Informatics Institute Annual Report 004 Chapter introduction

Books, bookchapters and special issues

[1] M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra. Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004. Proceedings, Part I, in series Lecture Notes in Computer Science, vol. 3036, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22114-X.

[2] M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra. Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004. Proceedings, Part II, in series Lecture Notes in Computer Science, vol. 3037, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22115-8.
[3] M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra. Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004. Proceedings, Part III, in series Lecture Notes in Computer Science, vol. 3038, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22116-6.
[4] M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra. Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004. Proceedings, Part IV, in series Lecture Notes in Computer Science, vol. 3039, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22129-8.
[5] J.A. Kaandorp and R.A. Garcia Leiva. Morphological analysis of two- and three-dimensional images of branching sponges and corals. In A.M.T. Elewa, editor, Morphometrics - Applications in Biology and Paleontology, pp. 83-94. Springer-Verlag, 2004. ISBN 3-540-21429-1.
[6] P.M.A. Sloot, B. Chopard and A.G. Hoekstra. Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004. In series Lecture Notes in Computer Science, vol. 3305, Springer Verlag, Heidelberg, October 2004, ISBN: 3-540-23596-5.
Conference contributions
[1] A.M.M. Artoli, L. Abrahamyan and A.G. Hoekstra. Accuracy versus Performance in Lattice Boltzmann BGK Simulations of Systolic Flows. In M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra, editors, Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part IV, in series Lecture Notes in Computer Science, vol. 3039, pp. 548-555, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22129-8.
[2] H.S.M. Cramer, V. Evers, E.V. Zudilova and P.M.A. Sloot. Usability Evaluation of a Simulated Vascular Reconstruction System. In Proceedings of the VIRART Virtual Reality Design and Evaluation Workshop 2004, (CD-ROM, Panel VI (Design methods/process and evaluation)) University of Nottingham, United Kingdom, January 2004, ISBN 0 85358 123 1.
[3] J. Cui and J.A. Kaandorp. Mathematical modelling of calcium homeostasis in yeast cells. In Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB), (abstract) pp. 215, Glasgow, Scotland, UK, July 2004.
[4]D.P. Gavidia, E.V. Zudilova and P.M.A. Sloot. A Client-Server Engine for Parallel Computation of High-Resolution Planes. In M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra, editors, Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part III, in series Lecture Notes in Computer Science, vol. 3038, pp. 970-977, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22116-6.
[5] M. Gieles. E. Athanassoula and S.F. Portegies Zwart. The Effect of Spiral Arms on Star Cluster Evolution. AAS/Division of Dynamical Astronomy Meeting, vol. 35, pp. May 2004.
[6] E. Gorbachev Yu, M.A. Zatevakhin, A.A. Ignatiev, V.V. Krzhizhanovskaya. Simulation of heat and mass transfer processes in PECVD reactors for silicon films growth under the conditions of intense formation of higher silanes in the gas phase in The 5th Minsk International Heat and Mass Transfer Forum, MIF-2004. May 24-28, 2004. Minsk, Belarus. Book of abstracts, V. 1, pp. 301-302 (in Russian), Proceedings published on CD, index S04/4-08. Proceedings on the Web: http://relay.itmo.by/forum/mif5/S04/4-08.PDF
[7]Y.E. Gorbachev, V.V. Krzhizhanovskaya and P.M.A. Sloot. Using GRID technologies for simulation of complex physical-chemical systems. In Proceedings of the XI All-Russian conference Telematika '2004. (In Russian) pp. 165-167, Publ.: SPbSU ITMO "Informika", St. Petersburg, Russia, June 2004.
[8] Y.E. Gorbachev, M.A. Zatevakhin, A.A. Ignatiev and V.V. Krzhizhanovskaya. Virtual Laboratory for Research and Education. In XI International Conference on High Technologies and Quality of Education and Science. pp. 90-91, SPbSPU, St. Petersburg Polytechnic University, February 2004.
[9] K.A. Iskra, G.D. van Albada and P.M.A. Sloot. Towards Grid-aware Time Warp. In Proceedings of the 18th Workshop on Parallel and Distributed Simulation, pp. 63-70, IEEE Computer Society, Kufstein, Austria, May 2004, ISBN 0-7695-2111-8.
