The monthly newsletter from the National e-Science Centre
NeSC News
Issue 74 October 2009 www.nesc.ac.uk
The Meaning of Music
By Iain Coleman
When musicology began, back in the
19th century, it was all about trying
to produce authoritative editions of
music of the past, and analysing the
canon to discover universal principles
of music. This allowed scholars to
determine how well particular works
fit these principles, and to study how
these principles differ from culture to
culture.
This approach fell out of favour
after the Second World War. It
was seen as too nationalistic, and
comparative research became deeply
unfashionable. Musicology became
the study of music from a particular
culture within its cultural context.
The idea that there may be some
universal principles by which music
works was regarded as invalid.
With the rise of e-Science, the
pendulum has started to swing
back – at least, to some extent. The
insights of culturally-situated studies
have not been abandoned, but
computing technology is beginning to
show that some kinds of comparative
research may prove viable. The
e-Science Institute workshop on
“e-Science for Musicology”, held on
1-2 July as part of the eSI research
theme “e-Science for the Arts and
Humanities”, sought to explore
the new ways of understanding
and studying music that are now
becoming possible.
Computational linguistics has
been a core part of the Artificial
Intelligence programme from the
beginning. But there is little in
natural language processing that
emulates the common formulations
of humanistic research: computers
can’t give an insightful analysis
of a piece of poetry. The situation
is similar for musicology. Music is
a kind of abstract language, and
some linguistic analysis tools can be
usefully applied, but there are still
serious limitations.
figure out which tracks are covers
of the same songs? A computer can
readily tell that one track is bluegrass
while another is death metal, but in
order to recognise that they are both
“Stairway to Heaven” it needs to
learn to understand music in terms of
chord progressions and melody.
Music Information Retrieval (MIR) is
an attempt to automatically identify
musical objects within tunes. It first
started in the 1960s, but made little
progress due to a lack of data. Now,
thanks to the growth of networked
digital music collections, it is making
a comeback, as Stephen Downie
(University of Illinois at UrbanaChampaign) explained. MIR currently
suffers from two limitations that
have nothing to do with technology.
The first is simply that the field
is dominated by technologists,
and would benefit from greater
involvement by musicologists. The
second, related, problem is that MIR
is mainly concerned with Western top
twenty pop music – because few of
the technologists working in the field
understand other kinds of music.
At the heart of these difficulties is
the fact that music is not just a set
of physical sound waves that can be
measured in the lab. It is a cognitive
phenomenon. Music happens when
a human mind interprets sounds,
and studying it is as much about
psychology as it is about signal
processing.
As a technology-driven field, MIR has
historically concentrated on the kinds
of analyses that machines can do
well, such as fast Fourier transforms
of musical pieces. But there is much
more to how our minds understand
music than this. We principally follow
melodies and basslines, whereas
machines are better at identifying
instruments and timbres. Some
progress is being made by means of
the cover version challenge: given a
set of widely disparate cover versions
of various songs, can the computer
Geraint Wiggins (Goldsmith’s
College) illustrated this with a
set of simple experiments. He
demonstrated how human listeners
tend to hear rhythmic structure in
sound, even in a steady, uniform
beat, and can even manipulate their
own perception to hear different
illusory structures. These tricks are
the auditory equivalent of optical
illusions like the Necker cube.
Conversely, it is possible to interleave
melodies such that the listener
cannot disentangle them: the sound
is physically present, but the listener
can’t hear it. Music exists in the mind
– everything outside is just sound.
So are computers useless then? Far
from it. Computer models of cognitive
phenomena allow them to be tested
more quickly, more objectively
and indeed more ethically than in
experiments on humans. The key is
to be carefully reductionistic, taking
complex phenomena apart and
Issue 74, October 2009
The Meaning of Music
What do you know about
e-Research?
Continued
By Iain Coleman
studying them one piece at a time.
This approach is commonplace in the
sciences, but at odds with the holistic
approach usually employed in the
humanities.
