INFRASTRUCTURE
Sometimes you need large-scale
facilities to make major discoveries
Major
research
You need major databases, powerful computers and enormous
telescopes to do research with large amounts of data. NWO is
helping science with the necessary infrastructure.
Text: Adriaan ter Braack
NWO is investing in
large-scale research facilities
Good research facilities are
indispensable for top-flight
research. Think of telescopes,
ICT facilities and data collections. That’s why NWO is
providing long-term funding for
these facilities. Every two years,
eighty million euros goes to
large-scale research facilities,
scientists can reserve time on
the LISA and Cartesius supercomputers, and NWO provides
access to research facilities
abroad. As a result, Dutch
scientists can conduct research
using the Isaac Newton Group of
Telescopes on the island of La
Palma. Finally, NWO ensures that
the facilities at all NWO research
institutes are accessible to
researchers here and abroad. An
overview of all large-scale
facilities is available at www.
onderzoeksfaciliteiten.nl.
Scientists can use this website to
find out which equipment and
databases they can use for their
research. The site should also
promote cooperation in the
development of new facilities.
Twelve countries are
participating in the SKA
telescope. It will be built
between 2018 and 2020.
Biobank network
WHAT? BBMRI-NL (Biobanking and
BioMolecular Resources Research
Infrastructure The Netherlands), a partnership between Dutch biobanks with
collections of medical data and individuals’ biomaterial.
WHAT CAN YOU DO WITH IT? ‘Diseases
that we used to group together, such as
cancer, diabetes and cardiovascular
disease, turn out to consist of different
biological sub-types’, says scientific
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co-director Gerrit Meijer.
‘In order to study these properly, backed
up with enough statistics, we need a
constantly growing large collection of
data, samples and images of healthy
citizens and patients. That’s why we work
with biobanks both here and abroad,
whereby BBMRI-NL represents the Dutch
biomedical data, sample and image
collection. It’s important in health care
that prevention and treatment are as
customised as possible. Population-based
biobanks, in which people are monitored
in times of good health and illness over a
longer period, are crucial to a customised
approach. Combining different kinds of
data makes it easier to recognise a
subtype of a particular disease at an early
stage, for example.’
HAS IT ALREADY GENERATED NEW
INSIGHTS? ‘BBMRI-NL has already
completed a number of successful
Giant radio telescope
projects, such as Genome of the Netherlands. That project unravelled the
complete DNA sequences of 750 Dutch
people. This data collection is used
frequently in clinics and for research.
Now that the unravelling of DNA is
playing an increasingly important role in
the diagnosis of diseases as well, it’s
important to know what’s “normal”. The
Genome of the Netherlands is an important reference for that.’
Genetic material is kept in
these kinds of tubes.
WHAT? SKA (Square Kilometre Array),
a radio telescope consisting of 200
dish antennas in South Africa and
130,000 dipole antennas in Australia
which are connected via a fast
network of fibre optic links to a large
supercomputer. Together the collecting area of the antennas and dishes
approaches one square kilometre.
WHAT CAN YOU DO WITH IT? ‘SKA
is much more sensitive than other
radio telescopes, so we can detect
weaker signals and therefore look
back further in time,’ says Michiel van
Haarlem, head of SKA NL. ‘We hope
that will enable us to get a better
picture of the formation of the first
stars and galaxies. That, in turn,
should lead to a better understanding
of the fundamental laws of physics.
By studying pulsars, which are
remnants of a star after a supernova
explosion, we can put Einstein’s
general theory of relativity to the test.’
WHAT IS IMPORTANT IN SUCH A
PROJECT? ‘The scope and cost of
SKA are considerable, so international
cooperation is extremely important.
We’re trying to set up an international
treaty organisation that will have the
task of building and running the
telescope. Moreover, the extreme
sensitivity of SKA is only possible
thanks to the development of new
technologies, such as sensitive
antennas, fast, energy-efficient
computers and intelligent new
algorithms that process and visualise
the data. The amount and complexity
of data that SKA will generate is the
reason why there are plans to set up a
Science Data Centre in the Netherlands. That will give users access to
the telescope and archived observation data.’
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INFRASTRUCTURE
The supercomputer simulates research
that’s too expensive or dangerous
Proteins at work
WHAT? Proteins@Work, a research
facility for proteomics, the study of the
biological function of proteins in cells.
The facility provides access to techniques, equipment and expertise for
biology and biomedical researchers.
WHAT CAN YOU DO WITH IT? ‘Proteins
are produced by genes, which are
encoded in the DNA,’ says Albert Heck,
scientific director of the Netherlands
Proteomics Centre. ‘The specific composition of proteins determines whether a cell
– such as a skin cell, muscle cell or brain
cell – works. By studying these proteins,
and interaction, we can gain a better
understanding of how life works, and
that’s important for medical and biological research. It enables us to determine
the cause of diseases, for example, so we
can develop new therapies.’
