Coordinator:
Prof. Richard Villems
E-mail: rvillems@ebc.ee
Project duration: 01.02.03-01.02.06
EU funding: nearly 300 000 EUR
Estonian Biocentre has participated in the call for centres of
excellence within the INCO 2 package of FP5. Our proposal, titled
as Geneticists for the
Next Millennium (Genemill), was placed 3-5 during the evaluation
and we have received financing. While we now discussed among ourselves
whether to participate in a somewhat similar call, we first hesitated:
the named project is still ongoing and we have not yet exhausted
its possibilities. Probably, we thought, a repeated competition
may be seen as an attempt to become a sort of permanent salesman
of the same bag, wherever and whenever there is a market. Yet we
have decided to participate. Why did we change our mind?
First and foremost, the previous application was prepared more
than 2 years ago. Then, not much was known about the next FP and
the European Research Area initiative was in its embryonic stage.
And although the very final documents about the rules for the FP6
are not approved yet by the EP and by the Council, many and probably
the most essential aspects of it have became clear. Directly relevant
here is a turn from the financing of limited in scale joint research
projects, to networks of excellence and to integrated projects.
Bearing that in mind, we asked our international advisory board,
together with us (i.e. the local steering committee), to look over
the goals an aims ('workpackages") in our ongoing project,
as well as other developments during the last two years, in order
to make recommendations. The recommendation was to participate in
this competition. More specifically, it was pointed out by the board
that while the instruments of the ongoing project are, so to say,
overwhelmingly self-centred and in a way fragmented, the challenges
ahead need more clearly, say, even more narrowly, targeted actions.
In other words - to cover less different general activities, but
to make a clear stress to the networking with the excellence in
the field of life sciences and technologies. Primarily with the
excellence in Europe, but also keeping a close eye to the best in
US and, possibly, elsewhere. As the Advisory Board concluded:
carry on as you have done so far - look to excellence in abroad
and in directions where you have reached a real working collaboration
on equal footing, your own work is very likely excellent as well.
You will see that in the field of basic science and, sometimes even
more clearly, where you attract industrial partnership and private
resources in general. This, likely, will be your way into the ERA.
These recommendations of the Board led us to the understanding
that there is in fact not much use in copying the instruments of
the previous proposal: there is a need for new concepts. Furthermore,
it was now possible to capitalize from a significantly wider and
deeper long-term collaboration with different research centres and
industrial partners than 2-3 years ago. Notably, thanks to joint
research projects of FP5 we are involved in (or plan shortly to
join), but not at all only. The ongoing INCO 2 excellence centres
project opened additional possibilities, whereas rapid growth of
our spin-offs has opened altogether different directions and dimensions.
The third argument (or, rather, several such arguments) for the
participation can be seen as "local", but we have considered
it equally seriously. "Seriously" is a right word here
because all relatively large-scale projects like that, addressed
to not-so-prosperous conditions, rise a legitimate question - what
happens when the project is over? Say - you use your money to attract
lots of nice fellows, good lecturers etc. and, when it is over after
3 years or so, they pack up and leave - probably with the best among
your grad students. Let us here limit with a statement that although
we understand this sort of fears, our now already almost 10-year
experience makes us rather immune against them; we return to this
issue in more depth below (see also B4 and, in
particular, subsection C4).
Here, however, we briefly try to explain a relevant, but a more
general "Estonian-centred" point, why we believe that
the R&D activities of the Estonian Biocentre, and of this proposal,
are in a focus of the strategic vision of Estonia for the future
of R&D in this country and an additional guarantee for a sustainable
development. Namely, in December, 2001, Estonian Parliament approved
the presented by the Government "white book on R&D"
for Estonia for the next 4 year period (electronic version in English
is available at the www site of the Estonian R&D Council at
the Prime Minister: www.tan.ee).
It is the first such level R&D document for our country: former
versions have been governmental position papers, not legally binding
to any new administration. Only three "key areas" in the
field of R&D are now defined for Estonia, one of them being
biotechnology and, in its more detailed description, with a stress
on genomics and on molecular medicine in general - for healthcare
and industrial innovation. Its explanatory chapter includes also
gene technologies to be used to improve the quality of the environment.