One area in which the humanities
undoubtedly benefit from e-Science
is the creation of digital libraries. A
great deal of scholarship is about
engaging very closely with the
literature. For musicologists, a lot of
scholarship is literature based, so the
same advantages apply. But musical
materials – scores and recordings
– have only recently begun to be
available.
Technology is opening up new
possibilities for musicology: new
ways of studying musical history,
new relationships between pieces
of music, and new insights into
the musical role of the mind.
With scholars and scientists
working together, the potential for
understanding the role of music in
our lives has never been greater.
OMII-UK are looking for volunteers
to fill in a ten-minute survey.
Slides from this event can be
downloaded from http://www.nesc.
ac.uk/esi/events/996/
Find the survey here: www.tinyurl.
com/y9g9z29
BalticGrid-II 3rd All-Hands Meeting
Poznan, Poland. Photo by Mohylek
Digital editions allow scholars to
ask new kinds of questions, as
Richard Lewis (Goldsmith’s College)
explained. Whereas traditional
musicology which involves close
reading of a few pieces of music,
digital editions allow the large-scale
analysis of hundreds or thousands
of pieces of music, all at the same
time. They also allow a much more
expansive and flexible presentation
of material. Editors no longer need to
relegate explanatory information to
introductions or footnotes in order to
make an edition clear for performers:
editions can be used in different ways
by different types of reader.
This flexibility, however, does come
at a cost, according to Raffaele
Viglianti (King’s College London).
Editors need to extend their
repertoire beyond their traditional
roles of selection and interpretation,
to encompass writing code for the
digital presentation. Here, music
presents its own technological
challenges. XML is becoming the
standard for literary philology, but it
doesn’t allow overlapping hierarchies
– and music is full of these. Thus,
digital musicologists also need to
master the hacks and workarounds
that allow them to make their tools fit
their studies.
Completing the survey not gives
you the chance to win an Amazon
voucher, it also means that you
will be directly contributing to
development of the software and
support that is needed by the
research community.
The third BalticGrid-II All Hands meeting will be held in Poznań, Poland, on
December 9-10, 2009.
The BalticGrid Second Phase (BalticGrid-II) project began on May 1, 2008. It
aims to increase the impact, adoption and reach, and to further improve the
support of services and users of the recently created e-Infrastructure in the
Baltic States.
This will be achieved by an extension of the BalticGrid infrastructure to
Belarus; interoperation of the gLite-based infrastructure with UNICORE
and ARC based Grid resources in the region; identifying and addressing
the specific needs of new scientific communities such as nano-science
and engineering sciences; and by establishing new Grid services for
linguistic research, Baltic Sea environmental research, data mining tools for
communication modelling and bioinformatics.
Programme details, and registration information, can be found here: http://
www.balticgrid.eu/3rd_AHM
NeSC News
www.nesc.ac.uk
Issue 74, October 2009
New Edinburgh Physics and Astronomy site
The new website for the School of Physics and
Astronomy at the University of Edinburgh (one of the
founding departments of the NeSC) went live on Monday
28 September.
But this is more than just a new website. It is the first
phase of a move to a shared web infrastructure which
will provide a more robust and easily maintainable set
of participating sites. Anna Kenway, project manager
of the web project and Deputy Director of the eSI says:
“This is an example of a School wide solution, which will
be supporting specialised institute websites, including
EPCC’s and eSI’s, in addition to the main School site,
with all sharing a common infrastructure and content
management system (CMS), and most importantly,
a web team working together rather than as lone
developers assigned to individual projects”.
The new site uses the open source CMS Drupal (http://drupal.org/) which was chosen for its wide range of features
and large development community. The new website can be seen at: http://www.ph.ed.ac.uk/
Elsevier launches Computational Science Journal: JoCS
management components (e.g.
problem solving environments).
Elsevier, a publisher of scientific,
technical and medical information
products and services, has
announced the launch of the Journal
of Computational Science, or JoCS.
The Journal of Computational
Science aims to be an international
platform to exchange novel research
results in simulation based science
across all scientific disciplines. It
publishes advanced innovative,
interdisciplinary research where
complex multi-scale, multi-domain
problems in science and engineering
are solved, integrating sophisticated
numerical methods, computation,
data, networks, and novel devices.
