Developing and supporting eScience at the University of Cambridge

1
Developing and supporting eScience at the
University of Cambridge
Michael Simmons, Development Manager, eScience
Centre for Scientific Computing
2
eScience at Cambridge

• who we are
• what is eScience?
• our model
• what we do
• what we want to do

3
Centre for Scientific Computing

• CRC Professor Mike Payne FRS
• eScience
• Director Mark Hayes
• Grid Specialist Mark Calleja
• Development Manager Michael Simmons
• HPC
• Director Paul Calleja, two colleagues
• MPhil in Scientific Computing
• Director Nikos Nikiforakis
• Deputy Director Julian Huppert

4
What is eScience?

• eScience is "research into new ways of using the
  Internet to do science".
• access to web-enabled scientific applications
• compute grids based on software such as Condor
• data grids based on web-friendly technologies
  such as REST
• multi-party video conferencing and telepresence
  e.g. AccessGrid,
• remote graphical visualisation

5
eScience at Cambridge

• To support e-Science projects involving
  scientists and industry in the Cambridge region.
  (and beyond)
• To enable new scientific advances by using
  Grid-enabled applications to tackle Terascale
  problems.
• To develop new generic Grid-based tools for
  massive data handling, high-perfomance computing
  and visualisation applications on wide area
  networks.

6
eScience model

• identify academics with need for scientific
  computing
• propose or join project funding bids
• promote eScience support for researchers
• develop extended networks inside and outside the
  University
• develop collaborative bids with industry
• Services CamGrid, data issues inc semantic web,
  interoperability, specialist web applications
• We need to
• Recover costs
• Demonstrate added value
• Metrics resulting publications, academic
  satisfaction

7
Collaborators and funders include

• UK Research Funding Councils EPSRC, STFC, NERC
• Technology Strategy Board (formerly DTI
  Technology Programme)
• UK eScience programme SRIF
• JISC
• UK Department for Transport
• O2
• Nokia
• Symbian
• Siemens
• Rolls-Royce

8
Universities and industry

• Fruitful meetings/engagements, results
  orientated, to develop
• Good personal contacts, enthusiasm (cf Lambert
  Report 2005)
• Knowledge exchange
• mini projects to test the water
• Universities need to understand company drivers
  and vice versa
• Different companies do things differently, so do
  universities, but neither are homogenous masses
• Collaborative funding projects leveraging eg TSB,
  European, PIPSS etc

9
What do we do?

• CamGrid
• GridPP
• Mobile Environmental Sensing System Across a Grid
  Environment (MESSAGE) monitoring pollution
  exposure for individual cyclists and pedestrians.
• Telemedicine on the Grid demonstrating the
  capability of Grid technology to support
  multi-disciplinary meetings for the review of
  cancer diagnoses and treatment
• CancerGrid open standards for clinical cancer
  informatics

10
What do we do?

• MaterialsGrid a large scale dynamic database of
  materials properties
• SciBorg extracting the science from scientific
  publications
• National Transport Data Framework providing
  access to distributed sources of transport data
• EU-IndiaGrid joining European and Indian Grids
• CCPNGrid grid-enabled NMR structure calculations

11
CamGrid

• Started in Jan 2005 by five groups (now up to
  eleven 13 pools).
• UCS has its own, separate Condor facility known
  as PWF Condor.
• Each group sets up and runs its own pool, and
  flocks to/from other pools.
• Hence a decentralised, federated model.
• Strengths
• No single point of failure
• Sysadmin tasks shared out
• Free to join
• Free middleware
• Weaknesses
• Debugging is complicated, especially networking
  issues.
• Many linux variants can cause library problems.

Mark Calleja (Michael Simmons)
12
Mark Calleja
13
CamGrid participating departments

• Astrophysics
• Biological Sciences
• Biological and Soft Systems
• Cambridge eScience Centre
• Chemical Informatics
• Earth Sciences (2)
• High Energy Physics
• Materials Science
• National Institute for Environmental eScience (2)
• Oncology
• Semiconductor Physics

14
41 refereed publications to date
Credit Mark Calleja
15
Computational Strategies for the Study of Protein
Complex Structure and Assembly by Ion Mobility
Mass Spectrometry
Tara Pukala Department of Chemistry
16
Modelling the evolution of the influenza virus
David Burke Antigenic Cartography
Group Department of Zoology
17
Modelling the evolution of the influenza virus

• Structure Prediction
• Comparative modelling
• Based on xray structure of a strain of HA from
  1968
• Molecular Dynamics
• Monte Carlo simulations
• Which features of the protein structure change as
  the virus evolves?
• Can we quantify the antigenic change given the
  amino acid substitutions and subsequent structure
  prediction?

David Burke Antigenic Cartography
Group Department of Zoology
18
Genomic arrrays tools for cancer gene discovery
Ian Roberts Hutchison MRC Research Centre
19

20

21

22
www.ntdf.org.uk

23

24

• MESSAGE PROJECT in Cambridge (eScience,
  Chemistry, Computer Laboratory)
• Develop portable systems to collect data on
  pollution
• Collaborators O2, Nokia, Symbian, Alphasense
• Build sensor grid infrastructure
• Query database, personal look up
• With Imperial College, Southampton, Leeds,
  Newcastle universities
• Asthma peak flow metre trial

Credit Iq Mead
25
What have we done?

• EMGrid - Electromagnetic Scattering From
  Aircraft visualising complex 3D EM data
• Molecular Informatics - Molecular Standards for
  the Grid exploiting modern methods of
  information management to discover new molecular
  information
• CosmoGrid enabling UK cosmologists to make world
  class contributions from observation of the
  cosmic microwave sky

26
What have we done?

• GROWL a light-weight Grid services toolkit and
  applications
• FutureGrid a program for long-term research into
  Grid systems architecture
• Multicast Transport for Grid Computing reliable
  high-speed bulk data delivery using IP multicast
• Distance CFD Supercomputing for Industry
  understanding turbulent flow patterns in complex
  systems like gas turbines and aero engines

27
What do we want to do?

• Develop eScience model 2.0 with stakeholders
• Create grid collaborations with industry
  (including help develop more imense.coms,
  bridging the gap between commercial requirements
  and publically-funded eScience resources
• Develop networks and collaborative projects with
  industry leveraging appropriate funding
• Extend CamGrid to support more research projects,
  extend range
• Application of new technologies, eg GPUs,
  pilot/feasibility
• Virtualisation imense various virtual platforms,
  vms.
• Mobile grid sensors grid infrastructure

28
Camtology

• Project to create start up specialising in
  ontological search
• Joint venture between imense.com and iLexIR
• Will use grid via joint venture partners

29
Constellation
New company to commercialise GLite STFC support
30
What do we want to do?

31
Fold.it

32
reCaptcha

33
Akogrimo

34
Contact
Michael Simmons, Development Manager mps48_at_cam.ac.
uk 44 7764 199 221 44 1223 765518 eScience
www.escience.cam.ac.uk with links to past and
current projects and to CamGrid technical
details Presentations from CamGrid users
meeting http//www.dspace.cam.ac.uk/handle/1810/1
97075/browse-title Centre for Scientific
Computing www.csc.cam.ac.uk