Support

Support Options

  • Knowledge Base

    Find information on common questions and issues.

  • Support Messages

    Check on the status of your correspondences with members of the QUBES team.

Contact Us

About you
About the problem

Tags: C8. Data types

Description

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).

Resources (1-16 of 16)

  1. 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/qubesresources/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/qubesresources/publications/1326/?v=1

  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. Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

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

    By Adam Idica1, Jordan Thompson1, Irene Munk Pedersen1, Pavan Kadandale1

    University of California, Irvine

    In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research, published in CourseSource

    https://qubeshub.org/qubesresources/publications/1007/?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. The Ames Test

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

    By Nathan Goodson-Gregg, Elizabeth A. De Stasio

    Introduction to the Ames Test, published as GSA Learning Resource

    https://qubeshub.org/qubesresources/publications/987/?v=1

  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/qubesresources/publications/56/?v=4

  10. 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/qubesresources/publications/860/?v=1

  11. 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

  12. 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/qubesresources/publications/164/?v=2

  13. 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

  14. 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

  15. 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

  16. 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