Computational Science is a rapidly
growing multi- and interdisciplinary
field that uses advanced computing
and data analysis to understand
and solve complex problems. It
has reached a level of predictive
capability that now firmly
complements the traditional pillars of
experimentation and theory.
The recent advances in experimental
techniques such as detectors, on-line
sensor networks and high-resolution
imaging techniques, have opened
up new windows into physical and
biological processes at many levels
of detail. The resulting data explosion
allows for detailed data driven
modeling and simulation.
This new discipline in science
combines computational thinking,
modern computational methods,
devices and collateral technologies
to address problems far beyond
the scope of traditional numerical
methods.
NeSC News
Computational science typically
unifies three distinct elements:
• Modeling, Algorithms and
Simulations (e.g. numerical and nonnumerical, discrete and continuous);
• Software developed to solve
science (e.g., biological, physical,
and social), engineering, medicine,
and humanities problems;
• Computer and information science
that develops and optimizes the
advanced system hardware,
software, networking, and data
The journal welcomes original,
unpublished high quality contributions
in the field of computational science
at large, addressing one or more of
the aforementioned elements.
“Submit your paper now,” say the
editors. “You can submit full papers,
short communications and letters.
The first four issues will get a lot of
international attention and the papers
will be freely available in Open
Access.”
More information is available
here: http://www.elsevier.com/
wps/find/journaldescription.cws_
home/721195/description#description
www.nesc.ac.uk
Issue 74, October 2009
New consortium to embed e-Research technology
By Simon Hettrick, OMII-UK
‘In the last twelve months, people
have begun to think differently about
e-Research technology’ says Anne
Trefethen, Director of e-Research
South, ‘maybe it’s the recession
causing people to make more of
the resources available to them,
or maybe we’re starting to see the
benefits of [e-Research] technology
maturing’. Whatever the reason, eResearch South are experiencing
significant interest in their mission to
embed e-Research technologies in
the research community.
The e-Research South consortium
was formed in October last year from
groups based at the STFC and the
universities of Oxford, Reading and
Southampton. Each of the groups
has developed specialist expertise
in a different area of e-Research,
and has been very successful in its
own right. By bringing the groups
together, e-Research South has
created a consortium with the
skills needed to apply innovative
computing technology to problems
experienced by research projects
from a broad range of disciplines
– from musicology to medicine.
Understanding the requirements of
projects from such a diverse range
of disciplines can be challenging.
The solution used by e-Research
South is to embed developers. An
embedded developer spends time
working as a member of the project,
learning about their research and the
technology they require. This leads
to a comprehensive understanding
of the project’s requirements, and an
e-Research solution that matches the
project’s needs.
One of the challenges for e-Research
has been a lack of understanding of
the (admittedly, very new) technology
in the wider research community.
However, the success of e-Research
South seems to indicate that this
challenge is being met.
NeSC News
‘We’re succeeding in both reaching
new audiences and in deeper
engagement with researchers across
a variety of disciplines’ describes
Anne ‘we now have people knocking
at our door who wouldn’t have done
so only twelve to eighteen months
ago… it’s sometimes hard to keep up
with the interest’.
www.eresearchsouth.ac.uk
Some of e-Research South’s projects
Smart Labs
Smart Labs covers a number
of projects that are using new
technology to improve the recording
of information generated by
researchers, and to automatically
capture information about the
laboratory environment and
equipment.
The CombeChem and e-Bank
projects have already made a
huge impact on the worldwide
crystallography community (the
initial demonstrator area) and the
dissemination of data. Smart Labs
will develop the work of these two
projects, and implement it in new
projects starting at the universities
of Oxford and Reading, and at the
STFC.
NeuroHub
The NeuroHub project will help
neuroscientists to conduct more
productive research. A set of tools
will be developed that will allow
neuroscientists to construct their own
environment for research information.
This will be tailored to their needs,
and presented through a web 2.0
access layer or a local application.
