The NIBLSE community is coordinating an effort to collect, customize, and disseminate high quality bioinformatics learning resources. Below is collection of Bioinformatics Learning Resources including NIBLSE Incubators and CourseSource Bioinformatics resources.



NIBLSE is working with the Quantitative Undergraduate Biology Education & Synthesis Project (QUBES) to establish learning resource “incubators” to nurture the development and dissemination of promising lesson materials. 



NIBLSE is working with the CourseSource Project to articulate a Learning Framework for Bioinformatics which describes the learning goals and objectives relevant to undergraduate biological sciences majors. 

All learning resources have been reviewed and assigned NIBLSE Core Competencies. To see a full description, click the competency or visit the NIBLSE Core Competency page.

Click the icon to the right to download a guide on how to navigate a QUBES Database: database guide        Browse the Collection by Card

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     

C1

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
Lab, bioinformatics, Teaching material, Undergraduate, gene regulation, microRNAs, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, CourseSource
31
1
0
01.04.2019

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

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
introductory, quantitative biology, bioinformatics, microbiology, Teaching material, Lecture, Undergraduate, physics, HIV, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts, CourseSource, multiplicity of infection, Poisson Distribution
14
3
0
01.04.2019
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 National Ce
introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, CourseSource, autosome, homologous chromosomes, homologous recombination, sex chromosome, sex determination, sex reversal mutations
9
1
0
01.04.2019

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019
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, Teaching material, Undergraduate, DNA, BLAST, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, nucleotide sequencing
23
6
0
01.03.2019

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
introductory, behavior, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, drosophila, genetic basis, fruit flies
18
2
0
01.03.2019

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
287
39
2
05.28.2018

RNAseq data analysis using Galaxy

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

Version: 3.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, 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
232
31
0
11.13.2017
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, Lab, bioinformatics, predator-prey, Teaching material, High School, Undergraduate, NIBLSE, Less than 1 hour, C1. Role of bioinformatics, C6. Models
327
57
0
06.05.2017

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, Teaching material, Undergraduate, NIBLSE, incubators, C1. Role of bioinformatics, C4. Bioinformatics tools
100
25
0
06.05.2017

Back to top


C2

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019
Module using analogies to introduce students to genomics
bioinformatics, genomics, Teaching material, Lecture, Undergraduate, workflow, Graduate, Advanced, Less than 1 hour, C2. Computational concepts, CourseSource, analogies
12
4
0
01.04.2019

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.
introductory, Lab, bioinformatics, genomics, Teaching material, Lecture, Undergraduate, transcription, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts, CourseSource, exon, intron, splicing
12
1
0
01.04.2019

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019

Bioinformatics - Investigating Sequence Similarity

Adam Kleinschmit, Benita Brink, Steven Roof, Carlos Christopher Goller, Sabrina Robertson

Version: 4.0

This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, introductory, Lab, bioinformatics, sequencing, FASTA, NCBI, Teaching material, Undergraduate, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
620
131
0
12.04.2018

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
287
39
2
05.28.2018

RNAseq data analysis using Galaxy

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

Version: 3.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, 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
232
31
0
11.13.2017

Needleman - Wunsch Algorithm Exercise

Michael Sierk

Version: 3.0

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
237
469
0
06.05.2017

Back to top


C3

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

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
introductory, quantitative biology, bioinformatics, microbiology, Teaching material, Lecture, Undergraduate, physics, HIV, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts, CourseSource, multiplicity of infection, Poisson Distribution
14
3
0
01.04.2019

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.
introductory, Lab, bioinformatics, genomics, Teaching material, Lecture, Undergraduate, transcription, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts, CourseSource, exon, intron, splicing
12
1
0
01.04.2019

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, introductory, Lab, bioinformatics, sequencing, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
18
2
0
01.03.2019

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019

RNAseq data analysis using Galaxy

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

Version: 3.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, 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
232
31
0
11.13.2017

Back to top


C4

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
Lab, bioinformatics, Teaching material, Undergraduate, gene regulation, microRNAs, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, CourseSource
31
1
0
01.04.2019
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.
introductory, Lab, bioinformatics, Teaching material, Undergraduate, Protein Structure, Majors, More than 1 hour, genotype, phenotype, C4. Bioinformatics tools, C5. Data retrieval, CourseSource, computational modeling, central dogma, plant leaf structure
36
1
0
01.04.2019

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

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, Teaching material, Undergraduate, HIV, Advanced, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, nucleotide sequencing, phylogenetic tree, viral life cycles, mutation rates, reverse transcriptase sequences
12
1
0
01.04.2019
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 National Ce
introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, Majors, 1 Hour, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, CourseSource, autosome, homologous chromosomes, homologous recombination, sex chromosome, sex determination, sex reversal mutations
9
1
0
01.04.2019

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, introductory, Lab, bioinformatics, sequencing, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
18
2
0
01.03.2019