WHAT’S PROTEINS@WORK ALL
ABOUT? ‘You can study proteins by
measuring their unique fingerprint in cell
or tissue samples. Mass spectrometry
enables us to determine the identity, and
indirectly the function, of proteins,’ Heck
explains. ‘We do this with tens of thousands of proteins in a single experiment.
We create about one million fragments
from that, which are then analysed by
powerful mass spectrometers and
computers. These techniques require a
great deal of expertise and investment in
hardware and software.’
WHAT CAN YOU DO WITH THIS
KNOWLEDGE? ‘Proteomics enables you
to answer a lot of questions. How much of
a certain protein is present, or how do
proteins work together in a cell? Which
proteins are typical of a certain function
or disease? We already know how to
reprogramme skin cells into a stem cell.
Essentially this means reprogramming all
proteins present in a cell. Scientists can
now give cells new and specific commands. For example, a command to
repair tissue or a damaged organ. That’s
already happening in laboratories, with
cells in laboratory animals, but not in real
patients yet.’
All Dutch universities and a
number of scientific institutes
can use the calculating wizard
Cartesius.
Treasure collection
WHAT? PAN (Portable Antiquities of
the Netherlands), an online database
of private metal detector finds, so
that they become available for
scientific archaeological research.
WHAT CAN YOU DO WITH IT? ‘An
enormous amount of archaeological
objects have been collected from
Dutch soil in recent decades by
amateur archaeologists with metal
detectors,’ says Nico Roymans,
professor of archaeology at VU
University Amsterdam. ‘It concerns
thousands of collections that have
never been systematically inventoried, but which, taken together, are
of unique scientific value for the
history of the Netherlands. A
database ensures that this data is
not lost.’
HOW IS PAN BEING DEVELOPED?
‘A variety of aspects are important
to set up this infrastructure, such as
a good network of metal detectors
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in the Netherlands and a digital
database that is accessible to both
scientists and the general public. We
Archaeological
finds by
amateurs can
also be
valuable to
science.
also need a team of archaeologists
to make an inventory in the coming
years of all the collections in the
Netherlands. For the sake of continuity, the database will ultimately be
handed on to the Cultural Heritage
Agency following the project period.’
WHAT KIND OF ISSUES CAN PAN
HELP TO SOLVE? ‘The data can be
used for a broad range of archaeological and historical issues – for
example, to determine the population density of regions, inter-regional
commercial ties, the functioning of
market economies and migrations.
The database can also be used to
determine whether a site is interesting, archaeologically speaking, so
that it can be handled in an adequate manner. Battlefields, for
example, can be identified by the
concentration of fragments of
military equipment and musket
balls.’
A whopping
calculating wizard
WHAT? Cartesius, the Netherlands’
national supercomputer, which is
receiving a major update this year.
WHAT CAN YOU DO WITH IT?
‘Supercomputers are used for largescale technical-scientific calculations,’
says Chantal Cassee, head of communications. ‘It usually concerns simulations
of research that would normally be
impossible, too expensive, too dangerous or too extensive.’
IN WHOSE INTEREST IS IT?
‘From chemists who want to calculate
the structures and interactions of
molecules to climate scientists who test
models. Other uses include calculating
currents around ship propellers,
airplane wings and currents in blood
vessels and rivers. Supercomputers can
make faster, more sophisticated
calculations of all these processes.’
IS IT NECESSARY TO UPDATE A
SUPERCOMPUTER? ‘Supercomputers
become outdated as quickly as regular
PCs. In other words, what’s a supercomputer today will already be so outdated
in five years that it needs replacing. By
that time you can get a machine that’s
ten times as fast for the same price,’
says Cassee. ‘The gain in speed used to
come from faster processors, but today
it comes from a greater number of
processors.’
Humanities databank
WHAT? CLARIAH (Common Lab
Research Infrastructure for the
Arts and Humanities), an infrastructure that brings together
data and software from the
humanities and makes it accessible.
WHAT CAN YOU DO WITH IT?
‘Large amounts of data in the form
of text, images, structured
information and audiovisual files
will soon be available digitally,’
says Patricia Alkhoven, coordinator of external cooperation. ‘These
data make it possible to conduct
innovative research in the humanities, providing they are stored
according to internationally
recognised standards. Then all
digital sources can be linked to
each other, creating a gigantic
collection of data.’
WHAT DOES ITS DEVELOPMENT
ENTAIL? ‘The effectiveness of the
database relies completely on the
availability of standards that
everyone can use in their work,
the possibility of continuing to
work with old and trusted software and the willingness of
researchers to share their data
with others. We can develop
fantastic programs, but if not a single humanities researcher sees its
use, then the infrastructure will
become an amazing four-lane
highway that nobody drives on.’
WHAT CAN YOU RESEARCH
WITH CLARIAH? ‘Examples? How
do classic media (newspapers,
magazines, radio and TV) interact
with new social media, such as
Twitter, Facebook and blogs? Or
why have some regions in the
world been wealthy for so long
and others poor? How is our
language changing under the
influence of new media?’
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