The framework and tools developed
by e-Research South will be the
product of in-depth analysis of user
requirements, adaptation of existing
software, development of key missing
components and a tight collaboration
between neuroscientists,
technologists and resource providers
at the universities of Oxford, Reading
and Southampton.
Water resources
Ensembles of hydrological models
will be used to determine how the
availability of water resources will
change in the future. The ensembles
are based on multiple scenarios of
future hydrological conditions, and
require significant computing power
to model. The Reading Campus
Grid has been used to help reduce
computation time from 21 days to 9
hours.
At its heart, this project seeks a
solution to a common problem with
Climate modelling on Grids: different
models predict different outcomes.
Once headway has been made on
this problem, the project intends to
implement their solution with other
climate-modelling projects.
www.nesc.ac.uk
Issue 74, October 2009
NGS makes the headlines at EGEE’09
Many of the NGS staff were recently in Barcelona for the EGEE ’09
conference (http://egee09.eu-egee.org/). The NGS was a major partner in
the UKI Federation stand which featured five of the UK and Irelands major
grid organisations – NGS, GridPP, OMII-UK, NeSC and Grid Ireland. The
exhibition stand was extremely busy with a great deal of interest being shown
in the work that is happening here in the UK.
Interest was helped by the NGS Technical Director, Dr David Wallom, giving a
keynote address on the NGS to a pretty packed room. David talked about the
current state of the NGS and also where we were headed as an organisation
given the move towards an EGI. He described the wide range of resources
that we offer our users and highlighted the large number of institutions who
have signed up to become members of the NGS, realising the importance of
giving their researchers access to as wide a range of resources as possible.
The range of research performed using NGS resources was also highlighted
with David talking about many of our popular use case examples. This was
a great opportunity for the NGS to be showcased to a European (and further
beyond) audience at an important event and we would like to thank the
organisers for giving the NGS this opportunity.
Hot off the press!
The latest edition of the NGS
newsletter, NGS News, is available
now from the NGS website (www.
ngs.ac.uk/newsletter).
This quarter’s issue contains
articles on how the NGS and
GridPP are working closely together
to prepare for the future, a report
back from the 5th International
Conference on e-Social Science
in Cologne and updates on what’s
new at the NGS.
We are always looking for
interesting articles for future editions
of the newsletter. If you have
anything to contribute or an idea
for a future article please contact
the NGS Liaison Officer (Gillian.
sinclair@manchester.ac.uk).
NeSC News
Summer school inspires scientists to use
the NGS
This month the NGS hosted the
Advanced Distributed Services
Summer School 2009 at
Cosener’s House in Abingdon. 15
scientists working in UK research
collaborations attended to learn how
to employ the distributed computing
facilities available to them in the UK
in their research.
Speakers included Steven Newhouse
from CERN, Katy Wolstencroft from
the University of Manchester, David
Fergusson from Edinburgh, David
Wallom from Oxford in addition
to speakers from STFC. Topics
addressed included distributed
computing resources available in the
UK including practical usage of the
NGS and SRB, as well as specialist
tools such as Taverna.
In addition to the technical activities,
highlights included a joint networking
event at Wadham College, Oxford
with e-Research South and
participants at the international
XtreemOS summerschool.
The organisers said that the event
“exceeded all expectations” while
student feedback included “very good
content, enjoyed practicals” and
“most liked the chance to network,
find ideas and hear developments”.
www.nesc.ac.uk
Issue 74, October 2009
BioCatalogue: a curated catalogue of Web
Services for the life sciences
By Franck Tanoh, OMII-UK
Estimates place the number of life
sciences Web Services at over
6000. With so many Web Services
available, many life scientists find
it difficult to locate the services that
would be useful in their research.
Hence, the launch this June of the
BioCatalogue.
The BioCatalogue allows life
scientists to easily locate Web
Services of interest, and keep track
of any changes that may occur over
the lifetime of the Web Service.
This will significantly accelerate
the work of scientists in fields
such as medicine, agronomy and
pharmacology. The BioCatalogue will
also enable a wider adoption of Web
Services, which have become crucial
for the integration of data resources
and tools in the life sciences.
