Engaging researchers with
e-Infrastructure
Leaping hurdles: planning IT provision for research
6 June 2009
Neil Chue Hong / Steve Brewer
Web: www.omii.ac.uk
Email: info@omii.ac.uk
Engaging Research
with e-Infrastructure
• What do people want to
do? What are they doing
already?
• Trivial barriers can seem
insurmountable
• Demonstrate success and
inspire trust in eInfrastructure
• Get users to engage with eInfrastructure to improve
research output
Web: www.omii.ac.uk
• Interview researchers to
identify what works and
what’s needed
• Analyse requirements and
propose interventions
• Develop solutions and
disseminate best practice
www.engage.ac.uk
Email: info@omii.ac.uk
Engaging Research
with e-Infrastructure
Interviews
Wider
deployment
Projects
Dissemination
Web: www.omii.ac.uk
New requirements
Email: info@omii.ac.uk
Adoption
ENGAGE Researcher
Interviews
• 53 interviews
o
o
o
semistructured
36 face-to-face
17 telephone
• 60 people
• 24 institutions
• Triage process to
identify
development
projects and best
practice
Web: www.omii.ac.uk
Email: info@omii.ac.uk
The Analysis of
Data in ENGAGE
Interview
Summary
Transcription
1) Writes own software in Python - looking at better
ways of getting it used
2) Software works on multiple datasets mapping to
own data format
3) Cytoscape not automated. Cannot automate
visualisations.
4) Data visualisation is restricted as there are
multiple datasets to download and access
6) Runs take 1-2 weeks. Not interactive.
7) Cannot submit large jobs.
Obstacles
Best Practice
Interviews
1)
2)
3)
Sourcing a system on which to run the
services
Assumptions made by software installation
Assumptions made handling I/O with WS
framework
Timing issues when checking for secure
services
Teaching, admin and other research
commitments meant that the primary
researcher had insufficient time
Evaluation
Evaluation
Report
Web: www.omii.ac.uk
Commission
Tools not easily accessible to
other researchers
Unable to run large jobs on
current resources
Difficult to reuse / repurpose
workflows
1. Undertake feasibility study and
investigate making the protein sequence
databases available as web services
before the wrapped applications can use
their data.
2. Get the wrapped applications and
workflows to work in a production
environment on instituitional facilities
3. Investigate and carry out the migration
from the production environment to the
NGS.
Development
ProjectBrief
Email: info@omii.ac.uk
Project
First Phase ENGAGE
Development Projects
• High Throughput Humanities
for e-Research
• Exposing bioinformatic
programs as Web Services
• Protein Molecule Simulation on the Grid
• Enable workflows in a Shared
Genomics causality workbench
• Linking and Querying Ancient Texts
• SWARMCloud
• Rapid Chemistry Portals by Engaging Users
Web: www.omii.ac.uk
Email: info@omii.ac.uk
Second Phase ENGAGE
Development Projects
•
•
•
•
•
•
•
Monte Carlo Treatment Planning
Crystal Energy Landscape Application
Epigraphy and papyrology image
processing
Strengthening and support for
eMinerals RMCS system
Configuration parameters for the
GENIE simulator
Lab Blog Book
Strengthening and supporting the text
and data analysis toolkit OSCAR
Web: www.omii.ac.uk
Email: info@omii.ac.uk
Planning IT provision
Putting the
for research
Team together
Need to bring together
researchers, developers
and infrastructure
providers. Can be difficult
to retain experienced staff.
Lab Blog Book
Link researchers analysing
molecular structure and
function via crystallography
and MD simulation
Follow how researcher
constructs the DL Poly
simulation files, recreate
at Southampton, link it to
servers.
Evaluation improves the
usability of the work
Evaluating
Usage
Best Practice
Understand where
approaches can be
reused.
Virtual server provided
on NGS2 hosting Lab
Blog server. Databases
ported for wider use.
Working with IT
administrators makes
provisioning faster
Creating a
Common
language
Shared vocabulary for
information exchange
e.g. “analysis”,
“ontologies”.
Experience can make it
easier to broker this
process.
Unix, Apache 2, PHP 5,
MySQL 5, ImageMagick,
1GB storage.
Well defined requirements
drive wider infrastructure
adoption
Defining
Provisioning
Requirements
infrastructure
Web: www.omii.ac.uk
Email: info@omii.ac.uk
First Phase ENGAGE
Development Projects
•
•
•
•
•
•
HiTheR: implemented different document similarity algorithms, 75% reduction
in run-time on small Condor cluster, positive researcher evaluations - discovered
various chains of related articles and misclassified articles, looking to transfer to
NGS
Exposing bioinformatic programs as Web Services: Nine protein
sequence analysis applications hosted on 144 CPU cluster, workflows created
now in daily use by postgraduates, has impressed infrastructure providers
ProSim: Tools connected and made available in portal, workflows evaluated,
workshop ran from 20-24 April with 40 attendees
Shared Genomics: workbenches integrated leading to new ideas for innovative
user interfaces based on coverflow techniques
LaQuAT: three databases integrated, in different languages. researcher about to
complete formal evaluation
RCPER: 3 portals complete, 1 portal underway; 1 portal evaluated and about to
be used by 100+ undergraduates; dissemination at ScotChem workshop
Web: www.omii.ac.uk
Email: info@omii.ac.uk
Second Phase ENGAGE
Development Projects
• MCTP: new users at: Swansea, Galway and Liverpool making use of the
updated system;
• Crystal Energy Landscape application-CPOSS: 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: Project
complete and good progress achieved; Examining link to other projects
• Integration of image processing tools within the VRE-SDM: New
integrated system previewed at recent Image, Text, Interpretation
workshop in Oxford; user interface well received;
• Aladdin 2: a launchpad for the GENIE Earth-System Model:
Ported GENIE simulator now operational – configurable parameters can
be rendered; MatLab logic has been ported from GENIELab.
Web: www.omii.ac.uk
Email: info@omii.ac.uk
ENGAGE Summary
• From interview to exemplar project
showing the use of e-Infrastructure
Interview
Scenario
Project
Evaluation
• Provide publicly available information to
improve uptake
Interview
Scenario
Web: www.omii.ac.uk
Obstacles
Demo /
Best Practice /
Video
Email: info@omii.ac.uk
www.engage.ac.uk
Web: www.omii.ac.uk
Email: info@omii.ac.uk