Difference between revisions of "CS 618"
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This page will contain the course syllabus and plan for CS 618 Computational Biology for the summer of 2024. For now, it contains a list of topics that we will look at. The basic plan is to look at a number of projects that I have worked on in the past, and to look at key tools and algorithms used in computational biology and bioinformatics. | This page will contain the course syllabus and plan for CS 618 Computational Biology for the summer of 2024. For now, it contains a list of topics that we will look at. The basic plan is to look at a number of projects that I have worked on in the past, and to look at key tools and algorithms used in computational biology and bioinformatics. | ||
| − | Projects | + | =Projects= |
| − | + | '''Gene expression''' - determining key genes from gene expression datasets. Project is in R, uses Shiny, Datatables, ShinyProxy, Docker. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-bartlett.pdf | |
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| − | Topics/Concepts | + | '''Protein topology prediction''' - finding potential transmembrane proteins in genomes. Project is in Python, uses Javascript, NCBI, BLAST. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-hoffman.pdf |
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| − | + | '''Transcription factors''' - finding mutations to disable a transcription factor while still preserving others. Project is in Python, R, and/or C. Poster - https://cs.indstate.edu/info/posters/bd4isu2020-bennett.pdf | |
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| − | + | '''Gene expression''' - determining key genes in a particular dataset from fish. Poster - https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf | |
| − | + | ||
| + | '''Mass spectrometry data''' - keeping a database of mass spec data and searching through databases for new samples. Potential new project. | ||
| + | |||
| + | =Topics/Concepts= | ||
| + | '''Central dogma of genetics''' | ||
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| + | '''Biological data''' - different types of assays, etc. - how the data is produced, what the data looks like, etc. | ||
| + | |||
| + | '''Sequence alignment algorithms''' | ||
| + | |||
| + | '''Clustering techniques''' | ||
| + | |||
| + | '''Statistics''' | ||
Revision as of 22:13, 17 April 2024
This page will contain the course syllabus and plan for CS 618 Computational Biology for the summer of 2024. For now, it contains a list of topics that we will look at. The basic plan is to look at a number of projects that I have worked on in the past, and to look at key tools and algorithms used in computational biology and bioinformatics.
Projects
Gene expression - determining key genes from gene expression datasets. Project is in R, uses Shiny, Datatables, ShinyProxy, Docker. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-bartlett.pdf
Protein topology prediction - finding potential transmembrane proteins in genomes. Project is in Python, uses Javascript, NCBI, BLAST. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-hoffman.pdf
Transcription factors - finding mutations to disable a transcription factor while still preserving others. Project is in Python, R, and/or C. Poster - https://cs.indstate.edu/info/posters/bd4isu2020-bennett.pdf
Gene expression - determining key genes in a particular dataset from fish. Poster - https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf
Mass spectrometry data - keeping a database of mass spec data and searching through databases for new samples. Potential new project.
Topics/Concepts
Central dogma of genetics
Biological data - different types of assays, etc. - how the data is produced, what the data looks like, etc.
Sequence alignment algorithms
Clustering techniques
Statistics
