In 2006, a few large projects have been granted in the framework of "Big Infrastructures", for scientific research in the Netherlands. One of the awarded projects has been the BIG GRID project, proposed in collaboration by the National Computing Facilities foundation (NCF), the National institute for sub-atomic phyiscs (Nikhef) and the Netherlands Bio-Informatics Centre (NBIC).
Monday September 17th, 2007, the management team of the BIG GRID project organises the official launch event of the BIG GRID project. During a one-day symposium, with lectures from several scientific disciplines, attention will be given to the opportunities offered by the Netherlands Science Grid for scientific research.
Location of the symposium is the Science Park in Amsterdam, particularly in the Turing room (address: Science Park Amsterdam Congreszalen, Turingzaal, Kruislaan 413, 1098 SJ Amsterdam) How to get there?
Start of the program is at 10:00. Attending the symposium is without costs, registration can be done here.
09:30 10:00 Reception and
coffee 10:00 10:15 Jaap van den
Herik Opening 10:15 11:15 Bob
Jones
(CERN) 11:15 11:45 Break 11:45 12:10 Kors
Bos
(Nikhef) 12:10 12:35 Ron
Heeren
(AMOLF) Proteins,
Images, Collaborations and Lots of Data : Big Help
Needed 12:35 13:30 Lunch 13:30 13:55 Hanno
Holties
(Astron) 13:55 14:20 Peter
Doorn
(DANS) 14:20 14:45 Ton
Rullmann
(Organon) The
challenge of complex diseases: how virtual patients can make
a difference 14:45 15:00 Tea 15:00 15:25 Willem
Bouten
(UvA) 15:25 15:50 Arie
Kaizer
(Philips) 15:50 16:00 Jaap van den
Herik Wrap up 16:00 17:00 Drinks
The EGEE project and the future of European
grids
Enabling Grids for E-sciencE operates the world's largest multi-science Grid infrastructure. As flagship e-Infrastructure project of the European Commission, EGEE unites thematic, regional and national Grid infrastructures into a seamless whole, able to support scientists in their research 24/7. The users of the EGEE Grid are organised into Virtual Organizations, allowing them to share resources, codes, data and common tools specific to their fields of study. At present, more than 200 Virtual Organizations make use of EGEE, in fields from High Energy Physics and Biomedicine to Earth Sciences, Astronomy and Finance.
Coming to the end of its second phase, EGEE is looking toward the future of the programme and of Grid computing in general. A proposal for a third phase of the EGEE project is in preparation, with increased support for new scientific disciplines joining the Grid. EGEE is also taking an active role in the development of a European Grid Initiative (EGI) via a design study recently approved by the European Commission. EGI intends to build on emerging National Grid Initiatives, such as Big Grid in the Netherlands, to provide European-level coordination for Grid computing.
Dr Jones is the project director of the European Union financed EGEE project, which provides a production grid facility for e-Science in Europe.
Previous experience in the grid arena includes his mandate as technical coordinator and then deputy project leader for the EU DataGrid project (2001-2004), the flagship grid project of the European Union in its 5th Framework Programme.
Following a B.Sc. (Hons) in Computer Science from Staffordshire University, Bob joined CERN in 1986 as a software developer with the information technology department providing support for the LEP experiments. He completed his PhD thesis in Computer Science at Sunderland University while working at CERN and has been involved in several research projects for the future LHC accelerator.
He is a member of the ATLAS physics experiment collaboration and has previously been responsible for the online software group.
Dr Jones has lectured on software engineering related subjects at events such as the CERN School of computing.
Proteins, Images,
Collaborations and Lots of Data : Big Help Needed
Technological developments in the analytical bio-sciences have revolutionized the possibilities for genome, proteome and metabolome characterization. This revolution however has come with the awareness that a conventional basic academic approach (where a specific scientific detail or aspect is thoroughly investigated by a specialized research group) is becoming increasingly inadequate. More global approaches where various biological problems are studied in a more complete, interdisciplinary approach are being proposed in the field of systems biology. These studies require the intimate interaction between all basic sciences such as physics, mathematics, chemistry and biology. More importantly, this approach requires a psychological change in the attitude of participating researchers to be successful. It requires the researchers to put themselves in a vulnerable position in science through the open and unbiased exchange of data, insights, results, protocols, (processing) tools and information in general while the active research process is still going on. This change in perception needs an environment in which researchers feel comfortable to share their resources and results in complex collaborations even before publication.
