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Tags: C2. Computational concepts

All Categories (1-20 of 22)

  1. Sequence Similarity in Developmental Biology - A Bioinformatics Exercise Using Myostatin

    19 Jun 2019 | Teaching Materials | Contributor(s):

    By Barbara Murdoch

    Eastern Connecticut State University

    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...

    https://qubeshub.org/qubesresources/publications/1317/?v=1

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

    07 Jun 2019 | Teaching Materials | Contributor(s):

    By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5

    1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University

    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.

    https://qubeshub.org/qubesresources/publications/1092/?v=2

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

    29 May 2019 | Teaching Materials | Contributor(s):

    By Ami Erickson

    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...

    https://qubeshub.org/qubesresources/publications/1247/?v=1

  4. Sequence Similarity Resource Adaptation: Exploring Ebola Virus

    16 May 2019 | Teaching Materials | Contributor(s):

    By William Tapprich

    University of Nebraska-Omaha

    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...

    https://qubeshub.org/qubesresources/publications/1219/?v=1

  5. Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

    02 May 2019 | Teaching Materials | Contributor(s):

    By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Carlos Christopher Goller3, Sabrina Robertson3

    1. Adams State University 2. Fairmont State University 3. North Carolina State University

    This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    https://qubeshub.org/qubesresources/publications/56/?v=5

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

    28 Feb 2019 | Teaching Materials | Contributor(s):

    By Rachael St. Jacques1, Max Maza1, Sabrina Robertson2, Guoqing Lu3, Andrew Lonsdale4, Ray A Enke5

    1. Department of Biology, James Madison University 2. Department of Psychology & Neuroscience, University of North Carolina at Chapel Hill 3. Department of Biology and School of Interdisciplinary Informatics, University of Nebraska Omaha 4. ARC Centre of Excellence in Plant Cell Walls, Melbourne University 5. James Madison University

    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.

    https://qubeshub.org/qubesresources/publications/1092/?v=1

  7. Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Mark Phillip Peterson1, Jacob T Malloy2, Vincent P Buonaccorsi2, James H Marden3

    1. Viterbo University 2. Juniata College 3. Pennsylvania State University

    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...

    https://qubeshub.org/qubesresources/publications/1005/?v=1

  8. Making toast: Using analogies to explore concepts in bioinformatics

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Kate L. Hertweck

    University of Texas at Tyler

    Module using analogies to introduce students to genomics

    https://qubeshub.org/qubesresources/publications/1003/?v=1

  9. A Hands-on Introduction to Hidden Markov Models

    04 Jan 2019 | Teaching Materials | Contributor(s):

    By Tony Weisstein1, Elena Gracheva2, Zane Goodwin2, Zongtai Qi2, Wilson Leung2, Christopher D. Shaffer2, Sarah C.R. Elgin2

    1. Truman State University 2. Washington University in St. Louis

    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.

    https://qubeshub.org/qubesresources/publications/999/?v=1

  10. Bioinformatics / Neuroinformatics

    03 Jan 2019 | Teaching Materials | Contributor(s):

    By William Grisham

    University of California, Los Angeles

    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...

    https://qubeshub.org/qubesresources/publications/990/?v=1

  11. Bioinformatics - Investigating Sequence Similarity

    04 Dec 2018 | Teaching Materials | Contributor(s):

    By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Carlos Christopher Goller3, Sabrina Robertson3

    1. Adams State University 2. Fairmont State University 3. North Carolina State University

    This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    https://qubeshub.org/qubesresources/publications/56/?v=4

  12. Using DNA Subway to Analyze Sequence Relationships

    28 May 2018 | Teaching Materials | Contributor(s):

    By Jason Williams1, Ray A. Enke2, Oliver Hyman2, Emily Lescak3, Sam S Donovan4, William Tapprich5, Elizabeth F Ryder6

    1. DNA Learning Center 2. The Department of Biology, James Madison University; The Center for Genome & Metagenome Studies, James Madison University 3. University of Alaska 4. University of Pittsburgh 5. University of Nebraska-Omaha 6. Worcester Polytechnic Institute

    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.

    https://qubeshub.org/qubesresources/publications/165/?v=2

  13. RNAseq data analysis using Galaxy

    13 Nov 2017 | Teaching Materials | Contributor(s):

    By Matthew Escobar1, Sam S Donovan2, Irina Makarevitch3, Bill Morgan4, Sabrina Robertson5

    1. California State University San Marcos 2. University of Pittsburgh 3. Hamline University 4. The College of Wooster 5. North Carolina State University

    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    https://qubeshub.org/qubesresources/publications/118/?v=3

  14. Using DNA Subway to Analyze Sequence Relationships

    18 Oct 2017 | Teaching Materials | Contributor(s):

    By Jason Williams

    DNA Learning Center

    This is a bioinformatics exercise using DNA Subway

    https://qubeshub.org/qubesresources/publications/165/?v=1

  15. RNAseq data analysis using Galaxy

    01 Aug 2017 | Teaching Materials | Contributor(s):

    By Matthew Escobar

    California State University - San Marcos

    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    https://qubeshub.org/qubesresources/publications/118/?v=2

  16. Bioinformatics - Investigating Sequence Similarity

    05 Jul 2017 | Teaching Materials | Contributor(s):

    By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Komal Vig3, Carlos Christopher Goller4, Sabrina Robertson5

    1. Adams State University 2. Hampshire College 3. Alabama State University 4. North Carolina State University 5. NC State

    This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    https://qubeshub.org/qubesresources/publications/56/?v=3

  17. RNAseq data analysis using Galaxy

    03 Jul 2017 | Teaching Materials | Contributor(s):

    By Matthew Escobar

    California State University - San Marcos

    This is a bioinformatics exercise intended for use in a computer lab setting with life science majors.

    https://qubeshub.org/qubesresources/publications/118/?v=1

  18. Bioinformatics - Investigating Sequence Similarity

    05 Jun 2017 | Teaching Materials | Contributor(s):

    By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Komal Vig3

    1. Adams State University 2. Hampshire College 3. Alabama State University

    This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    https://qubeshub.org/qubesresources/publications/56/?v=2

  19. Needleman - Wunsch Algorithm Exercise

    05 Jun 2017 | Teaching Materials | Contributor(s):

    By Michael Sierk

    Saint Vincent College

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

    https://qubeshub.org/qubesresources/publications/28/?v=3

  20. Bioinformatics - Investigating Sequence Similarity

    31 Jan 2017 | Teaching Materials | Contributor(s):

    By Adam Kleinschmit1, Benita Brink1, Steven Roof2, Komal Vig3

    1. Adams State University 2. Hampshire College 3. Alabama State University

    This laboratory module, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

    https://qubeshub.org/qubesresources/publications/56/?v=1