Before ISMB`99 SGI had decided to donate an SGI 320 machine, the new Pentium-based NT desktop machine from SGI that combines SGI's graphics technology with the standard Intel platform, to award an outstanding paper presented during the ISMB Conference. During the conference SGI augmented this offer to two such machines for two papers. Out of all presented papers, the organizing committee of ISMB'99 has selected two papers for the two awards. The selection was based on quality of the work, significance of the work papers with junior first authors were given some preference papers involving members of scientific groups of members of the organizing committee were excluded. The two SGI machines were awarded to the papers Using the Fisher kernel method to detect remote protein homologies Tommi Jaakkola, Mark Diekhans, David Haussler Spatio-temporal Registration of the Expression Patterns of Drosophila Segmentation Genes Ekaterina M. Myasnikova, David Kosman, John Reinitz, Maria G. Samsonova The awards were conferred by Udo Leutz from SGI Europe.

SGI donated 120 hours of time on a 128 CPU SGI Origin 2000, for the award-winning crunch proposal. Among seven submitted proposals the organizing committee of ISMB'99 selected a proposal by David Gilbert from EBI/City University of London with the title Finding Patterns in Protein Structure Databases using Clique Detection John Carpenter from the High Performance Computing Section of SGI conferred the SGI-Crunch Award.