData

mzData mzData

analysisXML

analysisXML


WorkflowEngine

ServicesServicesPortal

Internet/Server

Administrator

Grid/CloudDeveloper

User

PortletsPortlets

Authentication

invokes

TOPP

TOPPAS

TOPP tools

based on call

convert


Current / future work• TOPP tools wrapped as Web services• Providing infrastructure (workflow engine)

• Converter TOPPAS to WS-BPEL


• 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


Semantic Grid Portal for Bioinformatic Workflows

WorkflowEngine

ServicesServicesPortal

Internet/Server

User

Grid/CloudDeveloper

Administrator

PortletsPortlets

Service Discovery

Engine

PortletsPortlets

Authentication

finds

invokes

added


Future work• TOPP tools wrapped as Web services• Evaluation of ontologies

• Evaluation of service discovery engines • Evaluation of editors for ontologies • Providing infrastructure


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


Achievements of IWPLS‘09• Special Issue in Journal „Concurrency and Computation: Practice and Experience“• IWPLS’10 • EU proposal EuSGE


EuSGE European Science Gateways for e-Science


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


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


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.


Thank you for your attention.

Documents

15.02.2010 Sandra Gesing [email protected] Division for Simulation of Biological Systems Eberhard-Karls-Universität Tübingen Portals for Life