Computational Science Laboratory

The Computational Science Laboratory investigates new algorithms for solving problems in computational biology, computational chemistry and computational physics. Emphasis is placed on finding efficient algorithms that can be run on parallel computers.

Resources

The Laboratory currently uses computational resources from the Fulton Supercomputing Center as well as 600-800 idle desktop nodes across the BYU campus that are managed by the DOGMA system.

Software

Several software packages have been developed by members of the laboratory including:

• GNUMAP maps reads from next-generation sequencers to genomic data.
• DOGMA uses idle computers as well as clusters and supercomputers for distributed scientific computing.
• The PSODA project provides a phylogenetic search tool that reads the same data file format as PAUP*.
• Members of the laboratory collaborate with the Department of Integrative Biology to develop software to analyze biochemical properties when performing alignment or phylogeny search. This software performs a detailed analysis of selection on amino acid properties using user-defined phylogenetic trees.
• The TCS project estimates gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented in TCS is also known as Statistical Parsimony, which is described in Templeton, A. R., K. A. Crandall and C. F. Sing. 1992.
• The ScaffoldScaffolder project is for haplotype-aware scaffolding of contigs. It also includes modules for solving the Contig Orientation Problem.

Funding

The laboratory is currently supported by an NSF grant to investigate hexapod phylogeny.