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C8. Describe and manage biological data types, structure, and reproducibility. This competency addresses two distinct concerns: 1) each of the varied ‘omics fields produces data in formats particular to its needs, and these formats evolve with changes in technologies and refinements in 24 downstream software; and 2) all experimental data is subject to error and the user must be cognizant of the need to verify the reproducibility of their data. Students need to develop an awareness of, and ability to, manipulate different data types given the versioning of formats. They also need to exercise caution, to carry out appropriate statistical analyses on their data as part of normal operating procedures and report the uncertainty of their results, and to provide the relevant information to enable reproduction of their results. 

  • Describe the various sequence formats used to store DNA and protein sequences (e.g., FASTA, FASTQ).
  • Understand the representation of gene features using Gene Feature Format (GFF) files.
  • Compare reproducibility of biological and technical replicate data (e.g., transcriptomic data) using statistical tests (Spearman rank test and false discovery calculations).

Teaching Materials (1-6 of 6)

  1. Genome Solver: Complete Set of Lessons

    23 Oct 2019 | Teaching Materials | Contributor(s):

    By Anne Rosenwald1, Gaurav Arora2, Vinayak Mathur3

    1. Georgetown University 2. Gallaudet University 3. Cabrini University

    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...

    https://qubeshub.org/publications/860/?v=2

  2. Using Synthetic Biology to Teach Data Science

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

    By Margaret S Saha1, Beteel Abu-Ageel1, Sanjana Challa1, Xiangyi Fang1, Chai Hibbert1, Anna Isler1, Elias Nafziger1, Adam Oliver1, Hanqiu Peng1, Julia Urban1, Vivian Zhu1

    College of William and Mary

    Abstract for poster on using synthetic biology to introduce students to meaningful data mining, analysis, and application to engineering novel biological constructs.

    https://qubeshub.org/publications/1326/?v=1

  3. Complete Set of Lessons

    01 Nov 2018 | Teaching Materials | Contributor(s):

    By Anne Rosenwald1, Gaurav Arora2, Vinayak Mathur3

    1. Georgetown University 2. Gallaudet University 3. Cabrini University

    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...

    https://qubeshub.org/publications/860/?v=1

  4. 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/publications/165/?v=2

  5. 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

  6. 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/publications/165/?v=1

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