C5. Find, retrieve, and organize various types of biological data. Given the numerous and varied datasets currently being generated from all of the ‘omics fields, students should develop the facility to: identify appropriate data repositories; navigate and retrieve data from these databases; and organize data relevant to their area of study in flat files or small local stand-alone databases.
RNAseq data analysis using Galaxy
02 Jul 2021 | Teaching Materials | Contributor(s):
By Matthew Escobar1, Sam S Donovan2, Irina Makarevitch3, Bill Morgan4, Sabrina Robertson5
1. California State University San Marcos 2. University of Pittsburgh 3. Hamline University 4. The College of Wooster 5. North Carolina State University
This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Inquiry-based hypothesis testing using phylogenetic trees in MEGA
17 Jun 2021 | Teaching Materials | Contributor(s):
By Kristin Hultgren
A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple...
Sequence Similarity: A Quick Introduction to Bioconductor
04 Jun 2021 | Teaching Materials | Contributor(s):
By Derek Edward Sollberger
UC Merced School of Natural Sciences
Following the Sequence Similarity exercises by Kleinschmit, et al., this tutorial will guide students in using the Bioconductor suite of R packages to likewise compute sequence similarity.
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 the PDB
This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures.
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.
BSL-4: Authorized Personnel Only
17 Aug 2020 | Teaching Materials | Contributor(s):
By Nicole Anthony
Biological Sciences, Toronto District School Board
National Center for Case Study Teaching in Science resource on the 2014 Ebola epidemic. This resource is also included in the NIBLSE Learning Resource Collection
Introduction to UNIX command line
22 Jan 2020 | Teaching Materials | Contributor(s):
By Serghei Mangul1, Kristen Butela2, Michael Sierk3, Lihua Stefan
1. University of California - Los Angeles 2. University of Pittsburgh 3. Saint Vincent College
A laboratory module for an upper-level undergraduate biology course in which students will be able to carry out simple tasks using the Unix command-line environment.
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.
A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!
07 Jun 2019 | Teaching Materials | Contributor(s):
By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5
1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University
This resource is a fun computer-based intro to command line programming. The activity takes FASTQ NGS data files and runs a fun program called FASTQE.
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
28 Feb 2019 | Teaching Materials | Contributor(s):
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
Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes
By Tara Phelps-Durr
This lesson is a five-week series of laboratory activities designed to help students transition from applying lower order thinking skills to the central dogma to applying higher-order thinking skills.