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, 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
1.3K
191
0
0
07.2021

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
2.8K
521
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, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Instructional Setting, Audience Level, Advanced, Activity Length, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
2.1K
195
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, Undergraduate, NIBLSE, Instructional Setting, Audience Level, Activity Length, Less than 1 hour, C1. Role of bioinformatics, C6. Models, Reviewed at NIBLSE, agent based modleing
2.6K
461
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, Undergraduate, NIBLSE, incubators, HIV, Audience Level, C1. Role of bioinformatics, C4. Bioinformatics tools, Recommended by NIBLSE
1.4K
278
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, 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
1.3K
191
0
0
07.2021

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, Undergraduate, NIBLSE, algorithms, incubators, Audience Level, Advanced, Activity Length, 1 Hour, C2. Computational concepts, Incubated at NIBLSE
1.3K
184
0
0
04.2020

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
2.8K
521
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, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Instructional Setting, Audience Level, Advanced, Activity Length, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
2.1K
195
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, 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
1.3K
191
0
0
07.2021

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

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
2.1K
286
0
0
10.2019

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
2.8K
521
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, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Instructional Setting, Audience Level, Advanced, Activity Length, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
2.1K
195
0
0
10.2017

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, Undergraduate, NIBLSE, incubators, HIV, Audience Level, C1. Role of bioinformatics, C4. Bioinformatics tools, Recommended by NIBLSE
1.4K
278
0
0
06.2017

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, Undergraduate, NIBLSE, incubators, RNAseq, Instructional Setting, Audience Level, Activity Length, More than 1 hour, C4. Bioinformatics tools, C5. Data retrieval, Reviewed at NIBLSE
1.5K
267
0
0
06.2017

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C5. Find, retrieve, and organize various types of biological data

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, 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
1.3K
191
0
0
07.2021

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
2.1K
286
0
0
10.2019

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
2.8K
521
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, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Instructional Setting, Audience Level, Advanced, Activity Length, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
2.1K
195
0
0
10.2017

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, Undergraduate, NIBLSE, incubators, RNAseq, Instructional Setting, Audience Level, Activity Length, More than 1 hour, C4. Bioinformatics tools, C5. Data retrieval, Reviewed at NIBLSE
1.5K
267
0
0
06.2017

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C6. Explore and/or model biological interactions, networks and data integration using bioinformatics

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
2.1K
286
0
0
10.2019
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, agent-based model, Lab, bioinformatics, predator-prey, Undergraduate, NIBLSE, Instructional Setting, Audience Level, Activity Length, Less than 1 hour, C1. Role of bioinformatics, C6. Models, Reviewed at NIBLSE, agent based modleing
2.6K
461
0
0
06.2017

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C7. Use command-line bioinformatics tools and write simple computer scripts

No resources found.

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C8. Describe and manage biological data types, structure, and reproducibility

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
2.1K
286
0
0
10.2019

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
2.8K
521
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, Undergraduate, NIBLSE, DNA Barcoding, DNA sequence, BLAST, multiple sequence alignment, DNA Subway, Instructional Setting, Audience Level, Advanced, Activity Length, Extended Project, C1. Role of bioinformatics, C2. Computational concepts, C4. Bioinformatics tools, C5. Data retrieval, C8. Data types
2.1K
195
0
0
10.2017

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C9. Interpret the ethical, legal, medical, and social implications of biological data

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
2.1K
286
0
0
10.2019

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Supplemental Resources for Instructors

A Critical Guide to the UniProtKB Flat-file Format

Teresa Attwood, GOBLET Foundation

Version: 1.0

This Critical Guide briefly presents the need for biological databases and for a standard format for storing and organising biological data.
NIBLSE, uniprot, GOBLET, InstructorResources
805
202
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
1.0K
272
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
1.0K
262
0
0
12.2020

A Critical Guide to Unix

Teresa Attwood, GOBLET Foundation

Version: 1.0

This Critical Guide in the Introduction to Bioinformatics series briefly introduces the Unix Operating System, and provides a subset of some of the most helpful and commonly used commands....
NIBLSE, UNIX, basic UNIX commands, GOBLET, InstructorResources
802
210
0
0
12.2020

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