Progress 09/01/23 to 01/15/25
Outputs
Target Audience:Researchers and technicians with limited bioinformatic experience who are conducting studies/surveys (often agricultural) that require insect diagnostics. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
To support the bioinformatic pipelines, I learned about software management, namely workflows and software containerization. Workflow tools (I learned Common Workflow Language) provide an infrastructure to set up and run a sequence of tasks, for example, when importing sequence data and calling genotypes. Software containerization creates a portable, isolated environment that has the main programs and their dependencies; this makes it easier to run programs across different computing environments. I learned how to make Docker containers, which is a popular open-source platform for containerization.
Publications
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Progress 09/01/23 to 08/31/24
Outputs
Target Audience:Researchers monitoring invasive or pest insects for phytosanitary purposes. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? I developed teaching experience by creating and teaching an introductory bioinformatics workshop at the Univeristy of Iceland. This was a week-long, bootcamp-style workshop (Bioinformatics, from Command Line to Genomes) on bioinformatics and data analysis in population genomics at the University of Iceland from May 13 - 16th 2024. How have the results been disseminated to communities of interest? Publication on diagnostic marker selection in the journal Bioinformatics. Publicly available code on GitHub. What do you plan to do during the next reporting period to accomplish the goals? For the first objective, I will develop the code for the API that allows different bioinformatic software/pipelines to interact. For the second objective, I will develop the GUI that allows users to interact with the software without command-line experience. The third objective is to document and demonstrate the utility of the software with publicly available tephritid data. This is contingent on the first two objectives, however, I should be able to start on this objective while the other two are in progress.
Impacts
What was accomplished under these goals?
The first objective is software development, where I develop an analysis pipeline with a universal application programming interface (API) that allows the pipeline programs to share data. I am learning the necessary Python coding skills and have researched bioinformatic programs for the pipeline. Because this project is intended for non-model systems and emerging pests, I also thought about programs that streamline the development of new diagnostic panels. Thus, I co-authored an R package, snpAIMeR (https://github.com/OksanaVe/snpAIMeR), that helps select panel markers from a set of candidate markers. The paper for this program was published at the journal Bioinformatics. The second objective addresses software accessibility, where I develop a graphical user interface (GUI) for point-and-click analysis (instead of expecting users to know command line). Here, I am learning the necessary Python coding including the Tkinter library for creating GUI applications and the Bokeh library for interactive data visualization.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2024
Citation:
Vertacnik, K. L., Vernygora, O. V., & Dupuis, J. R. (2024). snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics. Bioinformatics, btae377.
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