Session 36 - Engage Results

OMII-UK @ ISSGC09

13 July 2009, ISSGC09, Sophia Antipolis, Nice, France
Steve Brewer / Neil Chue Hong

Web: www.omii.ac.uk Email: info@omii.ac.uk

OMII-UK: Software Solutions for e-Research

• Expertise OMII-UK is an open-source
organisation set up by the EPSRC to
• Open Source provide software and services to help
the UK research community adopt e-
• E-Research Research practices and technology.
• Software
The role of OMII-UK is evolving into one
• Services of cultivation rather than purely
development and custodian: the aim is
to sustain community software through
Currently funded by EPSRC,
JISC and others various channels of support


Mission: sustainability

• OMII-Uk’s mission is to cultivate and
sustain community software important
to research

Facilitating mutual benefit between all participants


Software sustainability

Cultivation: utopian goal for software sustainability
AHE – Application hosting environment
SPAM-GP - Shibboleth-based portal presentation manager

WSRF::Lite – Perl-based API for SOAP
RAPID – Portlet generation tool (JSDL)
CPOSS – Crystal Energy Landscape Application


Services for eResearch software

Innovator Design /Code Testing / Dev
Governance
s Evaluation Infrastructure

Integratio Packaging Documentation
n /porting and Training

Software
Deployment Promotion +
Providers Deploymen
Analysis Exploitation
t
Software
Community Software
Improvemen
Development Support
t
Requirement
Information Software
Users s
Provision Contributions
Gathering


OMII-UK Cycle for Software Sustainability
Domain Best practice;
expertise Process

Software products; Requirements
Community gathering
services

Standards;
Market
Information
research

Specialist Software
Development expertise


Engage Initiative: Science through software

• How do scientists use computers?
• What do scientists want from computers?
• Where can scientists go for support?


JISC-funded ENGAGE Initiative achievements

1. talked to ~50 researchers
o Detailed picture emerged of the UK e-Research community
o Computationally intensive research is being conducted across all
domains: papyrology, climate modelling, choreography…
2. review of best practices and lessons learned is underway
o Interviews transcribed and analysed
o 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.



How do scientists use computers?
50 interviews
across many
domains

Transcripts Triage process to
reviewed and guide project
analysed funding

Best practices
extracted


What do scientists want from computers?


Engaging Research
with e-Infrastructure

Interviews

Wider
deployment
Projects

Dissemination

New requirements www.omii.ac.uk
Web: Email: info@omii.ac.uk
Adoption

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


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


• 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


Monte Carlo treatment Planning

User Web
Web portal services NGS
requests
resources

• Remote access via portal
RTGrid
• Web services – requests Database
• Experiment manager for
simulation jobs
Experiment
• Computational resources Manager
Condor pool
where jobs are done
• RTGrid database provides Jobs took 159.45 hours on single machine
• 18.1 hours on Condor cluster
persistent storage of info
• 7.2 hours on NGS


CPOSS: Crystal Energy Landscape Application

• MOLPAKDMAREL: Centre Web Server

for Theoretical and MOLPAKDMAREL WSDL

Computational Chemistry at For Each (of the ?)
Limit to n
UCL and the department of MOLPAK DMAREL VISULISER POLYUTUL

computing at UCL
• five interacting workflows MOLPAK WSDL VISULISER WSDL

along with six Web Services MOLPAK2CML
Process

• BPEL Web Services shaded Generate JSDL
StoreResults

grey JOB MANAGER
GENHTMLPAGE

• replace dmarel with dmacrys DMAREL WSDL

• Replication of the execution JOB MANAGER WSDL
PLOT

For Each (of the 200)

stages on Legion and the NGS GridSAM MOLPAK2CML Generate JSDL

as well as to still allow
execution on Condor Test Successful JOB MANAGER MOLPAK2CML


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
• configure and execute GENIE with
has enabled Open University
real-time visualisation of key variables
students to acquire a stand-alone • XML extension for tutorial examples
simulator that allows them to create • GENIElab s/w enables multiple runs
real-time models of various earth on remote resources eg. NGS
projections with a small number of • ease of use reduces barriers to uptake
variables to control • access for students, teachers and
policy makers


Integration of image processing tools within the VRE-SDM (Oxford)

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.
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

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


OSCAR3 – text mining for chemistry

Project objectives:
• Refactored OSCAR software
• OSCAR-UIMA integration
• Improved OSCAR software
developer-user documentation
• OSCAR unit test
infrastructure OSCAR3 architecture at outset
• Improved SourceForge
community support
• Successfully completed test
process report


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


OMII-UK: sustainable community software

“You know, when you collaborate with people,
there's no rules about anything.”
Therman Statom


Session 36 - Engage Results

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Session 36 - Engage Results