David Hart

• Indiana University Bloomington

GeneIndex is an open-source program that locates words of any length k specified by the user in a sequence. GeneIndex is useful for understanding the structure of entire genomes or very large sets of genetic sequences, particularly in finding highly repeated words and words that occur with low frequency. GeneIndex accepts DNA sequences in FASTA for...

Maximum likelihood analysis is a powerful technique for inferring evolutionary histories from genetic sequence data. During the fall of 2003, an international team of computer scientists, biologists, and computer centers created a global grid to analyze the evolution of hexapods (arthropods with six legs). We created a global grid of computers usin...

Summary form only given. As the first geographically distributed supercomputer on the top 500 list, the AVIDD facility of Indiana University ranked 50^th in June of 2003. It achieved 1.169 tera-flops running the LINPACK benchmark. Here, our work of improving LINPACK performance is reported, and the impact of math kernel, LINPACK problem s...

Not Available

The revolution in life sciences research brought about by the sequencing of the human genome creates new challenges for scientists and new opportunities for computing support organizations. This may involve significant shifts in computing support strategies, particularly as regards interacting with life sciences researchers who maintain a medical p...

The recent revolution in biomedical research opens new possibilities for applications of parallel computing. This chapter discusses three parallel applications useful in medicine and bioinformatics, PENELOPE, GeneIndex, and fastDNAml, in terms of their scaling characteristics and the way they are used by biomedical researchers. PENELOPE is a code t...

Indiana University and IBM, Inc. have a very strong history of collaborative research, aided significantly by Shared University Research (SUR) grants from IBM to Indiana University. The purpose of this document is to review progress against recent SUR grants to Indiana University. These grants focus on the joint interests of IBM, Inc. and Indiana U...

This paper describes the parallel implementation of fastDNAml, a program for the maximum likelihood inference of phylogenetic trees from DNA sequence data. Mathematical means of inferring phylogenetic trees have been made possible by the wealth of DNA data now available. Maximum likelihood analysis of phylogenetic trees is extremely computationally...

Supercomputers were once regarded as being of very limited use - of interest to a very few national centers and used by a small fraction of researchers at any given university. As scientific research becomes more and more dependent upon management and analysis of massive amounts of data, advances in human knowledge will become increasingly dependen...

Supercomputers were once regarded as being of very limited use - of interest to a very few national centers and used by a small fraction of researchers at any given university. As scientific research becomes more and more dependent upon management and analysis of massive amounts of data, advances in human knowledge will become increasingly dependen...

Polar plots of various types of anisotropic data are often approximated by ellipses and used by earth scientists as part of the interpretation process. FITELLIPSE, a code to calculate the orientation and values of the major and minor axes of a best-fit ellipse to anisotropic data, is written using Maple, a standard commercial software. A nonlinear...

Indiana University has a decades-old research relationship with IBM. This relationship has expanded and deepened significantly in the past two years, in large part thanks to the SUR grants awarded by IBM to IU, totaling $2.45M (retail value) in IBM high performance hardware.