The NIBLSE community is coordinating an effort to collect, customize, and disseminate high quality bioinformatics learning resources. The current collection is displayed in two formats (table and card) below. 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 download a guide on navigating QUBES tables:

 guide to qubes database thumbnail

 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

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, Incubated at NIBLSE
46
28
0
05.29.2019

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
bioinformatics, 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
129
18
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, bioinformatics, 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
110
17
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
quantitative biology, bioinformatics, microbiology, physics, HIV, CourseSource, multiplicity of infection, Poisson Distribution, introductory, Teaching material, Lecture, Undergraduate, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts
67
11
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
bioinformatics, 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
55
10
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, 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
57
7
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, DNA, BLAST, nucleotide sequencing, Teaching material, Undergraduate, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval
94
17
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
behavior, 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
64
12
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
517
114
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
349
46
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
506
83
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
148
36
0
06.05.2017

Back to top of cards


C2

This exercise leads upper level biology majors in an inquiry-based excursion to determine how similar the signaling molecule, myostatin, is between humans and mice, using a basic set of bioinformatics tools and concepts.
bioinformatics, sequencing, FASTA, NCBI, Developmental Biology, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, myostatin, muscle, DNA mutation, Lab, Teaching material, Lecture, Undergraduate, Homework, Advanced, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
29
71
0
06.19.2019

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
257
39
0
06.07.2019
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, Incubated at NIBLSE
46
28
0
05.29.2019
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
103
106
0
05.16.2019
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
142
17
5
05.02.2019

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, bioinformatics, 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
110
17
0
01.04.2019
Module using analogies to introduce students to genomics
bioinformatics, genomics, workflow, CourseSource, analogies, Teaching material, Lecture, Undergraduate, Graduate, Advanced, Less than 1 hour, C2. Computational concepts
84
14
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.
bioinformatics, genomics, transcription, CourseSource, exon, intron, splicing, introductory, Lab, Teaching material, Lecture, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts
75
14
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, 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
57
7
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
517
114
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
349
46
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
457
704
0
06.05.2017

Back to top of cards


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, bioinformatics, 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
110
17
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
quantitative biology, bioinformatics, microbiology, physics, HIV, CourseSource, multiplicity of infection, Poisson Distribution, introductory, Teaching material, Lecture, Undergraduate, Majors, Less than 1 hour, C1. Role of bioinformatics, C3. Statistical concepts
67
11
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.
bioinformatics, genomics, transcription, CourseSource, exon, intron, splicing, introductory, Lab, Teaching material, Lecture, Undergraduate, Advanced, Majors, Non-majors, 1 Hour, C2. Computational concepts, C3. Statistical concepts
75
14
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, bioinformatics, sequencing, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
65
11
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, 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
57
7
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
349
46
0
11.13.2017

Back to top of cards


C4

This exercise leads upper level biology majors in an inquiry-based excursion to determine how similar the signaling molecule, myostatin, is between humans and mice, using a basic set of bioinformatics tools and concepts.
bioinformatics, sequencing, FASTA, NCBI, Developmental Biology, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, myostatin, muscle, DNA mutation, Lab, Teaching material, Lecture, Undergraduate, Homework, Advanced, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
29
71
0
06.19.2019

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
257
39
0
06.07.2019
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, Incubated at NIBLSE
46
28
0
05.29.2019
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
103
106
0
05.16.2019
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
142
17
5
05.02.2019

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
bioinformatics, 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
129
18
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.
bioinformatics, Protein Structure, 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
94
11
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, bioinformatics, 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
110
17
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, 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
294
51
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
bioinformatics, 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
55
10
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, bioinformatics, sequencing, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
65
11
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
bioinformatics, NCBI, BLAST, colon cancer, pedigree, genetic testing, APC, introductory, Teaching material, Undergraduate, Majors, C4. Bioinformatics tools, C5. Data retrieval
94
12
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, 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
57
7
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, DNA, BLAST, nucleotide sequencing, Teaching material, Undergraduate, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval
94
17
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
behavior, 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
64
12
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, DNA, ames test, assay, Lab, Teaching material, Undergraduate, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
75
11
0
01.03.2019

Complete Set of Lessons

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

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 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
229
4
0
11.01.2018

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
infectious disease, experimental design, bioinformatics, Ebola, 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
185
23
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
517
114
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
148
36
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
194
30
0
06.05.2017

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C5

This exercise leads upper level biology majors in an inquiry-based excursion to determine how similar the signaling molecule, myostatin, is between humans and mice, using a basic set of bioinformatics tools and concepts.
bioinformatics, sequencing, FASTA, NCBI, Developmental Biology, NIBLSE, algorithms, BLAST, multiple sequence alignment, CourseSource, myostatin, muscle, DNA mutation, Lab, Teaching material, Lecture, Undergraduate, Homework, Advanced, 1 Hour, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types, Incubated at NIBLSE
29
71
0
06.19.2019

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
257
39
0
06.07.2019
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, Incubated at NIBLSE
46
28
0
05.29.2019
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
103
106
0
05.16.2019
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
142
17
5
05.02.2019

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
bioinformatics, 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
129
18
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.
bioinformatics, Protein Structure, 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
94
11
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, bioinformatics, 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
110
17
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, 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
294
51
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, bioinformatics, sequencing, introductory, Lab, Teaching material, Undergraduate, Majors, More than 1 hour, C3. Statistical concepts, C4. Bioinformatics tools, C5. Data retrieval
65
11
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
bioinformatics, CourseSource, genomic wide association studies, UCSC genome browser, single nucleotide polymorphism, Lab, Teaching material, Undergraduate, Advanced, More than 1 hour, C5. Data retrieval, C9. Implications
77
13
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
bioinformatics, NCBI, BLAST, colon cancer, pedigree, genetic testing, APC, introductory, Teaching material, Undergraduate, Majors, C4. Bioinformatics tools, C5. Data retrieval
94
12
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, 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
57
7
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, DNA, BLAST, nucleotide sequencing, Teaching material, Undergraduate, Less than 1 hour, C1. Role of bioinformatics, C4. Bioinformatics tools, C5. Data retrieval
94
17
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
behavior, 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
64
12
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, DNA, ames test, assay, Lab, Teaching material, Undergraduate, Advanced, Extended Project, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
75
11
0
01.03.2019

Complete Set of Lessons

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

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 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
229
4
0
11.01.2018

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
infectious disease, experimental design, bioinformatics, Ebola, 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
185
23
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
517
114
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
349
46
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
194
30
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, 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
57
7
0
01.03.2019

Complete Set of Lessons

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

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 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
229
4
0
11.01.2018
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
506
83
0
06.05.2017

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C7

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
257
39
0
06.07.2019

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, bioinformatics, 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
110
17
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, plant biology, plant pathology, Online course, Teaching material, C7. Scriptin