Informatics Institute Annual Report 004 Chapter introduction

Tools for Knowledge Capture and Communication

A set of tools has been constructed that is currently being used by domain experts (mainly ecologists) to capture and share knowledge among experts, stakeholders and learners. The latest versions of this software produced in 2004 are: GARP (version 2), VisiGarp (version 2.04), and HOMER (version 2.1) (http://hcs.science.uva.nl/projects/GARP/.) GARP is a domain independent qualitative reasoning engine that allows users to simulate the behaviour of systems using a command-based interface. VISIGARP is a graphical interface to GARP that allows users to select, run and inspect qualitative simulation models by interacting with automatically generated visualizations. HOMER is a model-building environment that allows users to construct qualitative models using a graphical interface. Models constructed with HOMER can be exported as a set of files and used as input for GARP and/or VisiGarp.

Learning by modeling

Interactive Learning Environments that can be used by learners to learn while constructing. This is a special research track within the theme Qualitative Reasoning. It concerns research questions such as external representations, knowledge visualisation, and automated help. The Ph.D. project carried out by V. Bessa Machado showed that with careful designed diagrammatic representations novices were capable of using the model-building workbench MOBUM successfully. A multi-agent approach was developed to support the modelling process. The agents provided different kinds of help, such as general information on the formalisms and tailored feedback addressing the individual needs of a learner. Agents thus have scope, provide context-sensitive help, and are personified according to the type of support they provide. An evaluation study showed that such a help-system can effectively support users. V. Bessa Machado successfully defended her Ph.D. thesis on this topic in 2004 (promotor prof. dr. B.J. Wielinga and co-promotor dr. B. Bredeweg).

MONET network of Excellence

Monet is a European Network of Excellence in Model Based Systems and Qualitative Reasoning (MBS & QR) (Contract No: IST-33540). The Project brings together experts in these fields from Academia and Industry in order to realize the potential of this area. The primary aim being to bring these technologies to the point where they are of use to Industry and therefore forward the competitiveness of the joint economies of Europe. The methods used in MBS & QR are applicable to many and diverse areas of Research and Industry. Some applications are more developed than others; some are already in commercial use at this time. The Project aims to further the use of these technologies and then apply the lessons learned in their development to furthering the areas that are not quite so developed.

Portal on QRM

Due to the advanced representational features of Qualitative Reasoning, users find it often hard to use. One of the major problems with using Qualitative Reasoning is gaining the experience required to use them. Although the software is available (in our case freely so) if learners, teachers, stake-holders or domain experts want to use QR software it is difficult, if not impossible for them to do so unaided. A portal has been implemented that supports users of QR technology. The current version of the portal (version 2) includes information on QR ontologies, modelling and simulation (http://monet.aber.ac.uk/). There is an initial enumeration of typical examples and assignments, a list of FAQ and a glossary. The goal is to have this portal grow and support a community of practice on using and developing QR technology.
2005 and beyond
NaturNet-Redime is a EU FP6 STREP project that has just started (March 1^st, 2005). It will develop educational programmes to contribute to and accompany the design of the European Union’s Strategy for Sustainable Development. The technology produced will increase knowledge of the various factors that affect sustainable development. By building understanding of processes, decision makers, stakeholders, and citizens will be able to make more informed and equitable decisions. All materials will be available via the NaturNet-Redime (www.naturnet.org) web portal. Interaction with end users will provide feedback to ensure optimization.
The tools for knowledge capture and communication developed by our group will be the basis for the ecologist in the project to construct conceptual models. While collaborating with the experts, we will further improve our tools and develop means to support their usage. Three areas of research are planned. First, the integration of existing software packages into a seamless workbench for capturing and sharing ecological knowledge. Secondly, tools, method and support for a collaborative approach to modelling. Third, intelligent support and means for model-debugging to aid users (particularly, citizens and stakeholders) in their needs to created understanding and construct argumentation.