This rather complex document foresees organisational and financial
means to be used by the administration to achieve the named goals.
We mention it here in order to demonstrate that: (i) the current
project fulfils, in the most direct sense, one of the criteria for
the current call: relevance for the economy and/or the society
of NAS, listed under section C8 and (ii) also because strategic
decisions made in Estonia give an additional "insurance"
for sustainability of undertakings in the field of biomedical R&D
in this country.
It is worthwhile to add that the same document is now used as a
blueprint for relevant chapters in a new version of the Estonian
National Development Plan (referred now as Single Planning Document),
currently under preparation and to be presented to, and get approved
by, the EU, as a basis to distribute the Structural Funds of the
EU in future.
Finally, we trust that the overall spirit and the key positions
of our proposal are in a good conformity with the discussed earlier
in length and approved by the European Commission on 23.01.2002
a comprehensive plan for the development of life sciences and
biotechnology in Europe.
All these diverse components, taken together, convinced us to submit
the current proposal. From the Genemill proposal, we kept a central
introductory principle, defined as: this proposal is not to carry
out any particular scientific enquiry, neither developmental work
directly, because we have adequate means for that from different
sources.
Here we add: This proposal is to extend and to make more
efficient a platform for a successful entering of the Estonian Biocentre
into the European Research Area - in our particular field.
This is the objective of the proposal, further explained
as follows.
This single general objective covers different components. Instruments
for it (work packages) are outlined elsewhere in the proposal (section
B4). Although one may think about a long list of aspects indirectly
influencing successful participation of the Estonian Biocentre in
the ERA, many of them are beyond our effective control, there are
several, what we can affect and out of them we selected those
where an additional temporarily available resources can make a significant
difference.
Under "a platform" we keep in mind a variety of components,
depending primarily from us, like attractive research themes, good
equipment and premises and an adequate research support, efficient
electronic network and access to literature, friendly atmosphere
etc.
While seeking support under current call, our strategy to make
this platform more efficient, foresees many undertakings outside
this support scheme. In a way, they can be viewed as matching costs
above the usual research and teaching support, either national or
international. They include, in Summer 2002, a profound reconstruction
of premises for bioinformatics (planned 0.6 MEUR for construction
works and 0.2 MEUR for additional network equipment). It also includes
final planning of the third stage of the lab complex, possibly also
the beginning of its construction (about 3500 sq.m) within the next
3 years. An additional 1 MUSD recently received for sending our
postdocs abroad may be also viewed as "building a platform".
Thus, our sub-objectives are:
to build twinning relations with (a limited list of) scientific
institutions of recognized European and world level excellence
in research;
to open research themes and positions in EBC for an international
competition and to internationalise our graduate school.
to gather recognition as being among the leaders in the field
by organizing a continuous system of international/regional seminars,
hands-on training courses and workshops.
There seems to be a strong political will in the European Union
that quite a few associated countries will receive a call to join
the EU soon. Current political decisions of the member states suggest
that it should happen so that citizens of these countries may participate
in EP elections in 2004. In this sense it is seems that non of the
listed objectives would likely face setbacks for reasons outside
our control.
What, then, may be seen as problematic? Indeed, here is a question
about the objective. The ERA does not exist, so one cannot
enter it. At least not yet. Therefore, it would be more proper to
say that the proposal is an element, albeit a very small one, of
the creating of the ERA. Nevertheless, we can speak about FP6 and
our success in participation in its main instruments, as about a
verifiable indicator, but here the time horizon appears to be wider
than the duration of this call. On the other hand, the sub-objectives,
reflecting the content of work packages, are individually verifiable
and, together with many other necessary components would hopefully
create a synergistic effect expected. In particular, we view the
proposed twinning scheme as a beginning of organizing networking
of excellence under common research programme.
