The NIBLSE community is coordinating an effort to collect, customize, and disseminate high quality bioinformatics learning resources appropriate for undergraduate life science courses. Learning resources in this collection are organized below by NIBLSE Core Competencies; see the NIBLSE Core Competency page for full descriptions.

Bioinformatics Learning Resources for Genetics Courses. If you are looking to integrate bioinformatics lessons into an undergraduate genetics course, this list of learning resources is a great place to start.

C1. Role of Bioinformatics     C2. Computational Concepts     C3. Statistical Concepts     C4. Bioinformatics Tools

C5. Data Retrieval     C6. Model     C7. Scripting     C8. Data Types     C9. Implications     

Supplemental Resources for Instructors     

C1. Explain the role of computation and data mining in addressing hypothesis-driven and hypothesis-generating questions within the life sciences

RNAseq data analysis using Galaxy

Matthew Escobar, Sam S Donovan, Irina Makarevitch, Bill Morgan, Sabrina Robertson

Version: 4.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, bioinformatics, NCBI, Teaching material, mapping, Undergraduate, workflow, NIBLSE, Galaxy, RNAseq, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Incubated at NIBLSE
6
0
0
0
07.2021
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, Zika virus, introductory, Lab, Teaching material, High School, Reference material, Undergraduate, Homework, Majors, Non-majors, Less than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, Incubated at NIBLSE
67
8
0
0
06.2021

Yeti or not: Do they exist?

Keith Johnson, Adam Kleinschmit, Jill Rulfs, William (Bill) Morgan

Version: 3.0

Through this 4-part bioinformatics case study, students will be led through the forensic analysis of putative Yeti artifacts based on published findings.
case study, bioinformatics, NIBLSE, BLAST, 12S sequencing, Yeti, introductory, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C9. Implications, Incubated at NIBLSE, Reviewed at NIBLSE
358
266
0
0
12.2020

A Critical Guide to the PDB

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, GOBLET, InstructorResources, Article, Teaching material, Reference material, Undergraduate, Publication, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Recommended by NIBLSE
231
57
0
0
12.2020

A Critical Guide to BLAST

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, BLAST, GOBLET, InstructorResources, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
203
51
0
0
12.2020

Bioinformatics: the Power of Computers in Biology – a Practical Guide

Daniel Barker, Heleen Plaisier, Stevie Anne Bain, Teresa Attwood

Version: 1.0

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis.
NIBLSE, GOBLET, Teaching material, Undergraduate, C1. Role of bioinformatics, C4. Bioinformatics tools, C8. Data types, Recommended by NIBLSE
151
46
0
0
12.2020
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 sequences between Arabidopsis, moss and yeast.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, plant biology, NIBLSE, algorithms, incubators, Plant and Fungal Evolution, BLAST, multiple sequence alignment, CourseSource, phylogram, introductory, Lab, Teaching material, Undergraduate, Advanced, Majors, More than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
917
416
0
0
05.2019

Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

Adam Idica, Jordan Thompson, Irene Munk Pedersen, Pavan Kadandale

Version: 1.0

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
molecular biology, bioinformatics, NIBLSE, gene regulation, microRNAs, gene expression, CourseSource, Lab, Teaching material, Undergraduate, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Recommended by NIBLSE
608
142
0
0
01.2019

Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Mark Phillip Peterson, Jacob T Malloy, Vincent P Buonaccorsi, James H Marden

Version: 1.0

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 various classroom settings, published in...
statistics, R programming language, bioinformatics, NIBLSE, RNAseq, gene expression, CourseSource, computer programming, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
778
204
0
0
01.2019

Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts

Eric T. Holland, Greg Manley, Tamara Chiba, Rona Ramos, Simon Mochrie, Jennifer Frederick

Version: 1.0

Lesson on what it means for biological processes to be Poissonian, published in CourseSource
quantitative biology, bioinformatics, microbiology, physics, NIBLSE, HIV, CourseSource, multiplicity of infection, Poisson Distribution, introductory, Teaching material, Lecture, Undergraduate, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts, Recommended by NIBLSE
469
111
0
0
01.2019
In this four- part guided activity, students will learn about the structure and function of human autosomal and sex chromosomes, view and interpret gene maps, and gain familiarity with basic bioinformatics resources and data through use of the...
bioinformatics, NIBLSE, CourseSource, autosome, homologous chromosomes, homologous recombination, sex chromosome, sex determination, sex reversal mutations, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, Recommended by NIBLSE
591
174
0
0
01.2019