[10] M.B.N. Kouwenhoven, A.G.A. Brown, A. Gualandris, L. Kaper, S.F. Portegies Zwart and H. Zinnecker. The Primordial Binary Population in OB Associations, in Revista Mexicana de Astronomia y Astrofisica Conference Series, (Provided by the NASA Astrophysics Data System ) pp. 139-140, August 2004.
[11] M.B.N. Kouwenhoven, S.F. Portegies Zwart, A. Gualandris, A.G.A. Brown, L. Kaper and H. Zinnecker. Recovering the primordial binary population using simulating observations of simulations. Astronomische Nachrichten Supplement, (Abstract) vol. 325, pp. 101, 2004.
[12] V.V. Krzhizhanovskaya, M.A. Zatevakhin, A.A. Ignatiev, Y.E. Gorbachev, W.J. Goedheer and P.M.A. Sloot. A 3D Virtual Reactor for Simulation of Silicon-Based Film Production, in 5th International Bi-Annual ASME/JSME Symposium on Computational Technologies For Fluid / Thermal / Chemical / Stressed Systems With Industrial Applications, held in conjunction with the ASME/JSME PVP Conference. In series ASME PVP, vol. 491, nr 2 pp. 59-68, San Diego / La Jolla, California, July 2004, ISBN 0-7918-4686-5.
[13] V.V. Krzhizhanovskaya, Y.E. Gorbachev and P.M.A. Sloot. A Grid-Based Problem-Solving Environment for Simulation of Plasma Enhanced Chemical Vapor Deposition. In Book of abstracts of the International Conference "Distributed Computing and Grid Technologies in Science and Education", pp. 89-90, JINR Dubna, Dubna, Russia, June-July 2004, ISBN 5-9530-0052-9.
[14] B. Leskes and P.M.A. Sloot. Unlearning Phenomena in Co-evolution of Non-uniform Cellular Automata. In P.M.A. Sloot, B. Chopard and A.G. Hoekstra, editors, Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004, in series Lecture Notes in Computer Science, vol. 3305, pp. 172-181, Springer Verlag, Heidelberg, October 2004, ISBN: 3-540-23596-5.
[15] B. Ó Nualláin and S. de Rooij. Online Suffix Trees with Counts. In Proceedings of the Data Compression Conference 2004, (accepted) IEEE Computer Society Press, 2004.
[16] K. Rycerz, M. Bubak, M. Malawski and P.M.A. Sloot. Support for Effctive and Fault Tolerant Execution of HLA-Based Applications in the OGSA Framework. In M. Bubak, G.D. van Albada, P.M.A. Sloot and J.J. Dongarra, editors, Computational Science - ICCS 2004: 4th International Conference, Kraków, Poland, June 6-9, 2004, Proceedings, Part III, in series Lecture Notes in Computer Science, vol. 3038, pp. 848-855, Springer Verlag, Heidelberg, June 2004, ISBN 3-540-22116-6.
[17] K. Rycerz, B. Bališ, R. Szymacha, M. Bubak and P.M.A. Sloot: Monitoring of HLA Grid Application Federates with OCM-G. In S.J. Turner, D. Roberts and L. Wilson, editors, Eighth IEEE International Symposium on Distributed Simulation and Real-Time Applications (DS-RT'04), pp. 125-132, IEEE, Budapest, Hungary, October 2004, ISBN 3-540-22116-6.
[18] P.M.A. Sloot, A. Tirado-Ramos, A.G. Hoekstra and M. Bubak. An Interactive Grid Environment for Non-Invasive Vascular Reconstruction, in 2nd International Workshop on Biomedical Computations on the Grid (BioGrid'04), in conjunction with Fourth IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004), (CD-ROM IEEE Catalog # 04EX836C) IEEE, Chicago, Illinois, USA, April 2004, ISBN 0-7803-8431-8.
[19] A. Tirado-Ramos, J.M. Ragas, D.P. Shamonin, H. Rosmanith and D. Kranzlmueller. Integration of Blood Flow Visualization on the Grid: the FlowFish/GVK Approach. In M.D. Dikaiakos, editor, Grid Computing: Proceedings of the 2nd European AcrossGrids Conference, Nicosia, Cyprus, in series Lecture Notes in Computer Science, vol. 3165, pp. 77-79, Springer Verlag, Nicosia,Cyprus, January 28-30 2004, ISBN: 30540-22888-8.
[20] L.R. Yungelson, G. Nelemans and S.F. Portegies Zwart. AM CVn systems as optical, X-ray and GWR sources. In Revista Mexicana de Astronomia y Astrofisica Conference Series, pp. 117-119, July 2004.
[21] K. Zajac, M. Bubak, M. Malawski and P.M.A. Sloot. Execution and Migration Management of HLA-Based Interactive Simulations on the Grid. In R. Wyrzykowski, J.J. Dongarra, M. Paprzycki and J. Wašniewski, editors, Parallel Processing and Applied Mathematics: 5th International Conference, PPAM 2003, Czestochowa, Poland, September 7-10, 2003. Revised Papers, in series Lecture Notes in Computer Science, vol. 3019, pp. 872-879, Springer-Verlag, Heidelberg, 2004, ISBN 3-540-21946-3.
[22] E.V. Zudilova and P.M.A. Sloot. Multi-modal Interaction in Biomedicine. In Y. Cai, editor, Ambient Intelligence for Scientific Discovery, in series Lecture Notes in Computer Science, vol. 3345, pp. 184-201, Springer-Verlag, Heidelberg, 2004.
Professional publications
[1] P.M.A. Sloot and A.G. Hoekstra: Virtual Vascular Surgery on the Grid, ERCIM news, October 2004.
Other products
Software
[1] The Dynamite software package for the checkpointing of PVM programs is available through

