Telemedicine with a bullet in the high performance computing TOP500 list

Mannheim 11 November 1999Skipping through the freshly published November 1999 TOP500 list of best performing supercomputers, it is hard to discover at first glance where high performance computing power is used for medical applications. A more profound investigation however reveals that the Cray, Fujitsu, IBM and SGI supercomputing systems are omnipresent in the delivery of all the necessary calculation power for protein and genome research, drugs design, 3D visualisation, virtual simulation technologies implemented in minimally invasive surgery, and training simulator and telerobotic system development. Believe it or not, telemedicine is scoring surprisingly high in the new release of the Supercomputer TOP500.


Five supercomputer sites, which show serious medical ambition, storm the charts with more than one system. The highest climber, spotted at rank 10 with an IBM SP Power3 machine, is the University of California San Diego Supercomputer Center, which is listed four times. Installed in 1999 as the largest system available to the United States academic community, this IBM SP will help researchers tackle demanding computing problems, such as simulating the nervous system. Other SDSC supercomputers, like Cray T3E, are used to perform genetic analysis.

Ranked at position 28 with the 1998 Cray T3E and listed a second time with the 1994 Cray T3D, is the Pittsburgh Supercomputer Center. PSC scientist Marcela Madrid has used both machines in order to carry out simulations of structure and movement of reverse transcriptase (RT), an HIV enzyme that is targeted by AIDS drugs. The results have shown a joint-like movement in the "thumb" region of the enzyme. Blocking this motion might be the key to designing more effective RT-inhibitor drugs. The Pittsburgh machines are equally applied in the areas of protein research and brainmapping.

NASA Ames Research Center is ranked three times with its SGI Origin 2000 systems. Aerospace telemedicine technology enables physicians to consult, diagnose, and plan treatments for patients in real time from a great distance using 3D images rendered on high performance computers. The concept of this virtual collaborative clinic has actually been set up to help doctors treat astronauts travelling in space and provide care for people in remote locations on earth. The Ames computers are able to perform sophisticated simulations for medical imaging.

The pharmaceutical industry is extremely well represented in the TOP500 list with the Bayer IBM systems ranked four times and the SGI Origin 2000 from Vertex Pharmaceuticals at 376. The Bayer pharmaceuticals business group develops, manufactures and markets prescription drugs for cardiovascular, infectious, central nervous system and respiratory diseases as well as for the immune system and metabolic disorders. Vertex is actively involved in AIDS and cancer research. The Fujitsu-Siemens hpcLine Cluster of the Paderborn Parallel Computing Center is ranked at 351. The center has co-ordinated the Esprit funded Phase project, for the design of a distributed pharmaceutical applications server to deliver the power of high performance computing onto the desks of small and medium sized industrial companies operating in the field of drug target identification and modelling.

The Forschungszentrum Karlsruhe is listed twice, first with a 1999 IBM SP Power3 at 349 and second with a 1997 Fujitsu VPP300/16 at 494. Here, the Kismet simulation software package has been developed for a virtual reality based training system to simulate diverse minimally invasive surgical tasks. The centre is also specialised in computer-aided diagnostics, telerobotics and 3D medical visualisation. The Georgia Institute of Technology listed at 434 with a 1997 IBM SP P2SC has similar interests. In this centre, virtual reality is combined with physical models in the design of simulators for endoscopy and eye surgery.

Two very well-ranked sites are the Italian supercomputing centre Cineca (47) and the Edinburgh Parallel Computing Centre (49), both hosting a Cray T3E. These two institutions have applied and are still using big parts of their high performance computing and networking facilities for bioimaging applications in various European projects. Examples at Cineca relate to the pre-operative planning of maxillo-facial surgery; parallel reconstruction of medical images; and hip prosthesis alignment. Edinburgh has gained a great expertise in 3D visualisation in projects that deal with intra-operative real time visualisation and instrument tracking in MRI (IRVIT); real time 3D system building applied to sonography (PARSEMED); and, recently with cardiac magnetic resonance imaging analysis (CAMRA).

Two Japanese centres have been ranked for their genetic research with the aid of supercomputers. The Human Genome Center (176) at Tokyo University hosts a 1998 Hitachi SR2201/256 which is used for the isolation of disease-associated or brain-fundamental genes and in the development of genome analysis methods. The National Institute of Genetics at Mishima has a 1995 Fujitsu VPP500/40 (188) for bioinformatics studies, including the search for homology against available nucleotide sequences and amino acid sequences; multiple-alignment to reconstruct phylogenetic trees; computer simulation on the basis of evolutionary models; and the prediction of protein structures from amino acid sequences.

The Hewlett-Packard V2500/HyperPlex (435), hosted in Milano at Cilea, the Lombard consortium for supercomputing, is used among other applications for the numerical simulation of the blood flow capacity in cardiac valves, in the case of malformation. Finally, ranked at 442, is the fastest IBM computer in the Netherlands, which is located at SARA, the centre for supercomputing at the University of Amsterdam. This machine is currently being applied in the Virtual Radiology Explorer project to generate and transmit 3D Magnetic Resonance Imaging (MRI) scans of the human body for detailed analysis from and back to the participating hospitals. Additionally, supercomputing power is used at SARA to visualise 3D medical data sets in the CAVE, and to create simulation techniques for surgical applications. For a complete survey of all the supercomputers listed, we refer to the TOP500 home page.

Leslie Versweyveld

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