Bioinformatics / Neuroinformatics

William Grisham

Version: 1.0

This module is a computer-based introduction to bioinformatics resources.  This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in answering research questions. Published in CBE-LSE
bioinformatics, NIBLSE, ImageJ, quantitative trait locus, QTL, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, Recommended by NIBLSE
435
126
0
0
01.2019
Modules showing how the NCBI database classifies and organizes information on DNA sequences, evolutionary relationships, and scientific publications. And a module working to identify a nucleotide sequence from an insect endosymbiont by using BLAST
NCBI, NIBLSE, DNA, BLAST, nucleotide sequencing, Teaching material, Undergraduate, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, Recommended by NIBLSE
577
200
0
0
01.2019

Behavioral Genetics: Investigating the genes of a complex phenotype in fruit flies

Craig E. Stanley, Jr., Charles Hadley S. King, IV, Michelle Thornton, Rob J. Kulathinal

Version: 1.0

Introductory genetics laboratory published as GSA Learning Resource
behavior, bioinformatics, NIBLSE, drosophila, genetic basis, fruit flies, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, Recommended by NIBLSE
548
143
0
0
01.2019

Using DNA Subway to Analyze Sequence Relationships

Jason Williams, Ray A. Enke, Oliver Hyman, Emily Lescak, Sam S Donovan, William Tapprich, Elizabeth F Ryder

Version: 2.0

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.
phylogenetics, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
1.5K
319
2
0
05.2018

DNA Subway Learning Resources

Jason Williams

Version: 2.0

DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.
phylogenetics, introductory, Lab, bioinformatics, Teaching material, High School, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Advanced, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
1.2K
65
0
0
10.2017
This resource is an exercise to introduce students to agent-based modeling of biological systems through working with a simple existing model.
simulation, ecology, introductory, NetLogo, agent-based modeling, agent-based model, Lab, bioinformatics, predator-prey, Teaching material, High School, Undergraduate, NIBLSE, Less than 1 hour, C1. Role of bioinformatics, C6. Models, Reviewed at NIBLSE, agent based modleing
1.4K
280
0
0
06.2017

Exploring HIV Evolution

Sam S Donovan, Tony Weisstein

Version: 2.0

In this activity you will study aspects of sequence evolution by working with a set of HIV sequence data from 15 different subjects (Markham, et al., 1998). You will first learn about the dataset, then study the possible sources of HIV for these...
Evolution, bioinformatics, sequencing, Teaching material, Undergraduate, NIBLSE, incubators, HIV, C1. Role of bioinformatics, C4. Bioinformatics tools, Recommended by NIBLSE
595
144
0
0
06.2017

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C2. Summarize key computational concepts, such as algorithms and relational databases, and their applications in the life sciences

RNAseq data analysis using Galaxy

Matthew Escobar, Sam S Donovan, Irina Makarevitch, Bill Morgan, Sabrina Robertson

Version: 4.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, bioinformatics, NCBI, Teaching material, mapping, Undergraduate, workflow, NIBLSE, Galaxy, RNAseq, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Incubated at NIBLSE
6
0
0
0
07.2021
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.
bioinformatics, sequencing, NIBLSE, multiple sequence alignment, Bioconductor, introductory, Lab, Teaching material, Undergraduate, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, Adapted at NIBLSE
41
18
0
0
06.2021
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, Zika virus, introductory, Lab, Teaching material, High School, Reference material, Undergraduate, Homework, Majors, Non-majors, Less than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, Incubated at NIBLSE
67
8
0
0
06.2021
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, phylogram, percent identity matrix, introductory, Lab, Teaching material, Undergraduate, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
48
9
0
0
06.2021
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 SARS-COVID 2 virus.
bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, introductory, Lab, Teaching material, Lecture, Reference material, Undergraduate, Homework, Advanced, Majors, Non-majors, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
221
27
0
0
05.2021

Yeti or not: Do they exist?

Keith Johnson, Adam Kleinschmit, Jill Rulfs, William (Bill) Morgan

Version: 3.0

Through this 4-part bioinformatics case study, students will be led through the forensic analysis of putative Yeti artifacts based on published findings.
case study, bioinformatics, NIBLSE, BLAST, 12S sequencing, Yeti, introductory, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C9. Implications, Incubated at NIBLSE, Reviewed at NIBLSE
358
266
0
0
12.2020

A Critical Guide to the PDB

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, GOBLET, InstructorResources, Article, Teaching material, Reference material, Undergraduate, Publication, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Recommended by NIBLSE
231
57
0
0
12.2020