To realize this environment there are a number of technological hurdles to take. The large volume of raw data that is being produced by various analytical techniques constitutes a major problem. In this lecture we will illustrate how a large scale project such as BigGrid can assist the analytical scientist in this "omics" era in dealing with this problem through the concise implementation of virtual laboratory concepts and technologies. One newly implemented approach to metadata management in virtual organizations is the knowledge exchange or "KnowEx" developed in the framework of the VL-e project. This approach facilitates the collaboration of researchers and allows the to share various resources.
We will use an ongoing international collaboration between a academic research hospital in the US and a macromolecular ion physics group in Amsterdam to demonstrate the need for these innovative approaches. This particular project is focused on the determination of peptide and protein distributions in breast cancer tissue sections by imaging mass spectrometry. In this collaboration a typical raw mass spectrometric dataset is between 100 Mbyte and 200 Gbyte in size. In addition extensive in-vivo MRI datasets as well as histopathological and biochemical data is generated on breast tumors grown in immune compromised mice. New high throughput processing and visualization tools as well as meta-data management tools are needed to be able to deal with this geographical distributed large datasets. Here BigHelp is needed…
Prof. Dr. Ron M.A. Heeren, FOM-institute for Atomic and molecular Physics
Ron M.A. Heeren obtained a PhD degree in technical physics in 1992 at the University of Amsterdam on plasma-surface interactions. After two years of post-doctoral work on FTICR mass spectrometry he joined the MOLART research team at the FOM-Institute for Atomic and Molecular Physics as a project leader, heading the instrumental developments for paint cross-section analysis in early 1995. In 1999 he started a research group focussing on macromolecular ion physics with high resolution mass spectrometry and the development of imaging mass spectrometry at AMOLF. In 2001 he was appointed professor at the chemistry faculty of Utrecht University lecturing on the physical aspects of biomolecular mass spectrometry. He is an active participant in the Netherlands Proteomics Centre and the Virtual Laboratory or e-sciences. His academic research interests are the fundamental studies of the energetics of macromolecular systems, conformational studies of non-covalently bound protein complexes, virtual laboratory technology and the development and validation of new mass spectrometry based proteomic imaging techniques for the life sciences. The mass spectrometric imaging facility at FOM-AMOLF under his supervision is used to study neurodegenerative diseases, the molecular basis of cancer and several drug metabolic projects including innovative nanoparticle based drug delivery systems.
E-Humanities,
e-social science and the grid
In the humanities and social sciences the availability of increasing amounts of digital data makes it necessary to explore new research methods and techniques. Not only an e-science has developed, but there are now also e-humanities and e-social sciences. Large digital collections of, for example, annotated speech and other language data (text, audio and video), data bases on population characteristics (census data, population registers), economic time series, and geospatial data require new approaches in fields such as phonetics, sociology, econometrics, demography, history, geography and archaeology. Nevertheless, grid applications in those fields are generally only just beginning. Data Archiving and Networked Services (DANS), the national centre for permanent access to research data for the humanities and social sciences, is exploring the potential of the data grid, but we are also interested in the linkage of heterogeneous data resources. In three proposals from the humanities and social sciences that are on the Roadmap of the European Strategy Forum for Research Infrastructures, the grid plays an important role. Already during the preparations of the Big Grid project, the exchange of ideas between scholars from the humanities and social sciences on the one hand, and the scientists initiating Big Grid on the other, have proven to be fruitful. Also in the Catch-programme (Continuous Access to Cultural Heritage) the successes of the interaction between computing scientists, humanities scholars and cultural heritage institutions are being reaped. It is expected that the collaboration in Big Grid will not only boost e-science, but the intensive collaboration between the "arts" and the "sciences" will also lead to innovations in the humanities and social sciences.
Peter Doorn is director of Data Archiving an Networked Services (DANS), the national centre for permanent access to research data for the humanities and social sciences. He studied human geography in Utrecht and defended his PhD there. He taught computing for historians at Leiden University between 1985 and 1997. He was director of the Netherlands Historical Data Archive and head of department at the Netherlands Institute for Scientific Information Services (NIWI).