Chapter 3 Applied Research and Education

The Laboratory for Computing, System architecture, and Programming
1. Computational Informatics
The knowledge acquired through Computational Science is vital to solve many important problems in contemporary society, not only in the general sense, through the development of know-how, solution techniques and tools, but also through the development of specific applications and Grid middleware.
The Grid promises to become an important paradigm for business computing and our efforts in developing grid based environments is therefore very relevant. Many of our applications have a clear societal relevance. As an example, consider the work performed for the vascular reconstruction. The societal relevance of the flooding crisis management application in the CrossGrid project has been dramatically demonstrated recently, with and estimated damage of over 10 billion Euros due to flooding in Germany alone. Finally, the HIV infection related work clearly is of high societal relevance.
2. Advanced Computing Systems Engineering
The social and technological relevance of our research is illustrated by the impact this research has for companies like Philips, where the architectures of consumer electronics become increasingly heterogeneous

and complex. Good tool support, to assist architects during all design stages, becomes more and more important for designing these systems. Another example is the introduction of road pricing along the Dutch roads, which has been a political issue for many years. In the CAPS group, we have concentrated on the technical issues of this subject. In both examples modeling and simulation of the systems play an important role in studying their behavior before they are actually built. The industrial benefit of our Virtual Laboratory research is illustrated by the opportunities offered to, for example, commercial aviation companies: using virtual laboratory infrastructures, companies like Boeing have access to a Virtual Wind Tunnel to perform large simulations needed for the design of new wind turbines for aircrafts.

3. Programming Methods and Programming Environments
In the Programming Methods and Environments programme, the general aim is to support the development of better software in a systematic manner. Design and analysis on the conceptual level both are indispensable for a better understanding of programming, programming languages and programmed systems. The connection between our different projects has always been the transfer of concepts and models to the experimental stream and to the scientific community.
Sophisticated tools based on a firm foundation are crucial for the gradual improvement of software engineering practices. The results of the Programming Environments project may have a major impact on the longer term software development strategies in industry. In the software IT industry, most development is about enhancing existing systems, for instance, providing new front-ends to established back-ends, capitalizing on existing relational technology for data storage, and building new interfaces to existing software assets. Organizations are more and more trying to find effective ways to reuse their investments in existing packages, data bases, and legacy assets. Evidently, more and more people working in the software engineering area will be working on existing systems. This project perfectly fits these needs from the IT industry.

The Intelligent Systems Laboratory Amsterdam
1. Intelligent Sensory Information Systems
ISIS has been awarded as one of three national centers in the IOP-program for industrial vision. Over the years, the IOP-project is performed in cooperation with Stork, Oce, Philips CFT, Philips Medical Systems, ENZA, TNO, DLO, Noldus, Nederlands Forensisch Instituut, SPC and a few other industries.

The AMIS project combines five computer science research schools of the Netherlands into one integrated project on image search. The emphasis towards multimedia is further developed through an ICES KIS II grant of MEuro 4 to the UvA and the CWI with additional support from Elsevier, Oce, TNO, Datadistilleries. The aim is to convert high level research in multi-media information analysis into demonstrators, half-products and other means of innovation in Dutch industry.

The European IMAT project is developed with support from a variety of industries in Europe.

We have set up a joint venture with TNO called MediaMill in the area of multi-media information analysis. And we commenced a cooperation with the Ducth Forensic Institute, Rijswijk.

In the context of the ICES KIS and IOP programs, we design and show demonstrators to a large variety of industries and institutions. Demonstrators are in the area of image search, the PictoSeek system as well as the Filter Image Browser, document image analysis, document genre classification and the MediaMill video indexer.

Based on our experience with SCIL-Image, an environment for image processing algorithms implemented for 10 years in a large number of scientific labs for image processing mostly within the Netherlands, we have concluded work on the object-oriented pattern-based Horus C++ package.