A Critical Guide to BLAST

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, BLAST, GOBLET, InstructorResources, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
203
51
0
0
12.2020

Needleman - Wunsch Algorithm Exercise

Michael Sierk, Sam S Donovan, Neal Grandgenett, Bill Morgan, Mark A. Pauley, Elizabeth F Ryder

Version: 4.0

This exercise is used in a sophomore-junior level bioinformatics course. The algorithm is introduced to the students who then complete the exercise.
bioinformatics, Teaching material, Undergraduate, NIBLSE, algorithms, incubators, Advanced, 1 Hour, C2. Computational concepts, Incubated at NIBLSE
442
71
0
0
04.2020

A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke

Version: 2.0

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.
data science, bioinformatics, next generation sequencing, quality control, FASTQ, genomics, programming, NIBLSE, linux, microbiome, Illumina sequencing, command line, FASTQE, FASTP, NGS analysis, introductory, Lab, Teaching material, Lecture, High School, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, Incubated at NIBLSE
1.1K
790
0
1
06.2019
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 sequences between Arabidopsis, moss and yeast.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, plant biology, NIBLSE, algorithms, incubators, Plant and Fungal Evolution, BLAST, multiple sequence alignment, CourseSource, phylogram, introductory, Lab, Teaching material, Undergraduate, Advanced, Majors, More than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
917
416
0
0
05.2019
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 between Ebola virus strains.
phylogenetics, bioinformatics, Ebola, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, introductory, Teaching material, Lecture, Undergraduate, Advanced, Majors, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
881
2.0K
0
0
05.2019
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, Zika virus, introductory, Lab, Teaching material, Undergraduate, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
1.7K
259
8
0
05.2019

Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Mark Phillip Peterson, Jacob T Malloy, Vincent P Buonaccorsi, James H Marden

Version: 1.0

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 various classroom settings, published in...
statistics, R programming language, bioinformatics, NIBLSE, RNAseq, gene expression, CourseSource, computer programming, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
778
204
0
0
01.2019
Module using analogies to introduce students to genomics
bioinformatics, genomics, workflow, NIBLSE, CourseSource, analogies, Teaching material, Lecture, Undergraduate, Graduate, Advanced, Less than 1 hour, C2. Computational concepts, Recommended by NIBLSE
437
115
0
0
01.2019

A Hands-on Introduction to Hidden Markov Models

Tony Weisstein, Elena Gracheva, Zane Goodwin, Zongtai Qi, Wilson Leung, Christopher D. Shaffer, Sarah C.R. Elgin

Version: 1.0

A lesson in which students will understand the basic structure of an HMM, the types of data used in ab initio gene prediction, and its consequent limitations.
Markov model, bioinformatics, genomics, NIBLSE, transcription, CourseSource, exon, intron, splicing, introductory, Lab, Teaching material, Lecture, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts, Recommended by NIBLSE
552
154
0
0
01.2019

Bioinformatics / Neuroinformatics

William Grisham

Version: 1.0

This module is a computer-based introduction to bioinformatics resources.  This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in answering research questions. Published in CBE-LSE
bioinformatics, NIBLSE, ImageJ, quantitative trait locus, QTL, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, Recommended by NIBLSE
435
126
0
0
01.2019

Using DNA Subway to Analyze Sequence Relationships

Jason Williams, Ray A. Enke, Oliver Hyman, Emily Lescak, Sam S Donovan, William Tapprich, Elizabeth F Ryder

Version: 2.0

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.
phylogenetics, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
1.5K
319
2
0
05.2018

DNA Subway Learning Resources

Jason Williams

Version: 2.0

DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.
phylogenetics, introductory, Lab, bioinformatics, Teaching material, High School, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Advanced, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
1.2K
65
0
0
10.2017

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C3. Apply statistical concepts used in bioinformatics

RNAseq data analysis using Galaxy

Matthew Escobar, Sam S Donovan, Irina Makarevitch, Bill Morgan, Sabrina Robertson

Version: 4.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, bioinformatics, NCBI, Teaching material, mapping, Undergraduate, workflow, NIBLSE, Galaxy, RNAseq, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Incubated at NIBLSE
6
0
0
0
07.2021

A Critical Guide to the PDB

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, GOBLET, InstructorResources, Article, Teaching material, Reference material, Undergraduate, Publication, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C5. Data retrieval, Recommended by NIBLSE
231
57
0
0
12.2020

A Critical Guide to BLAST

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, BLAST, GOBLET, InstructorResources, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
203
51
0
0
12.2020

Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Mark Phillip Peterson, Jacob T Malloy, Vincent P Buonaccorsi, James H Marden

Version: 1.0

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 various classroom settings, published in...
statistics, R programming language, bioinformatics, NIBLSE, RNAseq, gene expression, CourseSource, computer programming, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
778
204
0
0
01.2019

Infectious Chocolate Joy with a Side of Poissonian Statistics: An activity connecting life science students with subtle physics concepts

Eric T. Holland, Greg Manley, Tamara Chiba, Rona Ramos, Simon Mochrie, Jennifer Frederick

Version: 1.0

Lesson on what it means for biological processes to be Poissonian, published in CourseSource
quantitative biology, bioinformatics, microbiology, physics, NIBLSE, HIV, CourseSource, multiplicity of infection, Poisson Distribution, introductory, Teaching material, Lecture, Undergraduate, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts, Recommended by NIBLSE
469
111
0
0
01.2019

A Hands-on Introduction to Hidden Markov Models

Tony Weisstein, Elena Gracheva, Zane Goodwin, Zongtai Qi, Wilson Leung, Christopher D. Shaffer, Sarah C.R. Elgin

Version: 1.0

A lesson in which students will understand the basic structure of an HMM, the types of data used in ab initio gene prediction, and its consequent limitations.
Markov model, bioinformatics, genomics, NIBLSE, transcription, CourseSource, exon, intron, splicing, introductory, Lab, Teaching material, Lecture, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts, Recommended by NIBLSE
552
154
0
0
01.2019

Finding Selection in All the Right Places

Juliet F. K. Noor, Mohamed A. F. Noor

Version: 1.0

Lab introducing students to evolutionary genetics using bioinformatics and biocuration, published as GSA Learning Resource
genetics, bioinformatics, sequencing, NIBLSE, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, Recommended by NIBLSE
440
126
0
0
01.2019

Bioinformatics / Neuroinformatics

William Grisham

Version: 1.0

This module is a computer-based introduction to bioinformatics resources.  This easy-to-adopt module weaves together several important bioinformatic tools so students can grasp how each is used in answering research questions. Published in CBE-LSE
bioinformatics, NIBLSE, ImageJ, quantitative trait locus, QTL, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, Recommended by NIBLSE
435
126
0
0
01.2019

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C4. Use bioinformatics tools to examine complex biological problems in evolution, information flow, and other important areas of biology

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 phylogenies using the program MEGA, to test evolutionary hypotheses.
phylogenetics, bioinformatics, FASTA, NCBI, BLAST, multiple sequence alignment, CourseSource, Zika virus, MEGA, alcohol metabolism, Lab, Teaching material, Undergraduate, Homework, Advanced, 1 Hour, C4. Bioinformatics tools, C5. Data retrieval, Incubated at NIBLSE
43
12
0
0
06.2021
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.
bioinformatics, sequencing, NIBLSE, multiple sequence alignment, Bioconductor, introductory, Lab, Teaching material, Undergraduate, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, Adapted at NIBLSE
41
18
0
0
06.2021
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, Zika virus, introductory, Lab, Teaching material, High School, Reference material, Undergraduate, Homework, Majors, Non-majors, Less than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, Incubated at NIBLSE
67
8
0
0
06.2021
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, phylogram, percent identity matrix, introductory, Lab, Teaching material, Undergraduate, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
48
9
0
0
06.2021
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 SARS-COVID 2 virus.
bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, introductory, Lab, Teaching material, Lecture, Reference material, Undergraduate, Homework, Advanced, Majors, Non-majors, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
221
27
0
0
05.2021

The Ames Test

Nathan Goodson-Gregg, Elizabeth A. De Stasio

Version: 2.0

Introduction to the Ames Test, published as GSA Learning Resource
genetics, NIBLSE, DNA, ames test, assay, Lab, Teaching material, Undergraduate, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Recommended by NIBLSE
338
61
0
0
01.2021

Yeti or not: Do they exist?

