Genome Solver - A bioinformatics pipeline for community science

20 Feb 2024 | Contributor(s): Vinayak Mathur, Gaurav Arora, Anne Rosenwald | doi:10.25334/SEDX-YS29

The Genome Solver was an NSF-funded project developed as a way to train undergraduate life science faculty in basic web-based tools for bioinformatics. As part of the project we developed a one-day workshop consisting of bioinformatics modules on the theme of bacterial genomics, which we...

Lesson III - Annotation

30 Sep 2022 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/H8JF-G263

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.

Lesson II - Databases

30 Sep 2022 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/CQ4X-NH94

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.

Lesson II - Databases

30 Sep 2022 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/X55M-FZ44

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.

NIBLSE Collaborative Community Model for developing, disseminating, and assessing bioinformatics learning resources

08 Dec 2020 | Contributor(s): William (Bill) Morgan, Adam Kleinschmit, Anne Rosenwald, Eric Triplett, Mark A. Pauley, William Tapprich | doi:10.25334/QTEK-P378

The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a collaborative community model to facilitate the development, dissemination, and assessment of bioinformatics learning resources.

Genomics Lessons with GEA - RNA-Seq CURES

25 Nov 2020 | Contributor(s): Vince Buonaccorsi, Marcella Denise Cervantes, Douglas L Chalker, Maira Goytia, Wilson Leung, Laurel Lorenz, Laura Reed, Anne Rosenwald, Analyne Manzano Schroeder, Emily Wiley, Jason Williams | doi:10.25334/S21R-9364

Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch a CURE based on RNA-Seq data. We also developed a workflow for analysis of either prokaryotic or eukaryotic RNA-Seq data with existing tools.

Mini-Workshop August 14, 2020

28 Aug 2020 | Contributor(s): Vinayak Mathur, Anne Rosenwald, Gaurav Arora | doi:10.25334/R22A-ZT05

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.

Lesson VI - The Community Science Project

30 Sep 2022 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/NNHK-8A89

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.

Pre-lesson: Introduction to BLAST

05 Aug 2020 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/TY8V-G541

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.

Lesson VII - Synteny

05 Aug 2020 | Contributor(s): Gaurav Arora, Anne Rosenwald, Vinayak Mathur | doi:10.25334/SGQF-1W47

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.

Lesson III - Annotation

05 Aug 2020 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/JEY1-0927

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.

Module 6: Alternative Splicing

25 Jul 2020 | Contributor(s): Leocadia Paliulis, Anne Rosenwald | doi:10.25334/B3AH-GV62

This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs.

Module 5: The Need for an Open Reading Frame

25 Jul 2020 | Contributor(s): Carina Howell, Leocadia Paliulis, Anne Rosenwald | doi:10.25334/N11Z-PK53

In this module, students will learn to identify the open reading frames for a given gene, and define the phases of the splice donor and acceptor sites.

Module 4: Removal of Introns from pre-mRNA by Splicing

25 Jul 2020 | Contributor(s): Meg Laakso, Anne Rosenwald | doi:10.25334/030X-Q219

In this module, students will learn to identify splice donor and acceptor sites that are best supported by RNA-Seq data, and use the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.

Module 1: Introduction to the Genome Browser: What is a Gene?

25 Jul 2020 | Contributor(s): Joyce Stamm, Jennifer Kennell, Wilson Leung, Leocadia Paliulis, Srebrenka Robic, Anne Rosenwald | doi:10.25334/N0PH-7508

This lesson introduces the University of California Santa Cruz genome browser to students, walking them through some of the key features so that it can be used for analysis of gene structure.

The Genomics Education Partnership: Exploring best practices in implementation of a genomics CURE

23 Jul 2020 | Contributor(s): Matthew Wawersik, Anna Allen, Cindy Arrigo, Andrew Arsham, Daron Barnard, Rebecca Burgess, Justin DiAngelo, Jennifer Jemc, Christopher Jones, Lisa Kadlec, Adam Kleinschmit, Judith Leatherman, David Lopatto, Mollie Manier, Hemlata Mistry, Nathan Mortimer, Alexis Nagengast, Susan Parish, Anne Rosenwald, Joyce Stamm, Sarah Elgin, Laura Reed | doi:10.25334/6HS9-XM77

Since 2006, the Genomics Education Partnership (GEP) has incorporated authentic genomics research experiences into the undergraduate curriculum.

Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life sciences education

23 Jul 2020 | Contributor(s): William Morgan, Sam S Donovan, Hayley Orndorf, Sabrina Robertson, Elizabeth F Ryder, Michael Sierk, Anne Rosenwald, Elizabeth Dinsdale, Eric Triplett, Mark Pauley, William Tapprich | doi:10.25334/A6NR-TT57

To efficiently and effectively integrate bioinformatics instruction into undergraduate life science curricula, educators would benefit from open access, high-quality learning resources (LRs) for use in existing biology classes.

The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Barriers to Integration

23 Jul 2020 | Contributor(s): Anne Rosenwald, Elizabeth Dinsdale, William Morgan, Mark A. Pauley, William Tapprich, Eric Triplett, Jason Williams | doi:10.25334/NHB4-X766

The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote the use of bioinformatics and data science as a way to teach biology.

The Genomics Education Partnership: Introducing Undergraduates to Research by Engaging Them in Genome Annotation

23 Jul 2020 | Contributor(s): Sarah Elgin, Wilson Leung, Anne Rosenwald, David Lopatto, Charles Hauser, Catherine Reinke, Laura Reed | doi:10.25334/SFXW-PZ41

Since 2006, the Genomics Education Partnership (GEP; http://gep.wustl.edu) has helped faculty bring genomics research experiences into the undergraduate curriculum.

Genome Solver: Building faculty skills in bioinformatics

23 Jul 2020 | Contributor(s): Vinayak Mathur, Gaurav Arora, Vinodh Ganesan, Hita Gupta, Mariana Kazarian, Anne Rosenwald | doi:10.25334/G1B6-JJ53

Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based bioinformatics skills.

Genomics Education Alliance: A Collection of Posters for the 2020 BIOME Institute.

23 Jul 2020 | Contributor(s): Vince Buonaccorsi, Marcella Denise Cervantes, Douglas L Chalker, Anne Rosenwald, Emily Wiley, Jason Williams | doi:10.25334/90HY-1188

This is a collection of posters from members of the Genomics Education Alliance (GEA) that will be presented at the 2020 BIOME Institute.

Introduction to Genome Annotation

09 Jan 2020 | Contributor(s): Selene Nikaido | doi:10.25334/2ANZ-SV60

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.

Lesson VI - The Community Science Project

19 Nov 2019 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/MN0K-XB56

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.

Genome Solver: Complete Set of Lessons

23 Oct 2019 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/E4GQ-2S85

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.

Lesson V - Phylogenetics

22 Oct 2019 | Contributor(s): Anne Rosenwald, Gaurav Arora, Vinayak Mathur | doi:10.25334/HBAR-5X64

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.