Colon Cancer: A Case of Genetic Bad Luck

Anne M. Casper

Version: 1.0

Case study developed for an introductory genetics class published in the National Center for Case Study Teaching in Science
introductory, bioinformatics, NCBI, Teaching material, Undergraduate, BLAST, Majors, C4. Bioinformatics tools, C5. Data retrieval, colon cancer, pedigree, genetic testing, APC
14
3
0
01.03.2019

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019
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, Teaching material, Undergraduate, DNA, BLAST, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, nucleotide sequencing
23
6
0
01.03.2019

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
introductory, behavior, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, drosophila, genetic basis, fruit flies
18
2
0
01.03.2019

The Ames Test

Nathan Goodson-Gregg, Elizabeth A. De Stasio

Version: 1.0

Introduction to the Ames Test, published as GSA Learning Resource
genetics, Lab, Teaching material, Undergraduate, DNA, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, ames test, assay
15
1
0
01.03.2019

Bioinformatics - Investigating Sequence Similarity

Adam Kleinschmit, Benita Brink, Steven Roof, Carlos Christopher Goller, Sabrina Robertson

Version: 4.0

This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, introductory, Lab, bioinformatics, sequencing, FASTA, NCBI, Teaching material, Undergraduate, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
620
131
0
12.04.2018

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
introductory, infectious disease, experimental design, bioinformatics, Ebola, Teaching material, Lecture, High School, Undergraduate, Case It!, PCR, BLAST, multiple sequence alignment, Majors, Non-majors, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, Published in National Center for Case Study Teaching in Science, polymerase chain reaction, febrile illness, virus, ELISA, enzyme linked immunosorbent assay, filovirus, Africa
113
13
0
09.24.2018

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
287
39
2
05.28.2018

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, Teaching material, Undergraduate, NIBLSE, incubators, C1. Role of bioinformatics, C4. Bioinformatics tools
100
25
0
06.05.2017

RNA-seq Analysis

Bill Morgan, Matthew Reeder

Version: 2.0

In this computer lab module, students learn how to process an RNA-seq data set to identify differentially expressed genes (DEGs). The samples for this data set were collected from yeast cells expressing either a control gene or a pathogen...
Lab, RNA, sequencing, Teaching material, Undergraduate, NIBLSE, incubators, More than 1 hour, C4. Bioinformatics tools, C5. Data retrieval
143
22
0
06.05.2017

Back to top


C5

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
Lab, bioinformatics, Teaching material, Undergraduate, gene regulation, microRNAs, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, CourseSource
31
1
0
01.04.2019
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.
introductory, Lab, bioinformatics, Teaching material, Undergraduate, Protein Structure, Majors, More than 1 hour, genotype, phenotype, C4. Bioinformatics tools, C5. Data retrieval, CourseSource, computational modeling, central dogma, plant leaf structure
36
1
0
01.04.2019

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

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, Teaching material, Undergraduate, HIV, Advanced, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, nucleotide sequencing, phylogenetic tree, viral life cycles, mutation rates, reverse transcriptase sequences
12
1
0
01.04.2019

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, introductory, Lab, bioinformatics, sequencing, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
18
2
0
01.03.2019
To increase students' interest in their own genomes, this computer-based laboratory lesson is designed to be coupled with the opportunity for the students to be genotyped by the consumer sequencing company, 23andMe. Published in CourseSource
Lab, bioinformatics, Teaching material, Undergraduate, Advanced, More than 1 hour, C5. Data retrieval, C9. Implications, CourseSource, genomic wide association studies, UCSC genome browser, single nucleotide polymorphism
16
2
0
01.03.2019

Colon Cancer: A Case of Genetic Bad Luck

Anne M. Casper

Version: 1.0

Case study developed for an introductory genetics class published in the National Center for Case Study Teaching in Science
introductory, bioinformatics, NCBI, Teaching material, Undergraduate, BLAST, Majors, C4. Bioinformatics tools, C5. Data retrieval, colon cancer, pedigree, genetic testing, APC
14
3
0
01.03.2019

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019
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, Teaching material, Undergraduate, DNA, BLAST, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, nucleotide sequencing
23
6
0
01.03.2019

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
introductory, behavior, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, drosophila, genetic basis, fruit flies
18
2
0
01.03.2019

The Ames Test

Nathan Goodson-Gregg, Elizabeth A. De Stasio

Version: 1.0

Introduction to the Ames Test, published as GSA Learning Resource
genetics, Lab, Teaching material, Undergraduate, DNA, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, ames test, assay
15
1
0
01.03.2019

Bioinformatics - Investigating Sequence Similarity

Adam Kleinschmit, Benita Brink, Steven Roof, Carlos Christopher Goller, Sabrina Robertson

Version: 4.0

This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, introductory, Lab, bioinformatics, sequencing, FASTA, NCBI, Teaching material, Undergraduate, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
620
131
0
12.04.2018

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
introductory, infectious disease, experimental design, bioinformatics, Ebola, Teaching material, Lecture, High School, Undergraduate, Case It!, PCR, BLAST, multiple sequence alignment, Majors, Non-majors, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, Published in National Center for Case Study Teaching in Science, polymerase chain reaction, febrile illness, virus, ELISA, enzyme linked immunosorbent assay, filovirus, Africa
113
13
0
09.24.2018

