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  1. Module 2: Transcription Part I: From DNA Sequence to Transcription Unit

    Module 2: Transcription Part I: From DNA Sequence to Transcription Unit

    2020-07-25 20:04:08 | Teaching Materials | Contributor(s): Maria Santisteban, Alexa Sawa | doi:10.25334/53EH-4602

    This module illustrates how a primary transcript (pre-mRNA) is synthesized using a DNA molecule as the template. Students will learn about the importance of the 5' and 3' regions of the gene for initiation and termination of transcription.

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

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

    2020-07-25 20:03:07 | Teaching Materials | 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.

  3. GEA Introductory lesson on RNA-Seq

    GEA Introductory lesson on RNA-Seq

    2020-07-25 20:01:56 | Teaching Materials | Contributor(s): Jason Williams, Judy Brusslan, Ray Enke, Matthew Escobar, Vince Buonaccorsi | doi:10.25334/GM6A-VC81

    This RNA-Seq lesson uses the CyVerse VICE Platform and Jupyter notebooks to examine the expression of the leptin gene in samples from a mouse experimental design evaluating diet (high-fat vs. normal diet) and disease (cancer vs. normal tissue).

  4. GEA Introductory lesson on BLAST

    GEA Introductory lesson on BLAST

    2020-07-25 20:00:58 | Teaching Materials | Contributor(s): Justin DiAngelo, Alexis Nagengast, Wilson Leung, Douglas L Chalker | doi:10.25334/WQ1J-PW32

    The "Introduction to BLAST using Human Leptin" exercise aims to introduce students to the use of the Basic Local Alignment Search Tool (BLAST) to identify related sequences and compare similarity between them.

  5. Genome Solver: Building faculty skills in bioinformatics

    Genome Solver: Building faculty skills in bioinformatics

    2020-07-24 02:15:09 | Teaching Materials | 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.

  6. Integration of Bioinformatics into Life Science Curricula: Community Development, Dissemination, and Assessment of a NIBLSE Learning Resource

    Integration of Bioinformatics into Life Science Curricula: Community Development, Dissemination, and Assessment of a NIBLSE Learning Resource

    2020-07-23 14:24:32 | Teaching Materials | Contributor(s): Adam Kleinschmit, Rachel Cook, Barbara Murdoch, Elizabeth F Ryder, William Tapprich | doi:10.25334/F138-SS53

    Big data and computational tools have transformed the way we address biological questions. To prepare undergraduates for tomorrow’s challenges, life science curricula should integrate the understanding and use of these tools at all levels.

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

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

    2020-07-23 14:22:36 | Teaching Materials | 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.

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

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

    2020-07-23 14:22:20 | Teaching Materials | 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.

  9. Making bioinformatics tools classroom-friendly

    Making bioinformatics tools classroom-friendly

    2020-07-23 14:15:22 | Teaching Materials | Contributor(s): Jason Williams, Wilson Leung, Cornel Ghiban | doi:10.25334/F17W-PK51

    Poster on using Cyverse resources to make classroom that make using bioinformatics in the classroom a more manageable experience presented at the 2020 BIOME Institute: Cultivating Scientific Curiosity

  10. Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2

    Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2

    2020-07-18 20:22:36 | Teaching Materials | Contributor(s): Maria Shumskaya, Nicholas Lorusso | doi:10.25334/37N4-SW29

    Introduction into computational approaches in phylogeny and protein modeling based on coronavirus SARS-CoV-2 (caused COVID-19 pandemic). Two self-guided tutorials for standard lab classes of 2.5 hours. Level: undergraduate students majoring in biology.

  11. Yeti or not: Do they exist?

    Yeti or not: Do they exist?

    2020-05-14 17:59:40 | Teaching Materials | Contributor(s): Keith Johnson | doi:10.25334/6QTG-RQ39

    Through this 2-part bioinformatics case study, students will be led through the forensic analysis of putative Yeti artifacts based on published findings.

  12. Needleman - Wunsch Algorithm Exercise

    Needleman - Wunsch Algorithm Exercise

    2020-04-22 13:05:22 | Teaching Materials | Contributor(s): Michael Sierk, Sam S Donovan, Neal Grandgenett, Bill Morgan, Mark A. Pauley, Elizabeth F Ryder | doi:10.25334/H7KQ-F202

    This exercise is used in a sophomore-junior level bioinformatics course. The algorithm is introduced to the students who then complete the exercise.

  13. Population Demography in Swirl

    Population Demography in Swirl

    2020-02-12 20:27:04 | Teaching Materials | Contributor(s): Emily Weigel | doi:10.25334/NANC-M515

    The students will learn to generate, test, and graphically represent basic hypotheses on data distributions using large datasets.

  14. Genome Solver: Complete Set of Lessons

    Genome Solver: Complete Set of Lessons

    2019-10-23 15:16:23 | Teaching Materials | 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.

  15. Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Recent Activities

    Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE): Recent Activities

    2019-06-11 22:24:19 | Teaching Materials | Contributor(s): William Morgan | doi:10.25334/Q4J45K

    Presentation on NIBLSE at the 2019 Great Lakes Bioinformatics Conference

  16. A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

    A Fun Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!

    2019-06-07 20:09:22 | Teaching Materials | Contributor(s): Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke | doi:10.25334/Q4D172

    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.

  17. Expanding Undergraduate Participation in Computational Biology: Resources and Lessons Learned from a Hands-on Workshop

    Expanding Undergraduate Participation in Computational Biology: Resources and Lessons Learned from a Hands-on Workshop

    2019-06-05 04:12:45 | Teaching Materials | Contributor(s): Layla Oesper | doi:10.25334/Q46J13

    Presentation on computational biology in undergraduate education at the 2019 Great Lakes Bioinformatics Conference

  18. The ml4bio Workshop: Machine Learning Literacy for Biologists

    The ml4bio Workshop: Machine Learning Literacy for Biologists

    2019-06-03 02:59:00 | Teaching Materials | Contributor(s): Fangzhou Mu, Chris Magnano, Debora Treu, Anthony Gitter | doi:10.25334/Q44Q97

    Presentation on machine learning literacy for biologists at the 2019 Great Lakes Bioinformatics Conference

  19. Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

    Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

    2019-05-29 18:10:28 | Teaching Materials | Contributor(s): Ami Erickson | doi:10.25334/Q4H458

    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.

  20. Interdisciplinary biology education: a holistic approach to an intractable problem

    Interdisciplinary biology education: a holistic approach to an intractable problem

    2019-05-21 14:13:17 | Teaching Materials | Contributor(s): Kristin Jenkins | doi:10.25334/Q4M74V

    Presentation on interdisciplinary biology education at the 2019 Great Lakes Bioinformatics Conference