C8. Describe and manage biological data types, structure, and reproducibility. This competency addresses two distinct concerns: 1) each of the varied ‘omics fields produces data in formats particular to its needs, and these formats evolve with changes in technologies and refinements in 24 downstream software; and 2) all experimental data is subject to error and the user must be cognizant of the need to verify the reproducibility of their data. Students need to develop an awareness of, and ability to, manipulate different data types given the versioning of formats. They also need to exercise caution, to carry out appropriate statistical analyses on their data as part of normal operating procedures and report the uncertainty of their results, and to provide the relevant information to enable reproduction of their results.
Developing a phylogram from computational resources.
01 Jun 2021 | Teaching Materials | Contributor(s):
By Melanie Lenahan1, Shea Cinquemani1
Raritan Valley Community College
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."
31 May 2021 | Teaching Materials | Contributor(s):
By Alice Tarun
St. Lawrence University
The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the...
The Ames Test
08 Jan 2021 | Teaching Materials | Contributor(s):
By Nathan Goodson-Gregg, Elizabeth A. De Stasio
Introduction to the Ames Test, published as GSA Learning Resource
A Critical Guide to the UniProtKB Flat-file Format
05 Dec 2020 | Teaching Materials | Contributor(s):
By Teresa Attwood1, GOBLET Foundation
The University of Manchester, Manchester, UK
This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data.
A Critical Guide to BLAST
04 Dec 2020 | Teaching Materials | Contributor(s):
This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity.
Bioinformatics: the Power of Computers in Biology – a Practical Guide
03 Dec 2020 | Teaching Materials | Contributor(s):
By Daniel Barker1, Heleen Plaisier2, Stevie Anne Bain1, Teresa Attwood
1. The University of Edinburgh, Edinburgh, UK 2. Royal Botanic Garden, Edinburgh, UK
This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis.
Genome Solver: Complete Set of Lessons
23 Oct 2019 | Teaching Materials | Contributor(s):
By Anne Rosenwald1, Gaurav Arora2, Vinayak Mathur3
1. Georgetown University 2. Gallaudet University 3. Cabrini University
The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - no coding or scripting. These Lessons also work well in the undergraduate classroom, culminating with...
Using Synthetic Biology to Teach Data Science
26 Jun 2019 | Teaching Materials | Contributor(s):
By Margaret S Saha1, Beteel Abu-Ageel1, Sanjana Challa1, Xiangyi Fang1, Chai Hibbert1, Anna Isler1, Elias Nafziger1, Adam Oliver1, Hanqiu Peng1, Julia Urban1, Vivian Zhu1
College of William and Mary
Abstract for poster on using synthetic biology to introduce students to meaningful data mining, analysis, and application to engineering novel biological constructs.
Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach
29 May 2019 | Teaching Materials | Contributor(s):
By Ami Erickson
This laboratory module is a modification of the original published on CourseSource with a focus on plant biology. In the final activity, students conduct a BLAST to compare histone protein...
Sequence Similarity Resource Adaptation: Exploring Ebola Virus
16 May 2019 | Teaching Materials | Contributor(s):
By William Tapprich
University of Nebraska-Omaha
This adaptation of the sequence similarity resource provides biology students with a basic set of bioinformatics concepts and tools. These concepts and tools are used to explore relationships...
Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses
02 May 2019 | Teaching Materials | Contributor(s):
By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Carlos Christopher Goller3, Sabrina Robertson3
1. Adams State University 2. Fairmont State University 3. North Carolina State University
Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans
04 Jan 2019 | Teaching Materials | Contributor(s):
By Adam Idica1, Jordan Thompson1, Irene Munk Pedersen1, Pavan Kadandale1
University of California, Irvine
In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research, published in CourseSource
Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching
By Mark Phillip Peterson1, Jacob T Malloy2, Vincent P Buonaccorsi2, James H Marden3
1. Viterbo University 2. Juniata College 3. Pennsylvania State University
This lesson plan was created to teach RNAseq analysis as a part of GCAT-SEEK network. It is provided here, both in finished form and with the modifiable source code, to allow flexible adaptation to...
03 Jan 2019 | Teaching Materials | Contributor(s):
Bioinformatics - Investigating Sequence Similarity
04 Dec 2018 | Teaching Materials | Contributor(s):
This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
Complete Set of Lessons
01 Nov 2018 | Teaching Materials | Contributor(s):
Using DNA Subway to Analyze Sequence Relationships
28 May 2018 | Teaching Materials | Contributor(s):
By Jason Williams1, Ray A. Enke2, Oliver Hyman2, Emily Lescak3, Sam S Donovan4, William Tapprich5, Elizabeth F Ryder6
1. DNA Learning Center 2. The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University 3. University of Alaska 4. University of Pittsburgh 5. University of Nebraska-Omaha 6. Worcester Polytechnic Institute
This is a bioinformatics exercise using the DNA Subway Blue Line, a user-friendly pipeline of bioinformatics tools, to analyze a collection of mosquito DNA bar-code sequences.
DNA Subway Learning Resources
18 Oct 2017 | Teaching Materials | Contributor(s):
By Jason Williams
DNA Learning Center
DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.
This is a bioinformatics exercise using DNA Subway
05 Jul 2017 | Teaching Materials | Contributor(s):
By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Komal Vig3, Carlos Christopher Goller4, Sabrina Robertson5
1. Adams State University 2. Hampshire College 3. Alabama State University 4. North Carolina State University 5. NC State