The monthly newsletter from the National e-Science Centre
NeSC News
Issue 73 September 2009 www.nesc.ac.uk
When Microbes Meet Molecules
By Iain Coleman
Physics generally starts with very
simple models – point masses
moving on frictionless surfaces and
so forth – then builds up into more
complex and realistic descriptions
of the world. Biology does the
opposite, starting from big, complex
systems like trees, tigers or physics
professors, and teasing out the laws
and common structures that underlie
this complexity.
The two disciplines meet in the
middle with the study of bacteria.
To a physicist, mathematician or
computational scientist, a bacterium
is a complex dynamic system,
processing information about its
surroundings through a network of
chemical signals. To a biologist, a
bacterium is an incredibly simple
living system, displaying fundamental
processes in an uncluttered and
tractable form.
The research network StoMP
(stochastic dynamical modelling for
prokaryotes) combines these two
perspectives. At the 2009 StoMP
workshop, held at eSI on 13-16
July, microbiologists and physical
and computational scientists joined
forces to expose the inner workings
of bacteria.
Much of the workshop centred
around E. coli. This bacterium is
a notorious cause of nasty – and
sometimes fatal – illness, but it is of
interest to modellers because even
among bacteria it is a very simple
organism. It has a single signalling
pathway that conveys information
about the outside world to the motor
system, so that the bacterium will
move towards or away from attractive
or repellent chemicals.
models can capture the details of this
organism’s behaviour.
Judy Armitage (Oxford) contrasted
this with the more complex
Rhodobacter Sphaeroides bacterium,
which possesses two physicallyseparate signalling pathways. One
pathway carries information about
the external world, much like E. coli,
while the other transmits information
about the internal state of the
bacterium. So the motor system
can know not just “where is food?”
but also “am I hungry?”, enabling
more sophisticated behaviour.
Steven Porter (Exeter) showed
how modelling the response time of
Rhodobacter led to the prediction
that a novel posphatase must form
part of the cell’s signalling system: a
prediction that was later borne out by
experiment.
These investigations were
complemented by the more abstract
modelling of stochastic networks.
Intrinsic variability, environmental
changes and random fluctuations
can all affect the dynamics of a cell.
Guido Sanguinetti (Sheffield) showed
how these concepts can shed light
on the transition between aerobic
and anaerobic states, while Peter
Swain (Edinburgh) discussed how
cells can both exploit and regulate
stochasticity.
Simple as E. coli might be, it can
do a neat trick that you or I can’t.
It is able to switch its metabolism
in response to the environment: if
there’s plenty of oxygen, it will use
that, if not it will switch to anaerobic
respiration, and if it can do neither
it will settle for fermentation. Alison
Graham (Sheffield) presented
experiments aimed at finding out how
the components involved in these
processes are regulated, exposing
an E. coli culture to controlled
levels of oxygen in order to study
the transition between respiratory
states. James Moir (York) discussed
similar issues of respiratory pathway
choice in Neisseria meningitidis,
an organism responsible for both
septicaemia and meningitis, showing
how sophisticated mathematical
While modelling is helping to
understand the inner workings of
bacteria, the most striking impact of
physics on E. coli is also the most
literal. Microscopic objects, such
as dust particles, are subject to
Brownian motion, caused by random
buffeting by the molecules around
them. We don’t notice this in our daily
lives, being much too large to notice
these microscopic impacts, but E. coli
is small enough to be tossed around
by Brownian motion like a ship on a
stormy sea. Wilson Poon (Edinburgh)
showed how the bacterium’s taillike propeller also acts like a rudder,
helping it to stay on course despite
the tumult of its microscopic world.
Bacteria live at the interface between
physics and biology. As the StoMP
network shows, collaboration
between researchers in these
different disciplines can produce
deep insights into the structure and
behaviour of these most fundamental
of organisms.
Slides from this event can be downloaded from http://www.nesc.ac.uk/esi/events/962/
Issue 73, September 2009
e-Science Institute call for new Theme proposals
The e-Science Institute has issued a
fresh call for Theme proposals, with a
deadline October 16, 2009.
The aim of a Theme is to achieve
new insights into a specific topic
by investigating it in depth over a
sustained period.