Web Services are critical to the
effective linking of biological data and
computing resources, because they
enable complex querying, computing
and analysis to be performed on
biological data. This use of Web
Services has been identified by a
number of organisations, including
the EBI (European Bioinformatics
Institute), the NCBI (National Center
for Biotechnology Information) and
the DDBJ (DNA Data Bank of Japan).
All of these organisations now
provide Web Services to access and
analyse their resources.
Web Services may be a critical
resource, but they are not without
their drawbacks. They can be difficult
to locate, poorly described and poorly
documented. This lack of information,
especially that concerning the quality
of the Web Service, impedes the
wider adoption of Web Services
within the life science community.
The BioCatalogue will help scientists
to locate, register or annotate Web
Services. BioCatalogue also helps
scientists understand how to use
NeSC News
NeSC Public Lecture:
“Software Sustainability:
Looking Past the Myths”
the Web Service, and directs him
or her to useful information, such
as licences and restrictions. Web
Services are submitted to the
BioCatalogue and curated by service
providers, the community and expert
curators. Users of the catalogue
can add information about the Web
Services they have used by providing
feedback or comments, or they
can identify them for use by others
by tagging them, marking them as
favourite, or sharing them.
The BioCatalogue is a Ruby on Rails
application and follows the Web
2.0 principles of perpetual beta,
constant iteration, constant feedback
and constant improvement. The
BioCatalogue project leverages some
of its socio-technical elements from
the successful myExperiment project.
The BioCatalogue automatically
sources services and annotations
from existing registries, such
as BioMoby, seekda, feta,
programmableweb and Embrace. In
time, it will merge with the Embrace
registry, which was built as the
precursor to the BioCatalogue. The
functionalities of the catalogue
can easily be incorporated into
other applications through the
BioCatalogue API.
The BioCatalogue is more than
just a registry. It is a collaborative
environment where the community
can meet and contact the experts
that develop and use Web Services.
Carole Goble, one of the leaders of
the BioCatalogue project, describes
it as a ‘social gathering point for
crowd-sourced information about
the services.’ With over 1070 Web
Services and more than 100 users
recorded in the two months since
it came online, it appears that the
BioCatalogue is already drawing the
crowds.
www.biocatalogue.org
Neil Chue Hong
The National e-Science Centre will
host a public lecture by Neil Chue
Hong on October 29, at 4pm.
Sustainability is the ultimate goal for
any software. If a future for software
is not secured, the time and money
invested in its development is
wasted. With this level of importance
placed on sustainability, it is no
surprise that a number of myths have
sprung up around how to achieve it.
In this entertaining lecture, Neil
Chue Hong, Director of OMII-UK, will
challenge five myths that surround
the goal of software sustainability.
Neil will call upon OMII-UK’s long
history of working with projects
from the UK research community,
achieving software sustainability and
participating in sustainable projects.
After discussing the misconceptions
that led to the five sustainability
myths, Neil will describe OMIIUK’s route for achieving software
sustainability through engagement
with the research community.
The public lecture is open to all
interested parties in academia and
industry. There is no need to register
and those attending are invited to join
the team for tea and coffee at 17:00.
This Public Lecture is scheduled
to be webcast live. The link to the
webcast will appear one hour before
the meeting / webcast is due to be
broadcast.
www.nesc.ac.uk
Issue 74, October 2009
EGI Council elects chair
Per Öster, representative of the Finnish National Grid Initiative (NGI),
was chosen by the European Grid Initiative (EGI) Council members to
lead the project’s governing body.
This election constitutes another important step towards the
implementation of the EGI, which aims to establish a sustainable grid
service for the European scientific communities. This will be achieved
through the creation of a long-term, pan-European grid infrastructure.
A new legal entity (EGI.eu) is currently being established in
Amsterdam, and will act as the
coordinating body for EGI. Its main role will be to facilitate the
interaction and collaboration between the national grid infrastructures
of the different participating countries. Together EGI.eu and the NGIs
will operate and further develop the pan-European grid infrastructure,
in order to guarantee its longterm availability for performing research
and innovative work.