Industrial Applications of
Grids
For Philips Research an IT infrastructure geared towards the needs of researchers is an indispensable element. In recent years Philips Research has undergone a number of major changes. As a result of the focus shift at Philips, Philips Research has also changed its programme considerably. The adoption of the open innovation concept has resulted in an open organisation that enjoys strategic cooperation with companies, universities and other institutes. Facilities are shared with partners in order to improve cost-effectiveness and efficiency. The Research ICT Department has modified its strategy so as to facilitate Research's new wishes. An example of this is the expected increase in High Performance Computing in application areas such as medical imaging, bio-informatics and simulation of physical devices. This presentation deals with the above-mentioned changes, the way we are responding to them and the need for intensive support.
Dr. Arie J.M. Kaizer, Philips Research
Arie Kaizer was born in Amsterdam in 1950. He studied electrical engineering at Twente Technical University and joined Philips Research in 1976. He received a PhD from Eindhoven Technical University in 1986. He is currently manager of the ADICT (Adaptive and Dedicated ICT) section of the Research ICT Department.
Particle physics has been one of the major driving forces behind the development of computing and data grids. The large amount of data that will be produced when the LHC machine at CERN in Geneva will be switched on next year plus the widely dispersed user community make grid technology a necessity. The preparation for the data taking is in full swing and currently full scale tests are ongoing that already approach the rates and data volumes of what will be reached next year. Cosmic rays are used to test all sub-detectors, the trigger for the read-out and the accumulation of the data. Moreover this data is analised at CERN and exported to all remote centers around the world to be stored and further analised in quasi real-time. The remote centers, of which NIKHEF/SARA is an important one, will still have to make a big step up in resources to be able to reach the nominal values for the experiments.
Dr. Kors Bos, National institute for subatomic physics
Kors Bos got his degree in physics in Amsterdam and has since been working in particle physics experiments. He worked mostly on hadron physics and was almost always involved in the data acquisition or off-line analysis part of the experiment. He was a member of the UA1 collaboration at CERN and the D0 collaboration at Fermilab and at the latter started a Monte Carlo production project which eventually lead to the development of what would now be called grid techniques. Shortly after he was part of the people that proposed the European Data Grid project. Currently he is responsible for all computer operations of the ATLAS experiment which is in a steep ramp-up to physics data taking next year.
The challenge of complex diseases: how
virtual patients can make a difference
Most human diseases (cancer, arthritis, diabetes etc.) are complex: they are not caused by a single gene, but by many genetic and environmental factors, that differ from person to person. Disease is the outcome of the behaviour of the human body as an integrated system. Pharmaceutical researchers increasingly recognize that to make progress in developing more efficacious drugs, disease should be studied at the systems level. This is the field of systems biology and systems pharmacology [1]. Analysis of large data sets and computational modeling are indispensable. Modeling of human physiology has a long history. Advanced software tools and model engineering workflows are now available to generate disease models at the organ level [2]. Models can be specified to represent variations between patients, either based on hypotheses about disease mechanisms, on experimental clinical data or on a combination of these [3]. New treatments can now be tested on hundreds of virtual patients simultaneously, requiring extensive computational resources. The presentation will highlight the development of computational physiology, discuss the impact of virtual patient simulations on drug discovery and clinical practice, and look forward into the future of personalized medicine.
[1] J. van der Greef et
al., "Rescuing drug discovery: in vivo systems pathology and systems
pharmacology", Nature Rev. Drug Disc. 4, 961 (2005).
[2] J.A.C. Rullmann et al., "Systems biology for battling
rheumatoid arthritis: Application of the Entelos PhysioLab platform",
IEE Proc. Syst. Biol. 152, 256 (2005).
[3] W. Alkema et al., "Target validation in silico: does the
virtual patient cure the pharma pipeline?", Expert Opin. Ther.
Targets 10, 635 (2006).
Dr. Rullmann graduated from the University of Groningen in 1988, studying hydration of biomolecules with quantum mechanical and Monte Carlo simulation techniques. He then moved to the University of Utrecht, where he worked on determining protein structures using NMR and molecular dynamics simulations, and on methods for assessing the quality of NMR-derived structures. In 1998 he joined the Dutch pharmaceutical company Organon. In the bioinformatics group he was responsible for database management and for technology development. He co-developed the text-mining tool CoPub, now hosted by SARA. His research currently focuses on the application of systems biology to pharmaceutical research. He is project manager for the collaboration between Organon and the biosimulation company Entelos in the field of Rheumatoid Arthritis.