2. Intelligent Autonomous Systems
To promote robotics at a young age, the IAS-group has initiated in 2004 RoboCup Junior (http://www.robocupjunior.nl). RobuCup Junior is a special league in which children between 9 and 19 compete with robots of their own design. In cooperation with the Amstel Institute and Nemo annual workshops and competitions are organized. During these games the best teams are selected and may then participate in international competitions. RoboCup Junior consists of three leagues that are divided into a number of age groups from 9 to 19.

Peter van Lith and Jelle Kok were the scientific hosts of the Beta Festival, a yearly event to promote science in the Netherlands (http://www.studeren.uva.nl/betafestival/). This year the focus was on robotics.

3. Information and Language Processing Systems
In collaboration with colleagues at the Academisch Medisch Centrum (AMC) work continued on support tools for developing terminologies, such as debugging, explanation, and summarization.

We started the developement of a benchmark for XML query engines. The goal of this project is to improve existing, both commercial and open-source, programs. The benchmark discovered bugs in two of the three systems we tested. These have been reported to the developers of the query engines and fixed.

Using TREC evaluation measures, the search engine of the UvA website has been tested and compared to state of the art search engine technologies. This has resulted in a number of concrete recommendations to the ICT group of the Universiteit van Amsterdam.

Collaborative work with several cultural heritage partners was set up, and has so far lead to final year projects and/or drafts of research proposals. Contacts with Elsevier Science were re-newed, and possibilities for future collaborations in the area of semi-structured retrieval are being explored.

Finally, within the setting of the Adaptive Information Disclosure project, ontology-based search technology is being developed to support the literature search efforts of bio-informaticians.

The Laboratory for Human Computer Studies
Interapy

Interapy conducts research on Computer-mediated Therapy (CMT) using a structured approach administered via the WWW. Interapy is a company that grew out of collaborative research between participants from Psychology and Social-science Informatics (now HCS). An important class of treatments deals with Post-traumatic Stress Syndromes (PTSS).

Ontologies

The methods and tools developed as part of the ontology research activities were used to develop a number of ontologies for knowledge management application projects in two large companies.

Eduction

One outcome of the research performed by UvA within the THINKcreative network of experts - focused on the study of virtual/networked organizations – was editing a book on “Collaborative Networked Organizations”. This book is now being used by several Universities for graduate courses in this area.

Chapter 4 Facts and Figures

Financial paragraph (x 1000 Euro)

2005

Income

Lump sum (university funding) 3451

Income from research activities 3981

Other income 150
Total 7582

Expenses

Personnel 6100

Other expenses 2076

Total 8176
Net result -594

Human Resource Input in fte for 2004

Human Resource Input 2004	Funding	CSP			ISLA			HCS
		CI	ACSE	PMPE	ISIS	IAS	ILPS	HCS
Full Professor	1	1	2	0.6	1.2	1	0.75	1
	2
	3		0.4		0.2	0.2		0.4
Associate Professor	1	1	2	1	2	0.5		0.7
	2
	3							0.9
Assistant Professor	1	2	3	2	1.3	1.8	0.75	5.1
	2				0.7
	3		0.4			0.2		0.3
Post doc	1	1			2	0.6	3.6	1.7
	2	2	3		1	2.8
	3	1.2	2.8		3	3		2.8
PhD Student	1	1	1	1	1	1	1.5	1
	2	4.5	1		2	3	1.5	2
	3	5	3		2	1	0.75	8
Software Developers	1		1	1	1	1
	2
	3	6	9		2		1
Other	1		1.3	1	1	0.8
	2		1.5
	3	2.3	7.6		3
Guests		1				2	0.4	1.2

Research Input 2004	Funding	CSP			ISLA			HCS
		CI	ACSE	PMPE	ISIS	IAS	ILPS	HCS
Full Professor	1	0.4	0.4	0.2	0.6	0.3	0.38	0.5
	2
	3		0.2					0.3
Associate Professor	1	0.4	0.5	0.4	1	0.4
	2							0.2
	3	0.1	0.4					0.5
Assistant Professor	1	0.8	0.4	0.8	0.5	1	0.38	2.65
	2				0.7
	3		0.4
Post doc	1	0.4	0.3		1.1			1.15
	2	0.6	0.5			0.8	3.03
	3		4.8		2	2.4		1.35
PhD Student	1	0.7		0.7	2	0.7	0.56	0.75
	2	2.55			1.4	2.4	1.37	0.94
	3	3.3	4.4		2.6	1.4	0.87	1.24
Other	1			0.3		0.2
	2
	3	4.4	0.9		0.7
Guests		0.3				0.4	0.7