The European Research Area is itself
a new innovative concept and its development an evolutionary process,
needing also quite a few small revolutions in the attitude of not
only of the member state governments, but their research councils
as well, since they, by and large, represent fairly well scientists
of the countries. It would be a long way to go. But it starts now,
with FP6. Yet it would be a gross overestimation to say that because
of the innovative nature of the ERA, our particular approach here
is ipse facto automatically innovative. The first (sub)objective
- twinning with known centres of excellence, is innovative in our
concrete context but not necessarily in principle - good labs do collaborate
extensively anyway, including across borders. So do we as well, and
not only through FPs.
However, usually this sort of collaboration is project-based and
short-living. If to take a careful look to the new Finnish centres
of excellence, launched this January for a 6 year period, then there,
one may perhaps see arrangements, more close to the "twinning":
different research units from different universities agreed to collaborate
on the basis of relatively long programs, not just projects. There
may be examples like that elsewhere. In this sense our twinning
schemes may be considered innovative, though not original.
There is nothing innovative in our proposal to achieve opening
of research positions, including top positions, to international
competition - just a common practice in many EU countries, though
not in all. Yet it is quite innovative in Estonian conditions -
if not necessarily in words, then certainly so in practice. It should
be done, but per se it is but a remote prerequisite for the
ERA. The same concerns opening grad studies and postdocs positions
(and here we have already some positive experience): funds available
for mobility can be considered here as a vital component.
More innovative would be to test approaches for the opening of
long-term national research themes internationally. We are well
aware that this issue is currently debated quite extensively (e.g
in a recent issue of Science by G. Radda from MRC, EL. Winnaker
from DFG and H. Wigzell from Karolinska) and we are quite willing
to test it, e.g., at the level of the Estonian Gene Heritage program.
Possibly in some other close-to-industry projects as well - limiting
it here to the margin of pre-competitive applied biomedical research,
e.g. in DNA vaccines. Of course, the present proposal can only be
seen as a small-scale pilot in this direction.
In sum, a benevolent reader may hopefully see certain innovative
aspects in this proposal. Here, we keep in mind the instruments
to be applied, not science itself. There, we trust, an innovative
nature of our research and developmental work is less foggy.
The current work plan consists
of 4 work packages and is structured along the main activities of
the proposed project. Those activities will be carried out by targeted
measures. The proposed 4 work packages will help the centre to achieve
the objectives of the proposal, described above. The total funding
and time effort of all work packages is indicated in the cost summary.
Part of the main rationale of the work packages can
be described as "to see as well as to be seen": they address
using different instruments, our capacity to function efficiently
as a partner in the European Research Area. All four work packages
serve the same objective in different ways.
The first of them is the most traditional, opening
new possibilities for learning and serious intellectual contacts.
European genetics is not any longer what it was 30 years ago: the
number of excellent groups has increased very significantly and
new innovative methods of analysis are now coming from many centres
of different countries. This is why WP1 identifies of certain methods
of a specific value for the Estonian Biocentre and lists European
centres of advanced knowledge in the corresponding specific problems.
Again - neither of the lists should be taken as closed: the field
is very dynamic and new knowledge generated in a large number of
labs.
WP2 is quite different: its implementation may seem
business as usual for many advanced centres where all positions
are open for international competition, but it would be a big change
in a CEEC environment. However, this change in policy is not "abstract"
- its real aim is to facilitate opening of our long-term research
and development programs for European researchers. We bear in mind
Estonian Gene Heritage project, as well as our long-term projects
in other directions. The other idea behind this WP is to create
means for opening new directions much faster, by recruiting specialists,
active and experienced in a particular profile. They, in turn, will
have local young researchers and grad students growing under his/her
guidance. Junior positions are meant, in classical way, for postdoc
level applicants, who, also working as a part of a research team,
will have his/her own research plan and freedom within it. Senior
positions are planned for a particular field where the Centre seeks
for experts in a certain field of research/developmental area, where
such an expertise is needed for strengthening the position of the
Centre, its general R&D directions. In addition to finances
available from the project, the Centre will take a commitment to
guarantee, both for junior and senior positions, adequate means
for successful scientific work. Senior positions are maximum for
two years under this project, but the contract with the Centre can
be extended after this period using already different financial
sources.