Keith Johnson, Adam Kleinschmit, Jill Rulfs, William (Bill) Morgan

Version: 3.0

Through this 4-part bioinformatics case study, students will be led through the forensic analysis of putative Yeti artifacts based on published findings.
case study, bioinformatics, NIBLSE, BLAST, 12S sequencing, Yeti, introductory, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C9. Implications, Incubated at NIBLSE, Reviewed at NIBLSE
358
266
0
0
12.2020

A Critical Guide to BLAST

Teresa Attwood, GOBLET Foundation

Version: 1.0

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.
NIBLSE, BLAST, GOBLET, InstructorResources, Teaching material, Undergraduate, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
203
51
0
0
12.2020

Bioinformatics: the Power of Computers in Biology – a Practical Guide

Daniel Barker, Heleen Plaisier, Stevie Anne Bain, Teresa Attwood

Version: 1.0

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis.
NIBLSE, GOBLET, Teaching material, Undergraduate, C1. Role of bioinformatics, C4. Bioinformatics tools, C8. Data types, Recommended by NIBLSE
151
46
0
0
12.2020

BSL-4: Authorized Personnel Only

Nicole Anthony

Version: 1.0

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
infectious disease, experimental design, bioinformatics, Ebola, NIBLSE, Case It!, PCR, BLAST, multiple sequence alignment, Published in National Center for Case Study Teaching in Science, polymerase chain reaction, febrile illness, virus, ELISA, enzyme linked immunosorbent assay, filovirus, Africa, introductory, Teaching material, Lecture, High School, Undergraduate, Majors, Non-majors, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, Recommended by NIBLSE
1.1K
206
0
0
08.2020

Genome Solver: Complete Set of Lessons

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

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 an authentic community research project.
bioinformatics, NIBLSE, Bioinformatics Education, Bioinformatics and Genomics, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, C8. Data types, C9. Implications, Recommended by NIBLSE, introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, Homework, Majors, Non-majors, Extended Project
939
108
0
0
10.2019

A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke

Version: 2.0

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.
data science, bioinformatics, next generation sequencing, quality control, FASTQ, genomics, programming, NIBLSE, linux, microbiome, Illumina sequencing, command line, FASTQE, FASTP, NGS analysis, introductory, Lab, Teaching material, Lecture, High School, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, Incubated at NIBLSE
1.1K
790
0
1
06.2019
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 sequences between Arabidopsis, moss and yeast.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, plant biology, NIBLSE, algorithms, incubators, Plant and Fungal Evolution, BLAST, multiple sequence alignment, CourseSource, phylogram, introductory, Lab, Teaching material, Undergraduate, Advanced, Majors, More than 1 hour, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
917
416
0
0
05.2019
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 between Ebola virus strains.
phylogenetics, bioinformatics, Ebola, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, introductory, Teaching material, Lecture, Undergraduate, Advanced, Majors, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Adapted at NIBLSE
881
2.0K
0
0
05.2019
This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, bioinformatics, sequencing, FASTA, NCBI, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, CourseSource, phylogram, Zika virus, introductory, Lab, Teaching material, Undergraduate, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
1.7K
259
8
0
05.2019

Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

Adam Idica, Jordan Thompson, Irene Munk Pedersen, Pavan Kadandale

Version: 1.0

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
molecular biology, bioinformatics, NIBLSE, gene regulation, microRNAs, gene expression, CourseSource, Lab, Teaching material, Undergraduate, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Recommended by NIBLSE
608
142
0
0
01.2019
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.
bioinformatics, NIBLSE, Protein Structure, DNA, molecular modeling, genotype, phenotype, CourseSource, computational modeling, central dogma, plant leaf structure, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C4. Bioinformatics tools, C5. Data retrieval, Recommended by NIBLSE
509
124
0
0
01.2019

Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Mark Phillip Peterson, Jacob T Malloy, Vincent P Buonaccorsi, James H Marden

Version: 1.0

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 various classroom settings, published in...
statistics, R programming language, bioinformatics, NIBLSE, RNAseq, gene expression, CourseSource, computer programming, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C7. Scripting, C8. Data types, Recommended by NIBLSE
778
204
0
0
01.2019

Murder by HIV? Undergraduate edition

Naowarat (Ann) Cheeptham, Laura B. Regassa, Michèle I. Shuster

Version: 1.0

Bioinformatics case study focusing on phylogenetic tree interpretation, published in the National Center for Case Study Teaching in Science
case study, Resources @ NSF - NCCSTS, bioinformatics, NIBLSE, HIV, nucleotide sequencing, phylogenetic tree, viral life cycles, mutation rates, reverse transcriptase sequences, Teaching material, Undergraduate, Advanced, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, Recommended by NIBLSE
1.6K
307
0
0
01.2019
In this four- part guided activity, students will learn about the structure and function of human autosomal and sex chromosomes, view and interpret gene maps, and gain familiarity with basic bioinformatics resources and data through use of the...
bioinformatics, NIBLSE, CourseSource, autosome, homologous chromosomes, homologous recombination, sex chromosome, sex determination, sex reversal mutations, introductory, Lab, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, Recommended by NIBLSE
591
174