GeneCrunch and Europort, examples for Hierarchical Supercomputing at Silicon Graphics

The SGI POWER CHALLENGEarray TM represents a hierarchical supercomputer because it combines distributed and shared memory technology. We present two projects, Europort and GeneCrunch, that took advantage of such a configuration. In Europort we performed scalability demonstrations up to 64 processors with applications relevant to the chemical and pharmaceutical industries. GeneCrunch, a project in bioinformatics, performed an analysis of the whole yeast genome using the software system GeneQuiz. This project showcased the future demands of HPC in pharmaceutical industries in tackling analysis of fast growing volumes of sequence information. GeneQuiz, an automated software system for large-scale genome analysis developed at the EMBL /EBI , aims at predicting the function of new genes by using an automated, rigorous, rule-based system to process the results of sequence analysis and database searches to build databases of annotations and predictions. In GeneCrunch more than 6,000 proteins from baker's yeast, for which the complete genomic sequence was completed in 1996, were analyzed on a SGI® POWER CHALLENGEarray with 64 processors (R8000® at 90MHz) in three days rather than the seven months predicted for a normal workstatio

Molecular dynamics studies of the interface between a model membrane and an aqueous solution.

Molecular Dynamics (MD) computer simulation studies are reported for a system consisting of two model membranes in contact with an aqueous solution. The influence of the membrane on the adjacent liquid is of main interest in the present study. It is therefore attempted to make the system sufficiently large to encompass the entire region between bulk liquid and the membranes. The latter are modeled by two-dimensional arrays of COO- groups with rotational and translational degrees of freedom. The water molecules are represented by the well-tested TIP4P model. The intermolecular potentials are parametrized in terms of Coulomb interactions between partial charges on the molecular frames and empirical, mostly Lennard-Jones (12-6), interactions centered at the atomic positions. A strong layering of the liquid accompanied by an increase in average water density is found in the vicinity of the membrane. The structural perturbation reaches approximately 8 A into the liquid. We discuss the static structure in these layers in terms of atom-atom distance distribution functions and study the average orientation of the water molecule dipoles with respect to the membrane. From the distribution of the ions, we find that less than 50% of the surface charge of the membrane is neutralized by Na+ ions in the first layer above the membrane. A simplified model of the adsorption site of the ion on the membrane is developed from the distance distributions. Finally the hydration of the Na+ in the first adsorbed layer is discussed

Molecular dynamics study of the interface amphiphile molecules / ionic solution

A model of the interface between an ionic solution and amphiphile molecules is presented. This model resembles closely a Langmuir monolayer and has similarities with a biomembrane. Using the molecular dynamics simulation method the structural properties of this system are examined. The results are in good agreement with the available experimental data

GeneCrunch: Experiences on the SGI POWER CHALLENGEarray with Bioinformatics applications

Analyzing genomic data is a computationally intensive and complicated process in which scientists must typically choose among multiple databases and analysis methods and make expert judgements inspecting multiple results. GeneQuiz, an automated software system for large scale genome analysis developed at the EMBL/EBI, tackles this problem by using an automated, rigorous, rule-based system to select among the results of sequence analysis and database searches, builds informative annotation and aims at predicting the function of new genes. In a demonstration project more than 6000 proteins from the Baker’s yeast, for which the complete genomic sequence was completed in 1996, were analyzed on a Silicon Graphics POWERCHALLENGEarray with 64 processors (R8000 @90 MHz) so that the analysis could be completed in 3 days. The results of the analysis were published on two web servers as they were computed