WP3 - the twinning scheme - differs from both WP1
and 2 in a sense that it does not address any longer any special
know-how, method or project and does not rely that much on a concrete
person as such. Instead, it is aimed to build up long-lasting collaboration
with centres of excellence in research in areas, overlapping with
our strategic interests and where, as we believe, our own knowledge
is on the level what may make us partners for advancing an important
for European life sciences direction. Thus, it seeks not for projects
but for common programs where the partnership would allow a much
more powerful approach. It is also clear that such partnerships
cannot be build up from zero level within a period of a few years.
Therefore, this partnership is selected bearing in mind two criteria:
twinning partners must be top quality research centres and there
should have been real positive collaboration experience already.
Scientific reputation of the Sanger Centre, Cambridge University,
DKFZ and the two Italian centres of excellence in genetics hopefully
do not need advertising. Some of the listed twinning partners (Sanger
Centre, DKFZ) are large or very large research establishments with
diverse research programs. It should be understood that in this
case "twinning" covers only a subset of such large centres.
One may be a bit surprised seeing in this list an archaeological
institute (U. of Cambridge), but it happens to be so that this institute
became, within the last decade, one of the leaders in Europe in
the understanding of genetic history of modern humans (calling it
"archaeogenetics"): it turned now out that approaches
developed there (though not only there of course) turned out to
be of specific value also in the search for gene combinations behind
disease phenotypes.
WP4 may seem again more traditional and in a way
it is indeed. However, note that a significant part of it is covered
by hands-on training courses/seminars: the aim of them is to combine
here an advanced international lecture course with training in advanced
methods, where the elements of the latter have been developed "in
situ" - i.e locally. Hence, in rather direct way such courses
serve as an advert for our know-how and would, hopefully, facilitate
export capacity of our emerging biotech. Larger conferences are
well in the fields of general interest and there is little doubt
that they will be attended enthusiastically all over Europe and
from elsewhere. In fact, there is already certain pressure on us
to organize such meetings -e.g. to prolong successful GeneForum
series: this proposal would greatly help their organisation. And
there is a specifically valuable for us long-term strategy aspect
in it - bringing together genetics, ethics and entrepreneurship
at its best and opening such forums to a wide local audience as
well. It continues our ongoing effort to rise public awareness and
help them to formulate an informed consent in modern genetics, where
we have hold and continue to organise (co-organise and co-finance
with Estonian TV) TV debates, issue "Gene News" as a free
add to a major daily, publish books, including those for children
from the age of 7 - 10 years, etc. And we must admit that here,
the Estonian Government, Ministry of Social Affairs in particular,
has been very understanding and supportive. This traditional activity
of the EBC, also "bolstered" by applying, within the FP5,
to joint grants in the field of bioethics, will continue. It may
be added here that WP4 is not exhausting bi- and multilateral seminars/workshops
activity of the Centre: many such events have been, are, and will
be organised in coming years, often in quite informal basis, at
the level of workgroups, gathering together interested specialists.
Above (in B2), we have used a term "an efficient
platform" to enter the European Research Area. We are quite
convinced that fulfilment of the planned activities would indeed
make such a platform more efficient. Furthermore, we are also sure
that the change generated would be sustainable: Estonian academic
and applied research in molecular medicine is in a fast growth phase,
both public and private resources have increased significantly and
this tendency continues. Ideas what seemed beyond reasonable five
years ago, are at present in a phase of execution or at least advanced
planning. These ideas cover not just technologies but also rapid
growth in intellectual capacity. And we do not keep all eggs in
one basket - several parallel activities increase chances for a
continuous progress. The "platform building" has many
aspects and developments in different directions, beyond those covered
by the instruments proposed in this project.
