Supporting crossover between quantitative modelling
communities: final report
Muffy Calder∗,
Stephen Gilmore†,
Jane Hillston‡
February 25, 2008
1
Background
QEST is the leading international forum on
evaluation and verification of computer systems and networks, through stochastic models
and measurements, possibly incorporating nondeterministic behaviour. Quantitative properties
of interest include performance, reliability, availability, safety, security, survivability, correctness,
timeliness, and efficiency. Topics covered included
modelling formalisms and methodologies, measurements, analytical and numerical evaluation,
simulation and verification, and theory of probabilistic systems, as well as case studies showing
the role of quantitative evaluation in the design
of systems including computer architectures, distributed and fault tolerant systems, communication systems, embedded systems, web-based systems, safety-critical systems, tools and tool applications.
The meeting in Edinburgh in 2007 was the
fourth in the series. QEST 2006 was held in Riverside, California, USA. QEST 2005, was in Torino,
Italy. The inaugural meeting was QEST 2004 in Enschede, The Netherlands.
The invited speakers for QEST 2007 were:
This grant was to support the first co-located meeting between leading quantitative modelling conferences in systems biology and theoretical computer science.
Two major conferences in quantitative modelling — QEST and CMSB — met together for
the first time in Edinburgh in September 2007.
The QEST conference has as its focus performance
evaluation of computer and telecommunication
systems. The CMSB conference addresses the systems approach to computational biology in the application of stochastic simulation and numerical
integration to aid the understanding of the functioning of biological processes.
Despite the apparent difference in outlook, these
two scientific domains have much to offer each
other and first steps have been taken to transfer
ideas from one community to the other. The colocation of these two conferences in Edinburgh
(QEST at the beginning of the week, CMSB towards the end) offered a unique opportunity for
post-graduate training in this important area, and
for a meeting of two like-minded, but separate, research communities. Co-location enabled a significant number of researchers to attend both conferences.
2
2.1
• Luca Cardelli, Microsoft Research, Cambridge
• Robert Givan, Purdue University
• Jean-Yves Le Boudec, EPFL, Lausanne
The QEST 2007 meeting in Edinburgh also received sponsorship from the British Computer Society to the value of £1,000.
The QEST 2007 conference website is on-line at
http://www.qest.org/qest2007/.
The QEST 2007 conference was attended by 91
researchers.
The conferences
Quantitative Evaluation of SysTems (QEST)
The QEST 2007 conference took place in Edinburgh on 16th–19th September 2007. The general
chair was Professor Jane Hillston. The programme
chairs were Professors Marta Kwiatkowska (UK),
Mor Harchol-Balter (USA) and Miklos Telek (Hungary).
2.2
Computational Methods in Systems Biology (CMSB)
The CMSB 2007 conference took place in Edinburgh on 20th–21st September 2007. The co-chairs
∗ Department of Computing Science, University of Glasgow,
were Professor Muffy Calder and Dr Stephen
Glasgow
Gilmore.
† LFCS, School of Informatics, University of Edinburgh, EdCMSB is an international conference on Systems
inburgh
‡ LFCS, School of Informatics, University of Edinburgh, EdBiology with emphasis on computer science asinburgh
pects, in particular programming languages and
1
3.2
logical formalisms for describing, modelling, simulating and analysing cellular pathways (e.g., signalling, metabolic and control), and higher-level
aspects, such as intercellular signalling or development.
Topics covered included the application of formal methods to analyse biomolecular systems
such as formal models for regulatory, signalling or
metabolic networks. Both qualitative or quantitative analyses of biomolecular systems were considered, with quantitative models expressed in
differential, discrete and/or stochastic modellinglanguage frameworks. We note that numerical
evaluation of stochastic process models was covered in both CMSB and QEST.
CMSB 2007 was the fifth in this series of conferences. CMSB 2006 was held at the Microsoft
Research–University of Trento Centre for Computational and Systems Biology in Trento, Italy.
CMSB 2005 was co-located with the ETAPS computer science conference in Edinburgh, Scotland,
chaired by Gordon Plotkin. The 2004 event was
held in Paris under the joint chairmanships of Vincent Danos and Vincent Schachter. The inaugural
meeting was the 2003 event in Trento, under the
chairmanship of Corrado Priami.
The invited speakers for CMSB 2007 were:
Proceedings of the conference were published
by Springer in the Lecture Notes in Bioinformatics
(LNBI) series: Computational Methods in Systems Biology, International Conference CMSB 2007, Edinburgh, Scotland, September 2007 Proceedings,
Muffy Calder, Stephen Gilmore (Eds.), LNBI volume 4695, 2007.
A special issue of Theoretical Computer Science
(Series C) has been agreed and is currently in
preparation. The volume will include 6 invited papers, 1 paper from an invited speaker (Girolomi)
and an overview paper by Calder and Gilmore.
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• Mark Girolami, University of Glasgow
The CMSB conference also received sponsorship
from the e-Science Institute (to the value of £2,600
for speaker costs) and Microsoft Research, Cambridge (to the value of £1,000).