A theme typically consists of a
connected series of events, visitors
and workshops. It has to address
e-Science research in a deep
and sustained effort to advance
knowledge and capability in its area.
It is expected that the focus for a
theme’s activity will be at the eSI
in Edinburgh, but the organisers
are keen to engage in collaborative
activity with other centres and
institutes through satellite activity
such as associated workshops.
A theme is driven by a Theme Leader
(TL) who is in effect a funded longterm visitor to eSI and is committed
to the topic for its duration. The
TL is responsible for developing a
connected programme spanning
many months and ensuring that it
will engage leading researchers in
the specific field over an extended
period. The theme should bring
visitors to the Institute and other
e-Scientists to work with the TL
throughout its duration. Themes will
also contribute to the eSI’s summer
schools programme.
An ideal theme is one which
progresses the goals of a welldefined research community and
which will initiate research that will
have a wider impact once proven
in the original field. Today’s wealth
of digital data provides many new
research opportunities. The wouldbe leader(s) will have spotted a new
strategy to mine those opportunities.
They would like to dedicate more
time to developing their smart
idea and engaging colleagues in
raising the effort and exploiting
the advance. They will apply to
lead a research team, so that the
buy out allows them to invest the
time and the funds enable them
to bring in experts and initiate
collaborations. The support from eSI
will help them make their mark as the
creative minds behind the new idea.
More information is available on the
eSI Wiki: http://www.nesc.ac.uk/esi/
themes/index.htm
NeSC research team settles into new Informatics offices
Informatics Foyer
To better integrate the research being undertaken at the National e-Science Centre with the research at the School of
Informatics, the Research@Nesc team has moved offices, to the brand new Informatics Forum.
The team in their new workplace
Standing: Rob Kitchen, Gagarine Yaikhom, Prof. Malcolm Atkinson, Jano
van Hemert Seated: Liangxiu Han, Yin Chen, Laura Valkonen
The other members of the team, unable to attend the photo session, are
Chee Sun Liew, Jos Koetsier and David Rodriguez
NeSC News
Roof garden
www.nesc.ac.uk
Issue 73, September 2009
Grid Computing Now! wins further funding
The Grid Computing Now!
Knowledge Transfer Network, a
project run jointly by the National eScience centre and UK trade body
Intellect for the past four years, has
won funding for a further 18 months.
The KTN will become part of
the Digital Business KTN, which
will focus on three programmes:
Scalable Computing (building on
the foundations of Grid Computing
Now! with a focus on Cloud/Utility/
IT as a Service; Sustainability and
Distributed Applications/Services),
Cyber-Security and Location and
Timing. This new KTN will build a
close working relationship with the
Digital Communications KTN, and
the two are expected to merge in
March 2011.
Introduced in 2005, KTNs have
proven that they can bring about
collaboration between government,
academia and business, encouraging
different sectors of UK society to
share ideas and successfully partner
to deliver results.
The Technology Strategy Board,
the body responsible for the KTN
programme, would like to encourage
more knowledge transfer and
collaboration between KTN member
communities.
The memberships of all of the KTNs
will be brought together, but each
community will also remain intact
and identifiable, to keep delivering
the service that members have come
to reply upon, says Ian Osborne,
Project Director.
Ian Osborne, Project Director Grid
Computing Now/ Digital Business
Joint BELIEF-II and CHPC conference announced
The BELIEF-II consortium (www.beliefproject.org) and the Centre for High Performance Computing (CHPC) in South
Africa, are pleased to announce their upcoming joint conference which will be held on the 7-9 December 2009 at the
Sandton International Convention Centre in Johannesburg, South Africa.
The event will focus on Advancing research competitiveness through collaboration: towards an integrated South
African cyberinfrastructure and revolve around an exciting programme that covers an array of important topics like
eEducation, BioInformatics, e-Infrastructures for Social Science.
The event aims at highlighting the important results achieved by the Centre for High Performance Computing in South
Africa and at fostering dialogues to strength an integrated partnership amongst local and international stakeholders.
