session 36 - engage results
TRANSCRIPT
Web: www.omii.ac.uk Email: [email protected]
OMII-UK @ ISSGC09
13 July 2009, ISSGC09, Sophia Antipolis, Nice, France
Steve Brewer / Neil Chue Hong
Web: www.omii.ac.uk Email: [email protected]
OMII-UK: Software Solutions for e-Research
• Expertise• Open Source• E-Research• Software• Services
OMII-UK is an open-source organisation set up by the EPSRC to provide software and services to help the UK research community adopt e-Research practices and technology.The role of OMII-UK is evolving into one of cultivation rather than purely development and custodian: the aim is to sustain community software through various channels of support
Currently funded by EPSRC, JISC and others
Web: www.omii.ac.uk Email: [email protected]
Mission: sustainability
Facilitating mutual benefit between all participants
• OMII-Uk’s mission is to cultivate and sustain community software important to research
Web: www.omii.ac.uk Email: [email protected]
Software sustainability
Cultivation: utopian goal for software sustainability
SPAM-GP - Shibboleth-based portal presentation manager
WSRF::Lite – Perl-based API for SOAP
AHE – Application hosting environment
RAPID – Portlet generation tool (JSDL)CPOSS – Crystal Energy Landscape Application
Web: www.omii.ac.uk Email: [email protected]
Services for eResearch software
Design /Code
Evaluation
Integration
SoftwareSupport
Documentation
and Training
SoftwareImproveme
nt
SoftwareDeployme
nt
Promotion +
Exploitation
Innovators
Providers
Users
CommunityDevelopment
Requirements
Gathering
Testing / DevInfrastructur
e
Packaging/porting
Governance
DeploymentAnalysis
SoftwareContribution
s
Information
Provision
Web: www.omii.ac.uk Email: [email protected]
Software products;Community services
OMII-UK Cycle for Software Sustainability
Requirementsgathering
Softwareexpertise
Marketresearch
Domainexpertise
Best practice;Process
SpecialistDevelopment
Standards;Information
Web: www.omii.ac.uk Email: [email protected]
Engage Initiative: Science through software
• How do scientists use computers?
• What do scientists want from computers?
• Where can scientists go for support?
Web: www.omii.ac.uk Email: [email protected]
JISC-funded ENGAGE Initiative achievements
1. talked to ~50 researchers1. Detailed picture emerged of the UK e-Research community2. Computationally intensive research is being conducted across all
domains: papyrology, climate modelling, choreography…
2. review of best practices and lessons learned is underway1. Interviews transcribed and analysed2. Transciptions written-up as public articles for further
dissemination
3. a collection of focussed projects launched that take forward the most promising technologies identified in interviews
1. Projects developed where a significant and visible contribution to the community could be achieved in a relatively short time-frame.
Web: www.omii.ac.uk Email: [email protected]
Engage Initiative: Science through software
How do scientists use computers?
50 interviews across many
domains
Triage process to guide project funding
Best practices extracted
Transcripts reviewed and
analysed
Web: www.omii.ac.uk Email: [email protected]
Engage Initiative: Science through software
What do scientists want from computers?
Web: www.omii.ac.uk Email: [email protected]
Engaging Research with e-Infrastructure
Interviews
Projects
Dissemination
AdoptionNew requirements
Widerdeployment
Web: www.omii.ac.uk Email: [email protected]
ENGAGE Projects (phase 2)
7 projects funded across many domains:• CPOSS – Crystal Energy Landscape Application – upgrade and
NGS port• MCTP – Monte Carlo Treatment Planning – portal improvements• RMCS – Remote My Condor Submit – improved support• Aladdin2 – new interface for GENIE Climate Modelling application • eLab - Integrating field work with the e-Lab Notebook with
centralized services and archives• eSAD - Integration of image processing tools for epigraphy and
papyrology (eSAD) within the Documents and Manuscripts (SDM) VRE
• OSCAR – Chemistry-specific textmining application developed at Cambridge over last 5 years
Web: www.omii.ac.uk Email: [email protected]
ENGAGE Projects (phase 2) – outcome
7 projects results (1-4):Monte Carlo radiotherapy treatment planning (Cardiff)
Now complete; new users at: Swansea, Galway and Liverpool making use of the updated system
Crystal Energy Landscape application-CPOSS (UCL)New DMACRYS system now working; re-engineered workflows being evaluated by Sally Price’s research team at UCL
RMCS: Remote job submission for molecular simulation (Cambridge)
Project complete and good progress achieved
Integration of image processing tools within the VRE-SDM (Oxford)
New integrated system previewed at recent Image, Text, Interpretation workshop in Oxford; user i/f well received by papyrologists and epigraphers
Web: www.omii.ac.uk Email: [email protected]
• 7 projects underway (5-7):o Aladdin 2: a launchpad for the GENIE Earth-System Model
