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Tags: C2. Computational concepts

Description

C2. Summarize key computational concepts, such as algorithms and relational databases, and their applications in the life sciences. To make use of sophisticated software and database tools, students should have a basic understanding of the principles upon which these tools are based and should be exposed to how these tools work. 

  • Explain the underlying algorithm(s) employed in sequence alignment (e.g., BLAST).
  • Modify software parameters to achieve biologically meaningful results.
  • Explain how data are organized in relational databases (e.g., NCBI and model organisms
    databases).

All Categories (1-20 of 32)

  1. A Critical Guide to BLAST

    04 Dec 2020 | Teaching Materials | Contributor(s):

    By Teresa Attwood1, GOBLET Foundation

    The University of Manchester, Manchester, UK

    This Critical Guide in the Introduction to Bioinformatics series provides an overview of the BLAST similarity search tool, briefly examining the underlying algorithm and its rise to popularity.

    https://qubeshub.org/publications/2172/?v=1

  2. A Critical Guide to the PDB

    05 Dec 2020 | Teaching Materials | Contributor(s):

    By Teresa Attwood1, GOBLET Foundation

    The University of Manchester, Manchester, UK

    This Critical Guide in the Introduction to Bioinformatics series provides a brief outline of the Protein Data Bank – the PDB – the world’s primary repository of biological macromolecular structures.

    https://qubeshub.org/publications/2174/?v=1

  3. 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/publications/1092/?v=1

  4. 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/publications/1092/?v=2

  5. 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/publications/999/?v=1

  6. 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/publications/56/?v=1

  7. 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/publications/56/?v=2

  8. 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/publications/56/?v=3

  9. 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/publications/56/?v=4

  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/publications/990/?v=1

  11. 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/publications/1247/?v=1

  12. Developing a phylogram from computational resources.

    01 Jun 2021 | Teaching Materials | Contributor(s):

    By Melanie Lenahan1, Shea Cinquemani1

    Raritan Valley Community College

    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/publications/2404/?v=1

  13. DNA Subway Learning Resources

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

    By Jason Williams

    DNA Learning Center

    DNA Subway is a NIBLSE Recommended resource. This is a collection of learning resources associated with DNA Subway.

    https://qubeshub.org/publications/164/?v=2

  14. Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."

    31 May 2021 | Teaching Materials | Contributor(s):

    By Alice Tarun

    St. Lawrence University

    The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the...

    https://qubeshub.org/publications/2394/?v=1

  15. 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/publications/1003/?v=1

  16. 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/publications/28/?v=1

  17. 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/publications/28/?v=2

  18. 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/publications/28/?v=3

  19. Needleman - Wunsch Algorithm Exercise

    22 Apr 2020 | Teaching Materials | Contributor(s):

    By Michael Sierk1, Sam S Donovan2, Neal Grandgenett, Bill Morgan3, Mark A. Pauley4, Elizabeth F 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/publications/28/?v=4

  20. 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/publications/118/?v=1