Theses and Dissertations at Montana State University (MSU)
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Item Simulation of deformation of colliding objects using particle systems(Montana State University - Bozeman, College of Engineering, 1989) Koti, Shirish RaghunathItem Visualizing Monte Carlo computed radiation energy values by using a density emitter(Montana State University - Bozeman, College of Engineering, 1994) Donahue, Brett A.Item Visualization of light inside leaves of Saxifraga rhomboidea(Montana State University - Bozeman, College of Engineering, 2002) Brown, Lisa AnnItem Model implementation and image data compression in a decision support system(Montana State University - Bozeman, College of Engineering, 1997) Wang, XiaobeiItem Modeling the deformation of colliding objects(Montana State University - Bozeman, College of Engineering, 1991) Younkin, Chance ReedItem Numerical simulation of biofilm accumulation in pipelines(Montana State University - Bozeman, College of Engineering, 1992) Szego, SandorItem Natural modeling of quaking aspen(Montana State University - Bozeman, College of Engineering, 1993) Spear, Rita SteeleItem Metaprogramming bioinformatics in the postgenomic era(Montana State University - Bozeman, College of Engineering, 2006) Ohler, Nathaniel Tobias; Chairperson, Graduate Committee: Brendan MumeyThe number of bioinformatics programs available is continuously growing, along with the knowledge required to run each individual program. As more programs become available, more complex combinations of these programs are being used by scientists. Workflow engines attempt to remove repetitive procedures from these combinations by saving and executing any group of the programs as one larger "meta-program". The output of one program is automatically directed to the input of another thereby creating a "flow' of "work". The first part of this project is the design and development of an easy to use workflow editor that maintains the usability of the original programs and allows for the relatively simple addition of new programs. The result is a workflow editor that currently allows access to over 170 bioinformatics programs each with a simple, common, and descriptive interface. In the second part of this project a specific workflow application for protein antibody imprinting is examined. Part of the workflow is a program that produces a series of potential alignments for an antibody and a protein, has already been developed. An additional program is developed which uses a greedy search algorithm to select the "best" set of alignments. This alignment selection problem is shown to be NP-Complete. These programs represent a real world example of a bioinformatics workflow.