The CMSB 2007 conference website is online at http://conferences.inf.ed.ac.uk/
cmsb07.
The CMSB 2007 conference was attended by 85
researchers.
3.1
Research impact and benefit to
society
A significant outcome of this support was that it
allowed Dr Dan Gillespie to spend some time in
the UK. Gillespie is a remarkable scientist who did
seminal work on a stochastic algorithm for chemical reactions in the 1970’s. His work is now highly
relevant to systems biology and it was a privilege
to hear him talk about his original work and subsequent refinements (he is now retired, but this
appears to be a theoretical concept!). Not only
did he make a huge impact on his audience at
the CMSB conference talk but he attended every
single talk and engaged in numerous discussions
with researchers (so much so that he kept missing
lunch). Furthermore, he gave well publicised and
well attended seminars at Edinburgh and Strathclyde Universities.
The other direct beneficiaries of this grant were
the PhD students who had their experience of the
scope and application of quantitative methods enriched, and their horizons widened to encompass
applications of stochastic and quantitative modelling in other disciplines. The future economic
and social prosperity of the UK depends on having a substantial pool of post-graduates and researchers with interdisciplinary skills.
• Daniel T. Gillespie, Dan T. Gillespie Consulting,
Castaic, California
3
CMSB
Dissemination
QEST
Proceedings of the conference were published by
IEEE Computer Society Press as Fourth International Conference on the Quantitative Evaluation of
Systems, Mor Harchol-Balter, Marta Kwiatkowska
and Miklos Telek (Eds.), 2007.
Following on from the conference, a special issue of IEEE Transactions on Software Engineering
on Quantitative Evaluation of Computer Systems is
in preparation. The guest editors for the issue
are Jane Hillston, Marta Kwiatkowska and Miklos
Telek. Submission for the special issue closed in
mid-January. Papers are presently under review.
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Explanation of expenditure
Costs were for speakers, PhD students, and a joint
conference reception. Actual expenditure was
pretty much as planned, although some virement
across headings was necessary to allow Gillespie’s
extended visit. Note that each conference had one
invited speaker from USA and one from Europe.
The joint reception was held in the Fellow’s Library, Royal College of Surgeons, Edinburgh. It
was extremely well attended by both communities
2
and provided a good opportunity for informal discussion.
5.1
ally because an academic at the university was a
member of the conference programme committee
or steering committee. Usually, that member of the
academic staff was the PhD supervisor of the student who was applying.
Awards of QEST and CMSB Student Bursaries
5.1.3
We wanted to check about the allowability of these
on the EPSRC grant so we contacted Pamela Mason at EPSRC by telephone on 3rd July 2007. She
informed us that we could award bursaries to any
student irrespective of funding source and nationality but that the EPSRC would prefer that we
prioritised EPRSC students over non-EPSRC first,
and then after that UK over non-UK (but it is still
perfectly OK to award a bursary to a non-UK student). The meaning of “prioritise” here is to decide in favour of the UK student (say) in preference to an otherwise equal student from France
(say), not that all EPSRC and UK applications must
be funded irrespective of merit before any non-UK
application is considered. We acted on this advice
in assigning bursaries.
5.1.1
We received three applications where we decided
not to award any funds. This information is detailed in Table 5. In these cases there was no evident connection between the academic institution
and the conferences or between the research work
of the PhD students and the academic subjects of
interest to the conferences. None of the above students submitted a paper to either conference, so
we had no clear evidence of interest. Geographic
distance was also an important factor in these applications, with travel costs being so high that we
were not sure that the applicants could bear these
costs themselves. We were also running short of
funds at this stage, due to following the agreed
policy of prioritising EPSRC-funded students first,
UK-based students second, and others last.
Applications from UK students
5.1.4
We received five applications from students currently in receipt of EPSRC funding, and made the
awards of bursaries indicated in Table 1.
We received nine applications from students not
currently in receipt of EPSRC funding, but studying for PhDs at UK universities. These applications are detailed in Table 2.
5.1.2
Applications not funded
Summary of expenditure on student bursaries
We are confident that no EPSRC or UK student
has been disadvantaged. The assignments of bursaries have taken account of location in that (for
example) accommodation costs are not paid to any
Edinburgh applicant (because they already have a
residence in Edinburgh). Where the amount spent
on accommodation was less than the amount of
the bursary we agreed to pay reasonable subsistence costs to the students up to the value of the
award made. The summary statistics are as follows.
Applications from non-UK students
We received seven applications from students
studying for PhDs outside the UK. We supplemented these bursary awards with sponsorship
money obtained from the British Computer Society (BCS) for the QEST conference and sponsorship money obtained from Microsoft Research,
Cambridge (Microsoft) for the CMSB conference.
In three cases (McQuinn, Pradalier, and Rizk below) these students were co-authors of a paper accepted to one or other of the conferences. A further three of these applications came from students
who had a poster accepted at QEST (Dinulescu,
Remke and Taylor). This is very clear evidence
of interest in the subject matter of the conferences.
