Fall 2020: Investigating Microbial Communities
Course Objectives (CO) Fall 2020
Course Objectives (CO) – Fall 2020
- CO 1. Demonstrate laboratory skills required of a modern-day molecular biologist in the era of next-generation sequencing. This includes keeping detailed and accurate laboratory notes (e.g., electronic records for sequence analyses) and choosing appropriate sequencing based on goals.
- CO 2. Read a scientific article and evaluate how bioinformatics methods were employed by the authors to explore a particular hypothesis. [from CourseSource framework]
- CO 3. Given a scientific question, develop a hypothesis and define computational approaches that could be used to explore the hypothesis. [from CourseSource framework]
- CO 4. Use pre-existing tools to analyze a metagenomic data set to determine the set of organisms present in a metagenomic sample (e.g., 16s rRNA, Greengenes, mothur, etc.). [from CourseSource framework]
- CO 5. Interpret data and identify limitations related to metagenomic surveys.
- CO 6. Design a critical thinking scenario and explain analyses for hypothesis testing of metagenomic data.
Introduction and Charge
There is a massive amount of information about metagenomics! We can easily get overwhelmed by the number of tools, complex analyses, and large datasets. We have an opportunity to work together to summarize as a group concepts that are central to the understanding of the power and applications of metagenomics.
This document is your digital notepad. You have access to edit it as you wish, and we encourage you to use a rich array of resources at your disposal. Include links, edit for clarity, and summarize. We have provided the framework in terms of the learning outcomes for each session. It is up to you to work collaboratively to produce a summary for each session.
To work efficiently, we need some ground rules:
- Everyone is expected to contribute to the document during the week for that module/quest.
- You can suggest comments to your peers by clicking on “Suggesting mode” in the top right corner. You can also make comments and respond to your peers. I will moderate and resolve comments.
- The material you incorporate into this document is meant to help all of you understand the concepts and make use of the tools and analyses appropriately. As mentioned previously, the number of resources can be overwhelming.
- Select resources carefully: use reliable resources
- Cite your sources appropriately.
- Provide links when available.
- The material you incorporate here will be turned into short summary videos/recordings for each week. We will send out the summary recording along with a link to the text.
- You are responsible for reviewing the notes we create: they will appear on quizzes to promote your ability to retrieve this knowledge and promote long term memory.
- At the end of the semester, this document will become a virtual e-book we all contributed to and, as such, will be credited as authors. This document will be found here: https://metagenomics.pressbooks.com/
- You will be asked to sign a document acknowledging that it is ok for us to publish this content with or without your name as a contributor.
- The current content of the site will be replaced with what we create, becoming V2020.
We hope this challenge and opportunity motivate you to create a resource that you and others will benefit from. We have the support and expertise of the NCSU OPEN Incubator project. We are a community of scholars and want to create an OPEN set of resources for the broader community. Start creating in the open.
Contributors
Fall 2020 BIT 477/577 Metagenomics participants.
Your names below:
- Sam McMillan
- Savanna Smith
- Dawn M. Hull
- Lauren Anderson
- Rob Suppa
- Micaela Robson
- David Ramotowski
- Victoria McQuade
- Deniz Durmusoglu
- Matt McNulty
- Ourania Raftopoulou
- Lauren Pawlowski
- Pooja Parameswaran