Summing up, the following work packages are
proposed: · WP1 - Capacity building through know-how transfer and mobility
· WP2 - Opening Centre for European Research Area
· WP3 - Building Twinning Relations for the Networking of _______Excellence
· WP4 - Thematic conference and workshops
All measures proposed in this work plan will help
to: Increase our networking with
leading European research ___centres
Increase focusing our activities in terms of thematic
and ___regional coverage
Increase our human capacity, with particular attention
on ___young researchers
Increase our links and joint initiatives with social and
economic ___spheres of Estonia
Increase our participation in the forthcoming 6th Framework
___programme
Work
package number and title
WP1:
Capacity building through know-how transfer and mobility Type of activity : VR, CO
Relative start month: 0
Timetable: 36 months (0-36)
Objectives:
This work package aims at strengthening the human
potential and research capacity of the Centre through relevant know-how
transfer and outward short and medium term mobility of young and experienced
researchers from the Centre. In particular, we would like to facilitate
the training of our post-doctoral and PhD students at leading European
Research institutions.
Description of the contents, the
workplan, the steps, the approach or the methodology:
This work package includes measures related to short
and medium term outward mobility of our researchers. Researchers
from the centre will visit leading European research institutions
for a minimum period of 1 week and up to 1 year. The principle approach
would be that the more senior is the rank of researcher the shorter
is his/her stay at a given European research centre and thus more
junior researcher will stay abroad for a longer period. We however
consider that staying away for more than 1 year might already lead
to potential brain drain rather than expected know-how transfer.
Based on development objectives and thematic priorities of the Centre,
the following thematic fields are of particular interest for know-how
transfer and outward mobility:
development of algorithms to handle very
large data sets in genome-wide STR analysis; defining disease-associated
haplogroups and haplotypes
development of relational d-bases, bringing together
phenotypes, genotypes, "expressotypes" etc.
executing large-scale epidemiological studies
new approaches in establishing networks of protein
interactions in a living cell
pico- and atomol scale analytical methods in
genomics and proteomics
complex transgenic phenotypes
stem cell research
modelling of phylogenetic/population history
scenarios in time and space
dynamics of host-pathogen interaction.
Partners Involved
Besides and above possibilities, available in/through
several twinning partnerships, a much wider choice is kept in mind.
The following examples do not close the list:
BMC, Uppsala University
Rudbeck Centre, Uppsala University
Karolinska Institutet, Stockholm
Viiki Centre of Helsinki University
Medical Genetics, Rotterdam University
EMBL, Heidelberg
MRC Laboratory of Molecular Biology, Cambridge
Genethon, Paris
KTH, Stockholm
International Agency for Cancer Research, Lyon
Dept. Medical Biometry, Bonn- European Bioinformatics
Institute, Hinxton
Danish Centre for Human Genome Resarch, Aarhus
Genzentrum, Ludwig
Maximilians University, Munich
Deliverables, expected results,
milestone for the overall package:
Young researchers from the centre will visit European
research centres for total of 14 man months (D1)
Experienced researchers will visit European research
centres for total 3 man months (D2)
Increased scientific know-how and enhanced research
capacity
Work
package number and title
WP2:
Opening Centre for European Research Area Type of activity : V1, V2, V3, V4
Relative start month: 0
Timetable: 36 months (0-36)
Objectives:
This work package aims at opening all research
positions within the centre to the European academic community.
Description of the contents, the
workplan, the steps, the approach or the methodology:
We intend to use a package of measure to allow European
researchers to apply for available research position within the
Centre. Those measures range from advertising the positions in international
academic journals to specific grants for elected European researchers
to partially cover their opportunity and transition costs. A steering
committee, including several members of the International Advisory
Board (or appointed by), will screen applications. In case of junior
positions, the leader of the corresponding field will of course
be consulted and an exact research plan agreed already between a
successful applicant and the centre. Senior researchers will provide
their own research agenda, including suggestions on short lecture/seminar
courses for MSc and PhD students. They will also supervise grad
students and guide young researchers.The contract will be from 12
month, up to 2 years stay, at our Centre. In case of senior positions,
further extension will be made possible and negotiable from the
very beginning, but not under this project. The full package will
contain appropriate support for research, financed by the Centre.
