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Core Resources                           FMN Adaptations

Core Resources

Lesson I - Introduction to Genome Solver

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Part I is the Introduction to the Genome Solver Project.
Published on 10.2018
1.5K Views
1.3K Downloads
1 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

Lesson IV - Comparative Genomics

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson IV, Comparative Genomics, discusses some of the tools available for looking at genes across different genomes.
Published on 10.2019
1.1K Views
625 Downloads
0 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

Lesson V - Phylogenetics

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson V is an introduction to Phylogenetics.
Published on 10.2019
1.1K Views
1.5K Downloads
2 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

Lesson III - Annotation

Gaurav Arora

Version: 1.0 Adapted From: Lesson III - Annotation v1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson III introduces Annotation, or assigning meaning to all the A's, C's, T's, and G's.
Published on 10.2019
677 Views
156 Downloads
0 Adaptations

Lesson III - Annotation

Gaurav Arora

Version: 1.0 Adapted From: Lesson III - Annotation v1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson III introduces Annotation, or assigning meaning to all the A's, C's, T's, and G's.
Published on 10.2019
653 Views
145 Downloads
0 Adaptations

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.
Published on 10.2019
1.6K Views
190 Downloads
0 Adaptations
bioinformatics, NIBLSE, Bioinformatics Education, Bioinformatics and Genomics, C4. Bioinformatics tools, C5. Data retrieval, C6. Models, C8. Data types, C9. Implications, Recommended by NIBLSE, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, Extended Project

Lesson VII - Synteny

Gaurav Arora, Anne Rosenwald, Vinayak Mathur

Version: 3.0

The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.
Published on 08.2020
794 Views
663 Downloads
0 Adaptations
Bioinformatics Education, Introductory, Lab, Online course, Undergraduate, Faculty, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

Pre-lesson: Introduction to BLAST

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.
Published on 08.2020
753 Views
823 Downloads
1 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Undergraduate, Audience Level, Majors, Non-majors

Mini-Workshop August 14, 2020

Vinayak Mathur, Anne Rosenwald, Gaurav Arora

Version: 1.0

We reviewed the materials available on Genome Solver (other lessons here) and described our new python pipeline for examining horizontal gene transfer and a new synteny lesson in detail.
Published on 08.2020
718 Views
986 Downloads
0 Adaptations
Bioinformatics Education, Introductory, Lab, Online course, Lecture, Undergraduate, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, More than 1 hour, Fostering a Sense of Belonging, Promoting Engagement and Self-Efficacy

MiniWorkshop Follow-Up October 2, 2020

Gaurav Arora, Vinayak Mathur

Version: 1.0

A follow up to our mini workshop of August 14, 2020. Further information about the python pipeline for HGT and the new cytoscape lesson.
Published on 10.2020
665 Views
807 Downloads
0 Adaptations
Bioinformatics Education, Introductory, Lab, Online course, Lecture, Undergraduate, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour, Promoting Engagement and Self-Efficacy

Using Bioinformatics Activities to understand the Past and Present of SARS-CoV2

Gaurav Arora

Version: 1.0

We have designed a Bioinformatics activity that uses tools to identify the origins and mutations in the novel SARS-CoV2 strains.
Published on 06.2021
1.1K Views
88 Downloads
0 Adaptations
Introductory, Undergraduate, Audience Level, Majors, Non-majors, Promoting Engagement and Self-Efficacy, Accessibility

Lesson VI - The Community Science Project

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 2.0

Genome Solver's Community Science Project was developed as a way to use the skills taught in the previous lessons. We're asking members of the community to provide instances of potential phage genes embedded in bacterial genomes.
Published on 09.2022
92 Views
36 Downloads
0 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, Extended Project

Lesson II - Databases

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 3.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson II introduces the principal databases for microbial genomics.
Published on 09.2022
198 Views
38 Downloads
0 Adaptations
Introductory, Lab, Online course, Lecture, Undergraduate, Bioinformatics Education, Bioinformatics and Genomics, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

Lesson III - Annotation

Anne Rosenwald, Gaurav Arora, Vinayak Mathur

Version: 4.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Lesson III introduces Annotation, or assigning meaning to all the A's, C's, T's, and G's.
Published on 09.2022
154 Views
24 Downloads
0 Adaptations
Introductory, Lab, Online course, Lecture, Undergraduate, Bioinformatics Education, Bioinformatics and Genomics, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour

FMN Adaptations

BLAST-HGT PROJECT

Shawna Reed

Version: 1.0 Adapted From: Lesson V - Phylogenetics v2.0

Genome Solver modules were combined to make one project for students using tools within NCBI BLAST to explore phylogenetics and horizontal gene transfer from phage to Chlamydia.
Published on 01.2020
629 Views
530 Downloads
0 Adaptations

Introduction to Genome Annotation

Selene Nikaido

Version: 1.0 Adapted From: Lesson III - Annotation v2.0

This exercise is an adaptation of the Annotation Lesson by Rosenwald et al. It introduces the use of bioinformatics tools to extract information from genome databases. It is a basic lesson on genome annotation databases.
Published on 01.2020
1.3K Views
357 Downloads
0 Adaptations
microbiology, Genome annotation, Bioinformatics Education, Bioinformatics and Genomics, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Advanced, Activity Length, More than 1 hour, Promoting Engagement and Self-Efficacy

Databases: A Study of Influenza

Selene Nikaido

Version: 1.0 Adapted From: Lesson II - Databases v1.0

This lesson introduces the student to the Influenza Research Database. Students will select Influenza genome sequences to see how they are related. Students tests hypotheses about evolutionary ideas involving reassortment in Influenza.
Published on 01.2020
864 Views
340 Downloads
0 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, molecular evolution, Influenza, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Advanced, Activity Length, More than 1 hour, Promoting Engagement and Self-Efficacy

BLAST Exercises for Analyzing Cloning Results

Erin R. Morris

Version: 1.0 Adapted From: Lesson I - Introduction to Genome Solver v1.0

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. These activities have modified Lesson 1: Introduction to Genome Solver.
Published on 01.2020
776 Views
224 Downloads
0 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Lab, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Advanced, Activity Length, 1 Hour, More than 1 hour

Exploring the evolution of caffeine biosynthesis enzymes

Shuchismita Dutta

Version: 1.0 Adapted From: Lesson V - Phylogenetics v2.0

Caffeine is a very common stimulant consume worldwide as tea, coffee, mate, cocoa, and chocolate. Ever wondered why plants make caffeine? Do all caffeine producing plants have the same enzymes for caffeine biosynthesis?
Published on 01.2020
1.2K Views
266 Downloads
0 Adaptations
Bioinformatics Education, Bioinformatics and Genomics, Introductory, Lab, Online course, Lecture, Undergraduate, Homework, Instructional Setting, Audience Level, Majors, Non-majors, Activity Length, 1 Hour