LOFAR data distribution &
analysis
LOFAR is a revolutionary Radio Telescope newly developed at ASTRON. Scientific operation will start in 2008 and LOFAR is expected to be operating at nominal capacity by 2010. As more stations are coming online, the potential and real dataflows will increase dramatically to the point where PetaBytes of data storage, and processing facilities for it, are needed each year. The centralized LOFAR facilities will provide limited storage capacity for data at full time- and frequency resolution. For long(er) term storage data will be distributed after initial calibration and inspection, and in most cases reduction, to compute centres providing storage and processing services to the astronomical user community. The BIG GRID project will be a major facilitator in matching the storage and processing requirements in the Netherlands. Already, the LOFAR CS1 prototype is being used as a test platform for commissioning purposes and a start has been made with transferring data to EGEE based GRID facilities.
Dr. Hanno (H.A.) Holties, ASTRON
Towards a European Bird Migration System of
Systems
Willem Bouten, Judy Shamoun-Baranes, Maurice Bouwhuis, Giovanni Garofalo, Amnon Ginati
Collisions between birds and aircraft are estimated to cost civil aviation about 1.2 billion US dollars annually worldwide; and the risk birds pose to military and civil aircraft is increasing annually. The FlySafe Integrated Application Program of the European Space Agency aims at developing a sustainable service to enhance the military aviation flight safety by reducing the risk of bird strikes. This will be achieved by developing an information system that issues warnings about high bird densities to pilots, air traffic controllers, flight planners and bird control units. The system incorporates real-time and historic information on bird migration using a network of military radars, the European network of weather radars, several mobile radars, information from birds tracked with miniature GPS-tags, and predictions by bird migration models. UvA and SARA are working closely together to provide the data storage and computational infrastructure, to develop models, and to visualize all observations and model results. BIGGRID will hopefully support the harware infrastructure and the development of the "Virtual Lab for Bird Migration Modeling".
Willem Bouten did a MSc in Soil Physics and Soil Chemistry at the Agricultural University in Wageningen and a PhD in Hydrology and Meteorology at the Universiteit van Amsterdam. In his research he combines models and measurements to develop new theories and to build predictive models. Currently he leads the research group of Computational Geo-Ecology of the Institute for Biodiversity and Ecosystem Dynamics. This trans-disciplinary group aims at modeling the relations between biota and their environment. In the context of the BSIK program "Virtual Lab eScience" he is project leader of subprogram 1.4 Biodiversity. In this subprogram his group developed Bird Avoidance Models for enhancing flight safety. As a follow-up, Bouten is now scientific coordinator of a large European initiative (ESA FlySafe Bird Migration System of Systems) in which 13 European research institutes and partners of industry co-operate. Bouten is also scientific director of the Dutch Research School for Geo-ecology.
The Science Park Amsterdam in located in the east of Amsterdam.
At Schiphol, Amsterdam Airport, you can rent a car or take a taxi to get to Science Park (travelling time about 25 minutes). There is also a train station to Amsterdam Central Station.
First take the train to Amstel Station, or the metro 51, 53 and 54 to Amstel (ca. 10 minutes). Then take bus 40 or a taxi. There are taxi stops near all railway stations. From Central Station, it takes about 15 minutes to get to Science Park by taxi.
Another possibility is tram 9. The tram doesnt stop at Science Park but at a distance that takes about 20 minutes to walk (on the Kruislaan).
Bus 40 drives from Amstel Station to Muiderpoort Station, and vice versa, and stops both times at Science Park Amsterdam. Traveling time about 12 minutes.
It is also possible to rent a bicycle at Amstel Station; distance is 3 - 4 km.
All motorways to Amsterdam lead to the ring road A10. Take the Ring and exit on "S113/Watergraafsmeer" follow the signs Science Park and turn right into Kruislaan, drive along about 1 km and go trough the railway tunnel. After the tunnel take the second way left. The Turing Room is in the first building at your right site.