The EGI Council, which is made up of NGIs as well as other members
such as European institutions represented in the EIROforum will
Per Öster
govern the direction of the EGI collaboration on a long term basis, and
is therefore one of the key bodies in the EGI.
Per Öster has been working since 2007 as Director of Application Services at CSC, the Finnish IT
Center for Science. He has been also actively involved in the EGI Design Study (EGI_DS), in which he has been
responsible for the EGI promotion and links with other initiatives. In his statement to the Council members, Öster
emphasised the importance of creating a working atmosphere based on trust and transparency, and setting up good
working principles, in order that the Council can carry out its mission efficiently, and meet the future challenges.
“In the next few months, important tasks await the EGI Council, including ensuring the success of the EGI proposal
to the European Commission and establishing the EGI.eu organisation”, Öster said. “EGI is a fantastic opportunity
not only for scientific collaboration but also to make the latest and most advanced computing resources, applications,
tools, and data available to all European researchers. It is a great honour to me to be able to contribute to it as chair of
the EGI Council.”
More information: www.eu-egi.eu, press@eu-egi.eu
Introduction to Implementing Ontologies in the Web Ontology Language (OWL)
BioHealth Informatics group at
the University of Manchester
in partnership with NWeHealth
invite you to participate in the
internationally renowned OWL
Ontology tutorials, at the University
of Manchester on November 11-12,
2009.
This introductory ‘hands-on’
workshop aims to provide attendees
with both the theoretical foundations
and practical experience to begin
building OWL ontologies using the
latest version of the Protégé-OWL
tools (Protege4). It is based on
Manchester’s well-known “Pizza
tutorial” (see http://www.co-ode.org).
NeSC News
This tutorial will cover the main
conceptual parts of OWL through the
hands-on building of an ontology of
pizzas and their ingredients. A series
of exercises take attendees through
the process of conceptualizing the
toppings found on a pizza; the entry
of this classification into the Protégé
environment; the description of
many types of pizza. All this is set
in the context of using automatic
reasoning to check the consistency
of the growing ontology and to use
the reasoner to make queries about
pizzas. Since 2003 this tutorial, in
various forms, has been given over
20 times and been attended by
hundreds of budding ontologists.
The aims of this tutorial are to:
understand the use of ontologies,
understand statements written
in OWL; understand the role of
automatic reasoning in ontology
building; build an ontology and use
a reasoner to draw inferences based
on that ontology; gain experience
in the Protégé 4 ontology building
environment; and gain insight into
how OWL can play a role in semantic
metadata.
To register, and for further information
for advertised tutorials, please visit
the CO-ODE website at: http://www.
nweh.org.uk/ViewCourses.aspx
www.nesc.ac.uk
Issue 74, October 2009
Cyprus Insitute Job Opportunities
The Cyprus Institute (www.cyi.ac.cy) is a novel, non-profit research and educational institution, with a scientific
and technological orientation, pursuing issues of regional importance and of global significance in the Eastern
Mediterranean, the Middle East and North Africa.
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for the Computation-based Science and Technology Research Center
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Project Manager for the Computation-based Science and Technology Research Center (CaSToRC) - CaSToRC-09-03
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Computational Scientist to work in atmospheric and climate modelling Computation-based Science and Technology
Research Center (CaSToRC) - CaSToRC-09-05 http://www.cyi.ac.cy/node/477
For further information, the full job descriptions and salary details please contact castorc.info@cyi.ac.cy.
For full consideration, interested applicants should send a CV, a sample of their work and the names of three
contactable referees by e-mail to HR@cyi.ac.cy Recruitment will continue until the positions are filled.
Forthcoming Events Timetable
October
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
“Software Sustainability: Looking Past the NeSC
Myths” by Neil Chue Hong
http://www.nesc.ac.uk/esi/events/1017/
The impact and influence of Web 2.0based Services on e-Research
http://www.nesc.ac.uk/esi/events/1007/
November
3-4
eSI
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 November 2009 issue is October 16, 2009
NeSC News
www.nesc.ac.uk