The programme will explore the contributions and expectations from policy makers, research communities, ICT
vendors, industries, academia and EU funded projects. Recent progress in the South African (SAn) cyberinfrastructure
will be showcased, along with its role in South Africa and developments in Africa. Keynote research and application
results using the cyberinfrastructure will be illustrated, and the latest international developments will be discussed.
Abstract submission guidelines are available at http://www.chpcconf.co.za/CHPC-NM-2009-Abstract-template.pdf or
email Tracy Cadle (tracy@walthers.co.za). Each delegate will be allocated 20 minutes per presentation.
Important Dates:
Abstract submission: 02 October 2009
Notification of acceptance of the abstract: 30 October 2009
Registration Deadline: 30 October 2009
This symposium’s discussions will shape a position paper to be sent to key stakeholders and decision makers. Your
participation would therefore add considerable value in advancing the agenda of e-Infrastructure R&D in South Africa
& Europe in a way that can sustain development in both regions.
For more information and registration, visit http://www.chpcconf.co.za or contact Mary-Jane Kgatuke (Email:
mkgatuke@csir.co.za) and/or event@beliefproject.org
NeSC News
www.nesc.ac.uk
Issue 73, September 2009
Beyond the Repository Fringe
By Florance Kennedy
A successful follow-up to the Repository Fringe 08 un-conference
was held in the Informatics Forum on 30 and 31 July with almost
100 delegates attending. “Beyond the Repository Fringe”
consolidated its reputation for innovation by including what is
believed to be the first Pecha Kucha session session to be held in
Edinburgh or Scotland. Each presenter is allowed 20 slides, each
of which is shown for 20 seconds only. A presentation therefore
lasts 6 minutes and 40 seconds.
Delegates voted with gold nuggets into the cowboy hats last seen
decorating the busts in the Playfair Library a year before, and the
runaway winner was Julian Cheal from UKOLN (pictured)for his
show entitled “Repository Deposit using Adobe Air”. The other
winner of the week was Patrick McSweeney of Southampton who
took the Grand Challenge prize.
The opening keynote was a double act by Ben O’Steen and Sally
Rumsey of Oxford on “A sneak preview at the A-list stars of future
repositories: blockbuster technical developments and the cultural
drivers behind them”.
Clifford Lynch flew in for
Day 2 and thanks to the
extensive streaming,
blogging and tweeting,
managed a closing keynote
which included reference
to events he had not
witnessed in person.
Julian Cheal, winner of Pecha Kucha Session
The round tables held boardroom style generated a lot of interest and
participation, and tutorials and presentations rounded off the events for
which presenters had volunteered themselves. Two formal workshops on
Datashare and Digital Curation 101 were also held.
You can see details of presentations and photos at http://wiki.repositoryfringe.
org/index.php/Main_Page
Clifford Lynch in full flow at the
closing keynote.
Invitation to Condor Workshop at Cardiff University
The Advanced Research Computing Division is pleased to announce that it is holding a Condor Workshop at Cardiff
University in the UK on the 16th September 2009.
The target audience for this event is both administrators (and potential administrators) and end users of Condor
with the event split into two parts. The morning session will explore best practices of service provision and future
developments. The afternoon session will showcase the research that Condor is enabling, hopefully broadening its
potential use in your institution.
Registration for the workshop is now open; see http://www.cf.ac.uk/arcca/services/condor/workshop2009.html for
further information.
NeSC News
www.nesc.ac.uk
Issue 73, September 2009
NGS Innovation Forum ’09 – registration open!
The NGS is pleased to announce
that registration for the NGS
Innovation Forum ’09 is now open.
The event will be held in The Magic
Circle Headquarters in London on the
21st -22nd October.
The two day event will showcase
the impact that the NGS has had on
research in the UK, allow delegates
to find out more about using the NGS
in applied research, enable IT staff
to find out how their institution can
benefit from the NGS, and how you
can contribute to and influence the
future development of the NGS.
