Session 36 - Engage Results

Web: www.omii.ac.uk Email: [email protected]

OMII-UK @ ISSGC09

13 July 2009, ISSGC09, Sophia Antipolis, Nice, France

Steve Brewer / Neil Chue Hong


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


Mission: sustainability

Facilitating mutual benefit between all participants

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


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


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


Software products;Community services

OMII-UK Cycle for Software Sustainability

Requirementsgathering

Softwareexpertise

Marketresearch

Domainexpertise

Best practice;Process

SpecialistDevelopment

Standards;Information


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 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.



How do scientists use computers?

50 interviews across many

domains

Triage process to guide project funding

Best practices extracted

Transcripts reviewed and

analysed



What do scientists want from computers?


Engaging Research with e-Infrastructure

Interviews

Projects

Dissemination

AdoptionNew requirements

Widerdeployment


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

• 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


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


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


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.


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

• Improved SourceForge community support

• Successfully completed test process report

OSCAR3 architecture at outset


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

Education

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