Scientific Output 2004	CSP			ISLA			HCS	Total
	CI	ACSE	PMPE	ISIS	IAS	ILPS	HCS
Dissertations	1	1		1	1		3	7
Journal Articles	19	7	2	14	4	4	11	61
Books, bookchapters, special issues	6	12				1	6	25
Conference contributions	22	20	1	37	34	57	30	201
Reports			11		4	4	7	26
Professional publications	1	1	6	1				9

Appendices

Appendix 1 Publications
The Laboratory for Computing, System architecture, and Programming
1. Computational Informatics
Recent key publications

[1] K.A. Iskra, R.G. Belleman, G.D. van Albada, J. Santoso, P.M.A. Sloot, H.E. Bal, H.J.W. Spoelder and M. Bubak. The polder computing environment, a system for interactive distributed simulation. Concurrency and Computation: Practice and Experience, 14:1313-1335, 2002. Special Issue on Grid Computing Environments.

[2] J.A. Kaandorp, E.A. Koopman, P.M.A. Sloot, R.P.M. Bak, M.J.A. Vermeij and L.E.H. Lampmann. Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti). Phil. Trans. R. Soc. Lond. B, vol. 358 (1437), pp. 1551 - 1557. 2003.

[3] B.D. Kandhai, D. Hlushkou, A.G. Hoekstra, P.M.A. Sloot, H. van As and U. Tallarek. Influence of stagnant zones on transient and asymptotic dispersion in macroscopically homogeneous porous media. Physical Review letters, 88(23):234501:1-4, 2002.