(UEA/OU)• Ported GENIE simulator now operational – configurable parameters can be
rendered; MatLab logic has been ported from GENIELab
o Integrating field work with the e-Lab Notebook with centralized services and archives (Bangor, Southampton)
• Lab Blog book project linked to users at Bangor & Southampton who are engaged with projects based on the analysis of molecular structure and function both via experimental crystallography and molecular dynamics simulation; updated system now on NGS
o Refactoring of OSCAR3, migration to NaCTeM, modularisation and code hardening (Cambridge, Southampton, NaCTeM)
• Workshop in Cambridge (July 09; EPO, RSC, NaCTeM and others attended• UIMA demo underway; refactoring process guided by modular architecture
plan
Web: www.omii.ac.uk Email: [email protected]
Monte Carlo treatment Planning
• Remote access via portal• Web services – requests• Experiment manager for
simulation jobs• Computational resources
where jobs are done• RTGrid database provides
persistent storage of info
Web portal
Condor pool
NGS resources
Experiment Manager
RTGrid Databas
e
Web services
User reques
ts
Jobs took 159.45 hours on single machine• 18.1 hours on Condor cluster• 7.2 hours on NGS
Web: www.omii.ac.uk Email: [email protected]
CPOSS: Crystal Energy Landscape Application
Web Server
JOB MANAGER WSDL
GridSAM
Test Successful
MOLPAKDMAREL WSDL
MOLPAK DMAREL POLYUTULVISULISER
For Each (of the ?)
Limit to n
MOLPAK WSDL
JOB MANAGER
Generate JSDL
MOLPAK2CML
DMAREL WSDL
For Each (of the 200)
Generate JSDL
MOLPAK2CMLJOB MANAGER
MOLPAK2CML
VISULISER WSDL
StoreResults
Process
GENHTMLPAGE
PLOT
• MOLPAKDMAREL: Centre for Theoretical and Computational Chemistry at UCL and the department of computing at UCL• five interacting workflows along with six Web Services• BPEL Web Services shaded grey • replace dmarel with dmacrys• Replication of the execution stages on Legion and the NGS as well as to still allow execution on Condor
Web: www.omii.ac.uk Email: [email protected]
Aladdin2: a cross-platform GENIE launchpad for Research and Teaching
o GENIE project was established to deliver simplified and faster-running models of the Earth’s climate system
o GENIE users are thus able to model longer timeframes stretching over many thousands of years
o modular construction of this system has enabled Open University students to acquire a stand-alone simulator that allows them to create real-time models of various earth projections with a small number of variables to control
• configure and execute GENIE with real-time visualisation of key variables• XML extension for tutorial examples• GENIElab s/w enables multiple runs on remote resources eg. NGS• ease of use reduces barriers to uptake• access for students, teachers and policy makers
Web: www.omii.ac.uk Email: [email protected]
Integration of image processing tools within the VRE-SDM (Oxford)
Design choice criteria: development restricted to the two projects VRE-SDM user interfaces exist for researchers NGS uniform execution environment researcher developing the algorithms in the team rapid turn around from algorithm to installation compiled binary accessed with GridSAM WS i/f
Project management characteristics: bi-weekly and impromptu team meetings Online collaboration application close interaction between researcher and
developers issues easily and swiftly resolved:
understanding of the algorithms, correct operation and of the NGS, workflow of the image processing tasks, design of the data model GUI design of the portlet.
Web: www.omii.ac.uk Email: [email protected]
Integrating field work with the e-Lab Notebook
•Partners•People
•Processes •Services
•Interactions
UNSW is the University of New
South Wales
STFC is the Science and Technology
Facilities Council
Web: www.omii.ac.uk Email: [email protected]
OSCAR3 – text mining for chemistry
Project objectives:• Refactored OSCAR software• OSCAR-UIMA integration• Improved OSCAR software
developer-user documentation
• OSCAR unit test infrastructure
• Improved SourceForge community support
• Successfully completed test process report
OSCAR3 architecture at outset
Web: www.omii.ac.uk Email: [email protected]
User engagement: techniques and practices
• How do we manage the engagement process in practice?• Should this be handled at the project level or the domain level?• In practice the following points are relevant:
- user engagement is different for each project- similar techniques exist: workshops/training, web, forums, video
- important to identify the user community you wish to have at the end of your project and work towards that as goal(sustainability)
• Dissemination sources/subjects can be found by targeting either:- passive users in order to "promote" themselves- creators/champions at top to bring in more overall users
Web: www.omii.ac.uk Email: [email protected]
OMII-UK: sustainable community software
“You know, when you collaborate with people, there's no rules about anything.”
Therman Statom