Biomedical Grid Challenges: Two examples

Peter Sloot UvA

http://www.science.uva.nl/~sloot


An area with many requirements and challenges to grid technology is
social healthcare in general and (bio)medical sciences in
particular. In this context, issues such as remote access to patient
data, medical knowledge bases, and specialized medical instruments are
of utmost importance. For these applications, grid technology should
provide dedicated support such as strong security, distributed storage
capability, and high throughput across long distance networks.

Besides these immediate requirements, the computational resources of
the grid should provide the required performance for large-scale
simulations, which are of major importance to many areas of medical
sciences.

I will briefly discuss two examples of grid-based prototype systems
under development in my lab:

[1] Pre-treatment planning in vascular interventional and surgical
procedures, developed in the scope of the EU CrossGrid project. We
developed an agent-oriented architecture, the Interactive Simulation
System Conductor (ISS), for the design of interactive experiments. The
Vascular Radiology Explorer is a case study for these experiments. I
will present the architecture, functionality and
simulation-visualisation techniques that have been developed and the
end-user evaluation.

[2] A grid-based medical decision support system that integrates
access of distributed data from infectious disease patient databases,
literature on in-vitro and in-vivo pharmaceutical data, mutation
databases, clinical trials, simulations and medical expert knowledge.

The output of the system consists of a prediction of the drug
sensitivity of the virus generated by comparing the viral genotype to
a relational database, containing a large number of phenotype-genotype
pairs. Multivariate analyses combined with rule-based fuzzy logic are
applied to the integrated data and provides ranking of patient
specific drugs. In addition cellular automata based simulations are
used to predict the drug-behaviour over time. Access to and
integration of data is done through existing Internet servers and
emerging grid-based tools like Globus. Data presentation is done by
standalone PC based software, Web-access and PDA roaming WAP access.
The experiments were carried out on the DAS, a Dutch Grid testbed.

References:

Sloot P.M.A., Boucher C.A., Keulen W., Kiryukhin I., Saskov K.,
Boukhanovsky A.: A grid-based problem-solving environment for
biomedicine, Proc. of the 1st European HealthGrid Conference, Lyon,
France, January 2003, pp.300-323.

Sloot P.M.A., Albada van G.D., Zudilova E.V., Heinzlreiter P.,
Kranzlmüller D., Rosmanith H., Volkert J.: Grid-based Interactive
Visualisation of Medical Images, Proc. of the 1st European HealthGrid
Conference, Lyon, France, January 2003, pp.57-67.

E.V. Zudilova; P.M.A. Sloot and R.G. Belleman: A Multi-modal Interface
for an Interactive Simulated Vascular Reconstruction System, in Fourth
IEEE ACMI'02 International Conference on Multimodal Interfaces,
Pittsburgh, Pennsylvania, 14-16 October 2002, pp. 313-318. IEEE
Computer Society, Los Alamitos, California, USA, 2002.

A. Tirado-Ramos; K. Zajac; Z. Zhao; P.M.A. Sloot; G.D. van Albada and
M.  Bubak: Experimental Grid Access for Dynamic Discovery and Data
Transfer in Distributed Interactive Simulation Systems, in
International Conference on Computational Science 2003, Saint
Petersburg, Russian Federation, Springer-Verlag, Heidelberg, June
2003.

K. Zajac; A. Tirado-Ramos; Z. Zhao; P.M.A. Sloot and M. Bubak: Grid
Services for HLA-based Distributed Simulation Frameworks, in First
European Across Grids Conference, Santiago de Compostela, Spain,
Springer-Verlag, Heidelberg, February 2003.

Z. Zhao; G.D. van Albada; A. Tirado-Ramos; K. Zajac and P.M.A. Sloot:
ISS-Studio: a prototype for a user-friendly tool for designing
interactive experiments in Problem Solving Environments, in
International Conference on Computational Science 2003, Saint
Petersburg, Russian Federation, Springer-Verlag, Heidelberg, June
2003.

More: see:

http://www.science.uva.nl/research/scs/papers/sloot.html

http://www.healthgrid.org/

http://www.eu-crossgrid.org/