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Physical Sciences and Mathematics Commons™
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- Bioinformatics (2)
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Articles 1 - 6 of 6
Full-Text Articles in Physical Sciences and Mathematics
Examining Natural Resource Conservation: In The Classroom, Through Collaborative Conservation, And Across Public Communication Platforms, Shauni Seccombe
Examining Natural Resource Conservation: In The Classroom, Through Collaborative Conservation, And Across Public Communication Platforms, Shauni Seccombe
Graduate Student Portfolios, Professional Papers, and Capstone Projects
No abstract provided.
Modeling Stromatolite Formation With Diffusion-Limited Aggregation, Laura E. Stevens
Modeling Stromatolite Formation With Diffusion-Limited Aggregation, Laura E. Stevens
Graduate Student Theses, Dissertations, & Professional Papers
Stromatolites, microbialites, and other microbially induced sedimentary structures exist in the rock record as far back as 3.6 billion years ago and continue to form in the present day. Better characterizing these structures and better understanding how they form is crucial in distinguishing these biosignatures from similar, abiotic structures, which can help us to understand the conditions of early Earth and early Mars. To that end, I have modified DLA 3D EXT, an open-source stromatolite modeling program, to more closely reflect the process of microbial trapping-and-binding by filamentous microbes in a calcite-precipitating hot spring system. This modified program includes a …
Nitrogen Dynamics And Transport Along Flowpaths In A Rural Wetland-Stream Complex, Colton Kyro
Nitrogen Dynamics And Transport Along Flowpaths In A Rural Wetland-Stream Complex, Colton Kyro
Graduate Student Theses, Dissertations, & Professional Papers
Human activities have doubled the rate of nitrogen inputs onto the landscape resulting in elevated nitrogen concentrations in our streams. Anthropogenically applied nitrogen is largely transported to stream networks via groundwater movement. Groundwater discharge occurs in distinct points along a stream but whose influences can often persist far beyond that area due to insufficient biogeochemical removal of imported nitrogen potentially causing alterations in community structure and precipitating large algae blooms. To understand the factors governing nitrogen abundance in a historical polluted stream, I used a mass-balance approach to quantify groundwater-surface water interaction and the magnitude of groundwater nitrogen input and …
Soda: An Open-Source Library For Visualizing Biological Sequence Annotation, Jack W. Roddy, Travis J. Wheeler
Soda: An Open-Source Library For Visualizing Biological Sequence Annotation, Jack W. Roddy, Travis J. Wheeler
Graduate Student Theses, Dissertations, & Professional Papers
Genome annotation is the process of identifying and labeling known genetic sequences or features within a genome. Across the various subfields within modern molecular biology, there is a common need for the visualization of such annotations. Genomic data is often visualized on web browser platforms, providing users with easy access to visualization tools without the need for installing any software or, in many cases, underlying datasets. While there exists a broad range of web-based visualization tools, there is, to my knowledge, no lightweight, modern library tailored towards the visualization of genomic data. Instead, developers charged with the task of producing …
Sula Study Revisited: 20-Year Post-Fire Regeneration In The Southern Bitterroot Valley, Montana., Luke Alan Rymniak
Sula Study Revisited: 20-Year Post-Fire Regeneration In The Southern Bitterroot Valley, Montana., Luke Alan Rymniak
Graduate Student Theses, Dissertations, & Professional Papers
In the summer of 2000, a number of large fires burned in the southern Bitterroot Valley near Sula, Montana. Research was conducted in 2001 and 2003 in the fire-affected areas of the French Basin and Larid Creek areas in order to investigate the effects of environmental variables, fire severity, and post-fire management on vegetation regeneration. In 2020 these areas were remeasured to understand trends over time by evaluating the impact of these same factors 20 years post fire. The results showed that the effects of environmental variables, fire severity, and post-fire management on vegetation regeneration were varied. The most influential …
Ensemble Protein Inference Evaluation, Kyle Lee Lucke
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 …