[4] S.F. Portegies Zwart, H. Baumgardt, P. Hut, J. Makino and S.L.W. McMillan. Formation of massive black holes through runaway collisions in dense young star clusters. Nature, vol. 428, pp. 724-726, 2004.
[5] P.F. Spinnato, G.D. van Albada and P.M.A. Sloot. Performance modelling of distributed hybrid architectures. IEEE Transactions on Parallel and Distributed Systems, vol. 15, nr 1 pp. 81-92. January 2004.
[6] A. Tirado-Ramos, P.M.A. Sloot, A.G. Hoekstra and M. Bubak. An Integrative Approach to High-Performance Biomedical Problem Solving Environments on the Grid. Parallel Computing, vol. 30, nr 9-10 pp. 1037-1055, (Chun-Hsi Huang and Sanguthevar Rajasekaran, editors), 2004.
Dissertations
[1] Z. Zhao: An agent based architecture for constructing Interactive Simulation Systems, PhD thesis, Universiteit van Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada) December 2004.
Journal articles
[1] A.M.M. Artoli, B.D. Kandhai, H.C.J. Hoefsloot, A.G. Hoekstra and P.M.A. Sloot. Lattice BGK of flow in a symmetric bifurcation. Future Generation Computer Systems, vol. 20, nr 6 pp. 909-916, 2004.
[2] D. Chakrabarty and S.F. Portegies Zwart. An Inverse-Problem Approach to Cluster Dynamics. Astronomical Journal, vol. 128, pp. 1046-1057, September 2004.
[3] B. Chopard and A.G. Hoekstra. Guest Editorial, Computational science of lattice Boltzmann modelling. Future Generation Computer Systems, vol. 20, nr 6 pp. 907-908, August 2004.
[4] H.S.M. Cramer, V. Evers, E.V. Zudilova and P.M.A. Sloot. Context analysis to inform virtual reality application development. International Journal of Virtual Reality, vol. 7, nr 3 pp. 177-186, 2004.
[5] J.M. Fregeau, P. Cheung, S.F. Portegies Zwart and F.A. Rasio. Stellar collisions during binary-binary and binary-single star interactions. Mon. Not. Royal Astr. Soc., vol. 352, pp. 1-19, July 2004.
[6] A. Gualandris, S.F. Portegies Zwart and P.P. Eggleton. N-body simulations of stars escaping from the Orion nebula. Mon.Not.Royal Astron. Soc., vol. 350, pp. 615-626, May 2004.
[7] A.G. Hoekstra, J. van 't Hoff, A.M.M. Artoli and P.M.A. Sloot. Unsteady flow in a 2D elastic tube with the Lattice BGK method. Future Generation Computer Systems, vol. 20, nr 6 pp. 917-924, 2004.
[8] C. Hopman, S.F. Portegies Zwart and T. Alexander. Ultraluminous X-Ray Sources as Intermediate-Mass Black Holes Fed by Tidally Captured Stars. Astrophys. J. Let., vol. 604, pp. L101-L104, April 2004.
[9] R.M.H. Merks, A.G. Hoekstra, J.A. Kaandorp and P.M.A. Sloot. Polyp oriented modelling of coral growth. Journal of Theoretical Biology, vol. 228, nr 4 pp. 559-576, 2004.
[10 ] D. Merrit, S. Piatek, S.F. Portegies Zwart and M. Hemsendorf. Core Formation by a Population of Massive Remnants. Astrophys. J. Let., vol. 608, pp. L25-L28, June 2004.
[11] G. Nelemans, L.R. Yungelson and S.F. Portegies Zwart. Short-period AM CVn systems as optical, X-ray and gravitational-wave sources. Mon. Not. Royal Astr. Soc., vol. 349, pp. 181-192, March 2004.
[12] S.F. Portegies Zwart, J. Dewi and T. Maccarone. Intermediate mass black holes in accreting binaries: formation, evolution and observational appearance. Mon. Not. Royal Astr. Soc., vol. 355, pp. 413-423, December 2004.

[13] S.F. Portegies Zwart, P. Hut, S.L.W. McMillan and J. Makino: Star cluster ecology - V. Dissection of an open star cluster: spectroscopy, Mon. Not. Royal Astr. Soc., vol. 351, pp. 473-486, June 2004.

[14] S.F. Portegies Zwart, H. Baumgardt, P. Hut, J. Makino and S.L.W. McMillan. Formation of massive black holes through runaway collisions in dense young star clusters. Nature, vol. 428, pp. 724-726, April 2004.
[15] C.P. Salzberg, A.T. Antony and H. Sayama. Evolutionary dynamics of cellular automata-based self-replicators in hostile environments. BioSystems, vol. 78, nr 1-3 pp. 119-134, 2004.
[16] K.A. Semyanov, P.A. Tarasov, A.E. Zharinov, A.V. Chernyshev, A.G. Hoekstra and V.P. Maltsev. Single-Particle Sizing from Light Scattering by Spectral Decomposition. Applied Optics, vol. 43, nr 26 pp. 5110-5115, September 2004.
[17] M.S. Sipior, S.F. Portegies Zwart and G. Nelemans. Recycled pulsars with black hole companions: the high-mass analogues of PSR B2303+46. Mon. Not. Royal Astr. Soc., vol. 354, pp. L49-L53, November 2004.
[18] P.F. Spinnato, G.D. van Albada and P.M.A. Sloot. Performance Modeling of Distributed Hybrid Architectures. IEEE Transactions on Parallel and Distributed Systems, vol. 15, nr 1 pp. 81-92, January 2004.
[19] A. Tirado-Ramos, P.M.A. Sloot, A.G. Hoekstra and M. Bubak. An Integrative Approach to High-Performance Biomedical Problem Solving Environments on the Grid. Parallel Computing, vol. 30, nr 9-10 pp. 1037-1055, (Chun-Hsi Huang and Sanguthevar Rajasekaran, editors), 2004.