http://www.science.uva.nl/research/scs/Software

[2] Development of "Roche" binary evolution web interface:

http://carol.wins.uva.nl/~spz/act/roche/roche.html
[3] Development of "McScatter" hybrid software package for Monte-Carlo dynamics with binary evolution
http://manybody.org/McScatter.html
[4] MODESTA is a dedicated parallel computer platform for MOdeling DEnse STellar systems in Amsterdam. The machine became available for production on 2 October 2004 and is now working full time. Current performance is 1.01TFLOPs sustained speed. MODESTA has a dedicated web site: http://modesta.science.uva.nl/
Interviews e.d.
P.M.A. Sloot:

[1] Interview Time Magazine: http://www.time.com/time/nation/article/0,8599,574849-3,00.html

[2] Natuur, wetenschap en techniek, nr 12, 2004: Wetenschapper aan het woord: Boeken top 3 van Prof. Peter Sloot;

[3] AT 5: A commercial based on the theme “innovation” in the series for the campaign 'I Amsterdam' filmed at the Sciencepark, aired three times in December.

[4] 10 December 2004 VARA Interview: Vara: "Nieuwslicht", popular scientific program.

http://cgi.omroep.nl/cgi-bin/streams?/tv/vara/nieuwslicht/bb.20041210.asf
S.F. Portegies Zwart (selection):

[5] Sky & Telescope (August 2004, P.20) How to build a midsize black hole by Robert Naeye

[6] Radio (AM 747) program Hoe by Teleac (2 July 2004, at 13:00).

[7] Jornal de Ciencia (22 April 2004) Grupo propoe receita para buracos negros

[8] NRC Handelsblad (24 April 2004) Middelzware zwarte gaten

[9] Scientific American (28 April 2004) Colliding Stars May Form Intermediate Black Holes

[10] Sky & Teleskope (20 April 2004) Black hole construction zone by Robert Naeye

[11] Life on national radio VPRO Noorderlicht (20 April 2004) missende zwarte gaten in het heelal by van Hattum.