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
287
39
2
05.28.2018

RNAseq data analysis using Galaxy

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

Version: 3.0

This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.
Lab, 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
232
31
0
11.13.2017

RNA-seq Analysis

Bill Morgan, Matthew Reeder

Version: 2.0

In this computer lab module, students learn how to process an RNA-seq data set to identify differentially expressed genes (DEGs). The samples for this data set were collected from yeast cells expressing either a control gene or a pathogen...
Lab, RNA, sequencing, Teaching material, Undergraduate, NIBLSE, incubators, More than 1 hour, C4. Bioinformatics tools, C5. Data retrieval
143
22
0
06.05.2017

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C6

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, Teaching material, Undergraduate, ImageJ, C1. Role of bioinformatics, C2. Computational concepts, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, quantitative trait locus, QTL
11
0
0
01.03.2019
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, Lab, bioinformatics, predator-prey, Teaching material, High School, Undergraduate, NIBLSE, Less than 1 hour, C1. Role of bioinformatics, C6. Models
327
57
0
06.05.2017

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C7

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

An Introduction to the R Programming Environment

K. A. Garrett, P. D. Esker, A. H. Sparks

Version: 1.0

An online module introducing students and biologists to R, published in American Phytopathological Society
epidemiology, R, ecology, Online course, Teaching material, plant biology, plant pathology, C7. Scripting
12
2
0
01.04.2019

Introduction to UNIX command line

Serghei Mangul

Version: 1.0

These are materials for a Unix workshop with hands-on examples that requires no prior knowledge of Unix or programming.
introductory, Lab, Online course, Teaching material, Lecture, High School, Undergraduate, NIBLSE, Majors, Non-majors, More than 1 hour, C7. Scripting, Reviewed at NIBLSE, command line, UNIX, grep, sed, basic UNIX commands, bash script
201
41
0
07.31.2018

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C8

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
Lab, bioinformatics, Teaching material, Undergraduate, gene regulation, microRNAs, gene expression, Advanced, Extended Project, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, CourseSource
31
1
0
01.04.2019

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 CourseSource
statistics, introductory, Lab, bioinformatics, Online course, Teaching material, Lecture, Undergraduate, RNAseq, gene expression, 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, CourseSource, computer programming
31
1
0
01.04.2019

The Ames Test

Nathan Goodson-Gregg, Elizabeth A. De Stasio

Version: 1.0

Introduction to the Ames Test, published as GSA Learning Resource
genetics, Lab, Teaching material, Undergraduate, DNA, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, ames test, assay
15
1
0
01.03.2019

Bioinformatics - Investigating Sequence Similarity

Adam Kleinschmit, Benita Brink, Steven Roof, Carlos Christopher Goller, Sabrina Robertson

Version: 4.0

This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.
phylogenetics, introductory, Lab, bioinformatics, sequencing, FASTA, NCBI, Teaching material, Undergraduate, NIBLSE, algorithms, incubators, BLAST, multiple sequence alignment, Advanced, More than 1 hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
620
131
0
12.04.2018

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
287
39
2
05.28.2018

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C9

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, Teaching material, Undergraduate, HIV, Advanced, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, nucleotide sequencing, phylogenetic tree, viral life cycles, mutation rates, reverse transcriptase sequences
12
1
0
01.04.2019

Genes and Civil Liberties

Philip L. Bereano

Version: 1.0

This lesson focuses on examining civil liberties issues as they relate to genetic research. Students can choose to represent an organization, real or fictional, that will report to a task force on civil liberties issues. Published in AIBS
bioinformatics, bioethics, Teaching material, Undergraduate, DNA, C9. Implications, ethics, DNA profiling, DNA forensics
7
0
0
01.04.2019

For Sale: Iceland's Genetic History

Oksana Hlodan

Version: 1.0

Lesson on Iceland's genetic history, published in AIBS
genetics, population genetics, bioethics, Teaching material, High School, Undergraduate, C9. Implications, ethics, genome
18
1
0
01.03.2019
To increase students' interest in their own genomes, this computer-based laboratory lesson is designed to be coupled with the opportunity for the students to be genotyped by the consumer sequencing company, 23andMe. Published in CourseSource
Lab, bioinformatics, Teaching material, Undergraduate, Advanced, More than 1 hour, C5. Data retrieval, C9. Implications, CourseSource, genomic wide association studies, UCSC genome browser, single nucleotide polymorphism
16
2
0
01.03.2019

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
introductory, infectious disease, experimental design, bioinformatics, Ebola, Teaching material, Lecture, High School, Undergraduate, Case It!, PCR, BLAST, multiple sequence alignment, Majors, Non-majors, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C9. Implications, Published in National Center for Case Study Teaching in Science, polymerase chain reaction, febrile illness, virus, ELISA, enzyme linked immunosorbent assay, filovirus, Africa
113
13
0
09.24.2018

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