BDS 211

Use and Abuse of Data: Critical Thinking in Science

Critically examine how data analysis can support legitimate conclusions from biological datasets and also how biased sampling, misleading comparisons, and spurious reasoning can lead to false conclusions. Analyze data to break down the logical flow of an argument and identify key assumptions, even when they are not stated explicitly.


BDS 311

Computational Approaches for Biological Data

Real-world biological datasets to implement fundamental concepts of efficient algorithm design. Synthesize previously acquired knowledge and skills in biology and computer science to analyze, implement, and apply algorithms that process biological datasets, including large-scale datasets.

  • Prerequisites: (BI 212 OR BI 212H) AND (MTH 252 OR MTH 252H) AND CS 261 AND (BI 213 OR BI 213H) AND (ST 351 OR ST 351H) OR instructor consent
  • Co-requisites: None
  • Instructor: Dr. Tim Warren

BDS 406

Special Projects for Senior Students: Professional Skills

Reflect upon experiential learning projects and build professional skills, including oral and a hard-copy written presentations, building a curriculum vitae or resumé, preparing job or graduate school application, listening and responding to other student presentations.

  • Prerequisites: completion of Experiential Learning project
  • Co-requisites: None
  • Instructor: Dr. Jeff Chang

BDS 411

  (Under development)

Analysis of Biological Data: Case Studies

In BDS 411, we will explore the way that professional data scientists report biological data. From Science Magazine to 23andMe, this course will examine real biological data from world-class research labs and major corporations—and effective ways of communicating data science results. We will learn to identify the ‘Big Picture’ underlying data science investigations, generate testable hypotheses, and support analyses with eye-popping visuals. By the end of the quarter, students will have mastered several methods for communicating data science and learn to formulate research plans of their own. During the course, students will produce a data visualization dashboard that analyzes a real industry-produced dataset and an independent research proposal in the style of the NSF Graduate Research Fellowship Program.

This course fulfills the Baccalaureate Core requirement for the Writing Intensive Curriculum (WIC) category for students majoring in Biological Data Sciences majors.

  • Prerequisites: ((BI 311 OR BI 311H) OR (BB 314 OR BB 314H) OR MB 310) AND ((MTH 252 OR MTH 252H) OR MTH 228) AND CS 261 AND (ST 352 OR ST 412)
  • Co-requisites: None
  • Instructor: Dr. Sam Leiboff
  • Promo: BDS 411 graphic

BOT 460

Functional Genomics

Functional genomics describes a set of conceptual approaches and associated laboratory techniques that rely on large-scale DNA sequence datasets to investigate the function of, and interactions between, genes as well as their RNA/protein products. This course will provide an overview of these techniques, including a) approaches to predicting protein function based on sequence analysis, b) large-scale genetic approaches to identifying novel genotype-phenotype associations, and c) transcriptomic, proteomic and metabolomic approaches that reveal gene functions by measuring changes in abundance/modification of associated RNA transcripts, proteins and metabolites.

  • Prerequisites: (BI 311 with C- or better or BI 311H with C- or better) and (BI 314 [C-] or BI 314H [C-])
  • Co-requisites: None
  • Instructor: Dr. Jeff Anderson

BOT/BDS 474

  (Course under development)
Introduction to Genome Biology

The genome - that is, the entirety of the genetic information (DNA) that lies at the center of every living organism - plays a major role in defining biological species, from prokaryotic microbes to eukaryotic multicellular organisms. Genomes underlie and influence all biological phenomena, from biochemistry and development to evolution and ecology. However, genomes are huge - for example, the human genome is ~3 billion nucleotides in size - and so, until recently, very difficult to investigate. Recent technological advances, particularly in DNA sequencing, are producing unprecedented quantities of genome-scale data and enabling new insights into how genomes work. Incorporating these new types of information, BOT/BDS 474 Introduction to Genome Biology will first provide an overview of the ways in which genomes are organized and evolve, for example, via mutation or via mobile genetic elements like transposons. The course will then cover the mechanisms (e.g., transcriptional and epigenetic regulation) that link genomes to the characteristics of organisms - i.e., to phenotypes. Students will expand their domain knowledge in basic genetic, biochemical and cellular mechanisms, and will begin to learn how to ‘think big’ about experimental approaches to understanding genomes.


BOT 475

Comparative Genomics

Introduction to comparative genomics. Methods for genome assembly and annotation. Genomic approaches for the study of structural change, whole genome duplication, and gene family evolution. Lab topics include the analysis of next generation sequencing data and conducting comparative genomic analyses.

 


BOT 476

Introduction to Computing in Life Sciences

Introduction to management of large datasets (e.g., nucleic acids, protein), computer programming languages, application of basic mathematical functions, and assembly of computational pipelines pertinent to life sciences.


New Course

  (New course under development)

In this course, students will learn fundamentals in generating and using contemporary genomics data to study evolution of plant associated microbial communities as examples. Students are expected to have a fundamental understanding of genetic concepts and be familiar with evolutionary theory related to populations such as gene flow, genetic drift, selection, and mutation rates. In this course, students will learn genomic approaches including, but not limited to, comparative genomics, genome-wide association mapping, expression analysis, and metagenomics. These genomic approaches will be compared and contrasted and framed around fundamental concepts in genetics and evolution. Upon completion of the course, students will be proficient in formulating approaches for studying genetic and phenotypic diversity of populations. Further, students will be adept in analyzing and critiquing primary literature and developing related hypotheses testable with genomics data.


BDS 491

Capstone Projects in Biological Data Science I

Quantitative skills and biological thinking will be used to analyze and draw conclusions from real-world biological datasets. Projects will be completed in the context of small groups. This is a synthesis course that draws skills in mathematics, statistics, computer science, and biology.

  • Prerequisites: (ST 352 OR ST 412) AND (CS 162 OR BOT 476 OR BB 485 OR MTH 427) OR instructor consent
  • Corequisites: none
  • Instructor: Dr. Maude David
  • Course advertisement: BDS 491 flyer

BDS 492

Capstone Projects in Biological Data Science II

Quantitative skills and biological thinking will be used to analyze and draw conclusions from biological datasets retrieved in BDS 491. This is a synthesis course that draws skills in mathematics, statistics, computer science, and biology, in which the students will process their curated datasets and draw conclusions.

  • Prerequisites: BDS 491 OR instructor consent
  • Corequisites: none
  • Instructor: Dr. Maude David

Some courses that were previously listed under the Molecular and Cellular Biology Program (MCB) are now available as BDS courses.

BDS 599: These are a series of courses offered by the Center for Genome Research and Biocomputing. Topics include:

  • Command-Line Data Analysis
  • Data Programming in R
  • Environmental Sequence Analysis
  • GBS (Genotyping by sequencing)
  • Introduction to Unix/Linux
  • Introduction to R and RStudio
  • Python I
  • Python II
  • RNA Sequencing

Please note that courses are offered in different terms. Learn more about course workshops offered through CRGB