Our award to Schabauer was declined by him after
his plans changed.
Applications from non-UK students in Europe
are shown in Table 3. Applications from non-UK
students outside Europe are shown in Table 4.
All of the students who accepted our bursary
awards came from good academic institutions
where there was a clear connection to the communities of the QEST and CMSB conferences, usu-
Bursaries for attendance at QEST only
Bursaries for attendance at CMSB only
Joint bursaries for attendance at both
Total available from grant to spend:
Total spend on student bursaries:
10
9
3
£7450
£7390
Because the conferences are located in Edinburgh
they are very convenient and therefore naturally
attractive to students who are presently studying
in Edinburgh. Consequently more bursary applications came from Edinburgh than from any other
city. However, the grant holders wish to point out
that none of the students who received bursaries
are supervised by any of the grant holders. The
grant holders intended the money to be used to
grow the quantitative modelling community and
to increase participation at the conferences from
outside the existing community, and therefore instructed their own students not to apply for bursaries.
3
Student
Chen, Chih-Chun
Affiliation
UCL, UK
Komorowski,
Michal
Kwiatkowski,
Marek
Warwick,
UK
Edinburgh,
UK
Murphy, Elaine
Edinburgh,
UK
Imperial,
UK
Wagner, Daniel
Applied to
QEST CMSB
X
X
X
X
X
Awarded
CMSB student registration (£170) plus accommodation (£150)
CMSB student registration (£170) plus accommodation (£150)
QEST tutorial registration (£75) plus QEST
student registration (£285) plus CMSB student registration (£170)
CMSB student registration (£170)
QEST tutorial registration (£75) plus QEST
student registration (£285) plus accommodation (£200)
Subtotal of EPSRC spend: £1900
X
Table 1: Applications from EPSRC-funded students
Student
Bergmann, Daniel
Affiliation
Nottingham
Gkargkas,
Konstantinos
Gorry, Benjamin
Manchester
Applied to
QEST CMSB
X
X
X
Kalapanulak,
Saowalak
Pedersen, Michael
HeriotWatt, Edinburgh
HeriotWatt, Edinburgh
Edinburgh
Edinburgh
X
Rutkowski, Michał
Warwick
X
Saithong, Treenut
Trivedi, Ashutosh
Edinburgh
Warwick
X
Grov, Gudmund
X
Awarded
CMSB student registration (£170) plus accommodation (£150)
CMSB student registration (£170) plus accommodation (£150)
QEST tutorial registration (£75) plus QEST
student registration (£285)
QEST tutorial registration (£75) plus QEST
student registration (£285)
X
CMSB student registration (£170)
X
QEST tutorial registration (£75) plus QEST
student registration (£285) plus CMSB student registration (£170)
QEST tutorial registration (£75) plus QEST
student registration (£285) plus accommodation (£200)
CMSB student registration (£170)
QEST tutorial registration (£75) plus QEST
student registration (£285) plus accommodation (£200)
Subtotal of EPSRC spend: £3350
X
Table 2: Applications from non-EPSRC funded students in the UK
4
Student
Pradalier, Sylvian
Affiliation
Paris,
France
Remke, Anne
Twente,
Netherlands
Rizk, Aurélien
Paris,
France
Vienna,
Austria
Schabauer, Hannes
Applied to
QEST CMSB
X
X
X
X
X
Awarded
QEST tutorial registration (£75) plus QEST
student registration (£285) plus CMSB student registration (£170) [plus accommodation (£300, Microsoft)]
QEST tutorial registration (£75) plus QEST
student registration (£285) [plus accommodation (£200, BCS)]
CMSB student registration (£170) [plus accommodation (£200, Microsoft)]
Award declined by student
Subtotal of EPSRC spend: £1060
Table 3: Applications from non-UK students in Europe
Applied to
QEST CMSB
X
Student
Dinulescu, Monica
Affiliation
McGill,
Canada
McQuinn, Michael
Illinois,
USA
X
Taylor, Jonathan
McGill,
Canada
X
Awarded
QEST tutorial registration (£75) plus QEST
student registration (£285) [plus accommodation (£200, BCS)]
QEST tutorial registration (£75) plus QEST
student registration (£285) [plus accommodation (£200, BCS)]
QEST tutorial registration (£75) plus QEST
student registration (£285) [plus accommodation (£200, BCS)]
Subtotal of EPSRC spend: £1080
Table 4: Applications from non-UK students outside Europe
Student
Baig, Mirza Saqib
Affiliation
CDRI, India
Issa, Ntegeka
IICT,
Uganda
CDRI, India
Saeed, Uzma
Applied to
QEST
CMSB
X
X
Awarded
No award
Application
incomplete
No award
X
No award
X
Subtotal of EPSRC spend: £0
Table 5: Applications which were not funded
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6
Further activities
Following the success of both conferences, they
will be held again: QEST in September 2008 in St.
Malo, France and CSMB in October 2008 in Rostock, Germany. One of the invited speakers at
CMSB 2008 will be Jane Hillston.
6