The first day is primarily aimed
at researchers and will feature
presentations from existing NGS
users that will demonstrate how
the NGS has become a powerful
research tool in their area. There
will be plenty of opportunity for
delegates to contribute to the event
with 2 breakout sessions covering a
variety of topics including communitybased sessions where delegates
can meet other researchers in their
subject area. The break out sessions
currently in place are listed below but
further suggestions are welcome:
•
•
•
•
•
•
•
•
Data handling and integration
Site integration with the NGS
Software licensing
User support
User communities molecular modelling
User communities bioinformatics
User communities - social
sciences
User communities - human
biology
NGS staff will be on hand throughout
the event to speak to delegates
about how the NGS could aid their
research etc and, for existing users,
offering up to the minute advice on
optimising your jobs on the NGS.
The second day is primarily aimed
at those responsible for delivering
IT services in their institutions. It will
focus on the benefits to an institution
of NGS membership and how
institutions can get involved with the
NGS. There will be presentations
on the novel technologies already
available on the NGS as well as
cloud technology and the NGS as
well as a session on outreach and
user engagement in institutions.
Stairwell, Magic Circle Theatre
The event will be held in the exciting
surroundings of The Magic Circle
Headquarters which is a stones
throw from Euston train station. A
drinks reception will also be held
in the venue on the Wednesday
evening where participants will have
the chance to meet NGS users from
a wide range of research areas.
The event is free to attend but
registration is required. Delegates
are welcome to register for a
single day or the full event. Please
see the event page on the NGS
website to register (www.ngs.ac.uk/
innovationforum09).
Advanced Visualization on the NGS
The NGS is pleased to announce the addition of another resource to the NGS network. The STFC Visualization
cluster is now available through the NGS enabling NGS users to access the cluster through a range of toolkits to
analyse their data without having to download the datasets to their desk.
The Visualisation Cluster offers visualisation tools such as IRIS Explorer, ParaView, Visualisation ToolKit(VTK), IDL,
Chromium and Visit. The cluster is configured to be used as an interactive remote system with NGS, giving the
graphics power of cluster to your laptop/desktop.
Visualization cluster users are supported under the JISC funded vizNET (http://www.viznet.ac.uk) by the STFC team. Information on how to access this cluster is available on http://sct.esc.rl.ac.uk/viscluster/index.html. Please contact
Lakshmi Sastry (lakshmi.sastry@stfc.ac.uk) if you wish to make use of the system and require support.
NeSC News
www.nesc.ac.uk
Issue 73, September 2009
Forthcoming Events Timetable
September
8-10
Multicore Workshop - Exploiting
Multicore Processors: Challenges and
Programming Models
NeSC
http://www.nesc.ac.uk/esi/events/991/
9-11
DPA Authors’ Meeting
eSI
http://www.nesc.ac.uk/esi/events/1013/
14 & 22
Introduction to R Course
eSI
http://www.nesc.ac.uk/esi/events/1009/
14-15
IWPLS’09 International Workshop on
Portals for Life Sciences
eSI
http://www.nesc.ac.uk/esi/events/1000/
30-1
Mapping Information with and without
Geography: Approaches to Data
Visualization and Structure in the Arts,
Humanities and Social Sciences
eSI
http://www.nesc.ac.uk/esi/events/1005/
8
A Patient-Centred NHS - How MCNs Do
It
eSI
19
OMII-UK Board Meeting
NeSC
http://www.nesc.ac.uk/esi/events/997/
20
e-Science Directors’ Forum
NeSC
http://www.nesc.ac.uk/esi/events/989/
30
Introducing the JISC services: Back to the NeSC
Future
October
November
3-4
The impact and influence of Web 2.0based Services on e-Research
eSI
Improving Cancer Care for Children &
Teenagers in Scotland
eSI
December
16
http://www.nesc.ac.uk/esi/events/1012/
This is only a selection of events that are happening in the next few months. For the full listing go to the following
websites:
Events at the e-Science Institute: http://www.nesc.ac.uk/esi/esi.html
External events: http://www.nesc.ac.uk/events/ww_events.html
If you would like to hold an e-Science event at the e-Science Institute, please contact:
Conference Administrator,
National e-Science Centre, 15 South College Street, Edinburgh, EH8 9AA
Tel: 0131 650 9833 Fax: 0131 650 9819
Email: events@nesc.ac.uk
This NeSC Newsletter was edited by Gillian Law.
Email: glaw@nesc.ac.uk
The deadline for the October 2009 issue is September 18, 2009
NeSC News
www.nesc.ac.uk