Life Sciences Commons^™

Intelligent Resource Prediction For Hpc And Scientific Workflows, Benjamin Shealy

All Dissertations

Scientific workflows and high-performance computing (HPC) platforms are critically important to modern scientific research. In order to perform scientific experiments at scale, domain scientists must have knowledge and expertise in software and hardware systems that are highly complex and rapidly evolving. While computational expertise will be essential for domain scientists going forward, any tools or practices that reduce this burden for domain scientists will greatly increase the rate of scientific discoveries. One challenge that exists for domain scientists today is knowing the resource usage patterns of an application for the purpose of resource provisioning. A tool that accurately estimates these …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Using Deep Learning For Children Brain Image Analysis, Rafael Toche Pizano

Computer Science and Computer Engineering Undergraduate Honors Theses

Analyzing the correlation between brain volumetric/morphometry features and cognition/behavior in children is important in the field of pediatrics as identifying such relationships can help identify children who may be at risk for illnesses. Understanding these relationships can not only help identify children who may be at risk of illnesses, but it can also help evaluate strategies that promote brain development in children. Currently, one way to do this is to use traditional statistical methods such as a correlation analysis, but such an approach does not make it easy to generalize and predict how brain volumetric/morphometry will impact cognition/behavior. One of …

Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke

Computer Science and Computer Engineering Undergraduate Honors Theses

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …

Incorporating Demographic Structure And Variable Interaction Types Into Community Assembly Models, Akhil Reddy Alasandagutti, Nayan Chawla

Honors Theses

Theoretical studies of ecological food webs have allowed ecologists to remove the constraints of specific location and timescales from their study of ecological communities; food webs are generally complex and thus empirical study is difficult. Further, this theoretical approach allows ecologists to compare ecological processes and outcomes across any possible food web structures. However, these simulated communities are only as useful as the model from which they were constructed. Modifying existing considerations in these models, and generating new ones, are the jobs of theoretical ecologists that seek to achieve the shared goal of a majority of simulations: representation of real …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Maternal Proximity To Mountaintop Removal Mining And Birth Defects In Appalachian Kentucky, 1997-2003, Daniel B. Cooper

Theses and Dissertations--Public Health (M.P.H. & Dr.P.H.)

Background: Extraction of coal through mountaintop removal mining (MTR) alters many dimensions of the landscape, and explosive blasts, exposed rock, and coal washing have the potential to pollute air and water with substances known to increase risk of developmental and birth anomalies. Previous research suggests that infants born to mothers living in MTR coal mining counties have higher prevalence of most types of birth defects.

Objectives: This study seeks to examine further the relationship between MTR activity and birth defects by employing individual level exposure estimation through precise satellite data of MTR activity in the Appalachian region and maternal residence …