[12] Polskie radio (14 April 2004) Astronomia: Czarna dziura w budowie

[13] Aljazeera (15 April 2004) Missing link found in black hole by the editor

[14] de Volkskrant (18 April 2004) Amsterdammers vinden zwart gat by the editor

[15] BBC news (15 April 2004) New support for black hole theory by Paul Rincon

[16] cnn.com (14 April 2004) Colliding stars may create black holes by Robert Roy Britt

[17] Wissenschaft-online.de (14 April 2004) Sternencrash bei viel Verkehr by the editor

[18] Noorderlicht (VPRO) (14 April 2004) Middengaten by Maarten Keulemans

[19] Astronomy (March 2004) Black holes in the middle by Steve Nadis

[20] Sky & Telescope (4 Febr 2004) Stellar Breakups by Pamela L. Gay

2. Advanced Computing Systems Engineering
Recent key publications
[1] H. Afsarmanesh, V. Guevara-Masis, and L.O. Hertzberger. Management of Federated Information in Tele-assistance Environments. The Journal on Information Technology in Healthcare, 2 (2): 87-108, 2004.
[2] A.S.Z Belloum, D.Groep, L.O. Hertzberger, V. Korkhov, Cees T.A.M de laat, D. Vasunin. “VLAM-G: a Grid-based Virtual Laboratory” . Future Generation Computer System, 19, 2003, No 2, 209-217
[3] C. de Laat, E. Radius, S. Wallace. "The Rationale of the Current Optical Networking Initiatives", iGrid2002 special issue, Future Generation Computer Systems, volume 19 issue 6, 2003.
[4] A.D. Pimentel, L.O. Hertzberger, P. Lieverse, P. van der Wolf and E.F. Deprettere. Exploring Embedded-systems Architectures with Artemis. IEEE Computer, 34(11):57-63, 2001.
[5] Visser, H.H. Yakali, A.J. van der Wees, M. Oud, G.A. van der Spek and L.O. Hertzberger. “An hierarchical view on modelling the reliability of a dsrc-link for etc applications”. IEEE Transactions on Intelligent Transportation Systems, 3(2), June 2002.
Dissertations
[1] E.C. Kaletas: Scientific Information Management in Collaborative Experimentation Environments, PhD thesis, Universiteit van Amsterdam, Amsterdam. ISBN 90-5776-121-1. 2004.
Journal articles
[1] H. Afsarmanesh and L. M. Camarinha-Matos (Eds). International Journal of Networking and Virtual Organizations (Inderscience), Special issue on Infrastructures for new virtual organizations, Vol. 2, Nº 3, 2004.
[2] H. Afsarmanesh, V. Guevara-Masis, and L. O. Hertzberger. Management of Federated Information in Tele-assistance Environments. The Journal on Information Technology in Healthcare, 2 (2): 87-108, 2004.
[3] L.M. Camarinha-Matos and H. Afsarmanesh. A multi-agent based infrastructure to support virtual communities in elderly care. International Journal of Networking and Virtual Organizations, Inderscience, 2004 Vol. 2, No. 3, pp.246–266, ISSN 1470-9503, 2004.
[4] L.M. Camarinha-Matos and H. Afsarmanesh. TeleCARE: Collaborative virtual elderly care support communities. The Journal on Information Technology in Healthcare, Vol. 2, Issue 2, London, pp 73-86, ISSN 1479-649X, April 2004.
[5] C. Curti, T. Ferrari, L. Gommans, S. van Oudenaarde, E. Ronchieri, F. Giacomini, C. Vistoli. On Advance Reservation of Heterogeneous Network Paths. Future Generation Computer Systems Journal, 2004
[6] Y. Demchenko. Virtual Organisations in Computer Grids and Identity Management. Information Security Technical Report - Volume 9, Issue 1, January-March 2004, Elsevier, Pages 59-76
[7] E. C. Kaletas, H. Afsarmanesh and L. O. Hertzberger. A Collaborative Experimentation Environment for Biosciences. International Journal of Networking and Virtual Organizations, 2 (3): 209-231, 2004.