Provided calculation is based on one-year period, the following
positions will be announced during the coming three years:
2 junior researchers in the field of genome diversity
analysis
1 senior position in bioinformatics
1 senior position in cancer genomics
The time frame for filling these positions
is planned from the very beginning and bearing in mind that it would
be optimal if two senior positions - in bioinformatics and in cancer
genomics were filled as soon as possible. Junior research positions
in genome diversity will be announced in year 2 and 3.
Partners Involved
There are no specific fixed partners for this workplan,
though pro-active approach (e.g. partnerships to be organised via
twinning) will be of course used in addition to open advertising.
Deliverables, expected results,
milestone for the overall package:
Work
package number and title
WP3:
Building Twinning Relations for the Networking of Excellence Type of activity : VR, CO
Relative start month: 0
Timetable: 36 months (0-36)
Objectives:
We intend to introduce several twinning actions
with selected leading research institutions in Europe in order to
meet the specific needs of the Centre.
Description of the contents, the
workplan, the steps, the approach or the methodology:
Twinning arrangements are planned in the following
fields:
High-density, high-throughput genome analysis
for multifactorial diseases
Vector systems for DNA vaccination and gene therapy;
vaccine development and clinical trials
European and worldwide studies in human genetic
variation
Cell cycle regulatory networks, in particular
in cancer research
Twinning a subject of bi- and multilateral agreements,
defining workplan aims, timetables and delivery of tasks between
partners. Because the planned partnerships will be built up from
already existing professional contacts and collaboration, the implementation
of the twinning arrangements is expected to be a relatively fast
procedure. Twinning scheme will be based, first and foremost, on
a long-term common interests in one or other scientific or/and applied
research direction, i.e., it will be program- , rather than project-based.
The corresponding fields are listed above. Twinning will be implemented
by working out a common research agenda for a list of problems to
be addressed jointly. The main aspect here is to address a class
of problems (scope, depth), which would not likely be addressed
separately. Two-way study visits, joint colloquia and seminars will
be used at the initial stage for building up efficient "everyday"
contacts at all level of researchers. We consider this "human
aspect" in the twinning schemes most important: contacts at
the top level are necessary but not sufficient.
Partners Involved
The Wellcome Trust Sanger Institute, Hinxton,
UK
DKFZ (German Cancer Research Institute) in Heidelberg
Institute of Medical Technology, University of
Tampere, together with Finnish Immunotechnology plc, Tampere,
Finland
Department of Biochemistry and McDonald Institute
of Archaeological Research, Cambridge University, UK
Department of genetics, University of Pavia together
with Department of Genetics and Molecular Biology, University
of Roma "La Sapienza"
Deliverables, expected results,
milestone for the overall package:
7 Study visits (D5)
1 Brainstorm meeting (D6)
Published research works, performed in tight co-operation
with the twinning partners (D7)
Work
package number and title
WP4:
Thematic Conferences and Seminars Type of activity : CF, WS
Relative start month: 4
Timetable: 36 months (0-36)
Objectives:
This work package aims to organise several thematic
conferences and seminars during the project in order to increase
the overall visibility and international attraction of the centre.
Description of the contents, the
workplan, the steps, the approach or the methodology:
We intend to use this work package for organising
seminars and conference on selected topics, which are both relevant
to our research priorities and will be of broader interest to European
Research Community. For all planned conference we will establish
international steering committee. This work package also includes
covering costs related to inviting keynote speakers as well as limited
amount of travel grants for young researchers from European research
organisations. We intend to organise seminars and conferences in
the following thematic fields:
Yearly GeneForum conferences bringing together
scientists, entrepreneurs and bioethics specialist from Europe
and elsewhere, to present new knowledge and new ideas in a field
of genomics and postgenomics;
3 combined hands-on practical courses/seminars
in genome analysis
3 combined hands-on practical courses/seminars
in postgenomic tools
Partners Involved
ESF, NORFA, HUGO, FEBS, EMBO, NIH, Estonian Technology
Agency, Estonian Genome Foundation
Deliverables, expected results,
milestone for the overall package:
6 international practical courses/seminars
will be organised (D8)
3 international conferences will be organised
(D9)