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Tags: C2. Computational concepts

All Categories (1-17 of 17)

  1. Intro to Command Line Coding Genomics Analysis

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

    By Rachael St. Jacques1, Max Maza1, Ray A Enke1

    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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. Needleman - Wunsch Algorithm Exercise

    13 Oct 2016 | Teaching Materials | Contributor(s):

    By Michael Sierk1, Sam S Donovan2, Neal Grandgenett, Bill Morgan3, Mark A. Pauley4, Elizabeth Ryder5

    1. Saint Vincent College 2. University of Pittsburgh 3. The College of Wooster 4. University of Nebraska at Omaha 5. Worcester Polytechnic Institute

    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=2

  17. Needleman - Wunsch Algorithm Exercise

    03 Aug 2016 | 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=1