1) Brief description of your project: objectives, activities, impact
The aim of this project is to develop a course about “Bioinformatics”. This course will be taught to the students of the Biomedical Engineering Department, Faculty of Engineering, Minia University. The course contents are based on Open Educational Resources (OER). The final course will be an OER as it could be freely retained, reused, revised, remixed, and/or redistributed.
Searching for high quality resources is an essential step in the production of this project. Module 3 -in the OpenMed course- contains a wealthy collection of OERs which were used to find the appropriate resources. Then, localizing the content to the Biomedical Engineering students is the second step.
After downloading the required OERs, I remixed, modified, and updated them. I will promote my OER by informing my students about them. Also, I shared the links on social medias like Twitter and Facebook.
I will use Facebook group for online discussions with the students. Open Badges is a very motivating tool for students’ motivation.
The open licences that I applied to my project depended on the open licences of the OERs that I used in my project. I applied Attribution (BY), Share-alike (SA), and Non-commercial (NC) Creative Commons (CC) licences. The (BY) to have credits and reputation for me and my institution. The (SA) to not be more restrictive. The (NC) as it will be for educational purposes. I will not apply the No Derivative Works (ND) to let others remix or adapt for further courses. I applied the licences through: (https://creativecommons.org/share-your-work/). The course is released through open license and shared on the OER commons website <https://www.oercommons.org/authoring/26019-introduction-to-bioinformatics> making them publicly available.
About the language, English is the main foreign language in Arab Republic of Egypt. All the students of faculties in Egypt had been taught English for many years. So, I searched for OERs in English to use them in my course.
About the content, Bioinformatics is a multidisciplinary subject. It may be taught to students from different faculties like Faculty of Medicine, Faculty of Engineering, Faculty of Computer Science, and/or Faculty of Agriculture. I adapt the content of Bioinformatics to the Biomedical Engineering students by stressing on the applied algorithms, software programs, and equations that are used to solve a biological problem.
- Student/user feedback and open peer review
- Reputational benefits, recognition
- Reaching a wider range of learners
For my institution:
- Recognition and enhanced reputation
- Wider availability of their academic content
- Increased sharing of ideas and practice within the institution
Resources: • The resources used in the first lecture were from: 1- website “figshare.com”. (CC BY 4.0) https://figshare.com/articles/Bioinformatics_Introduction/1506799 https://figshare.com/articles/Bioinformatics_for_the_Public_Eye/763316 https://figshare.com/articles/Jobs_Posts_up_to_April_19th_2016/3185014 2- OpenCourseWare (OCW) “Bioinformatics and Computational Biology Solutions Using R and Bioconductor” offered by The Johns Hopkins University, 2006. (CC BY NC SA) http://ocw.jhsph.edu/courses/BioinformaticsComputationalBiology/PDFs/Lecture1.pdf • The resources used in the second lecture were from: 1- OpenCourseWare (OCW) “BIO101: INTRODUCTION TO MOLECULAR AND CELLULAR BIOLOGY” offered by Saylor Academy. https://learn.saylor.org/course/bio101 (CC BY 4.0) 2- Open Textbook “Concepts of Biology” offered by OpenStax College, Rice University. http://cnx.org/content/col11487/1.9 (CC BY 4.0) Chapter 8: Patterns of Inheritance, pp: 173-198 3- Open Podcasts and Video Content “Introduction to Heredity”, "Punnett Square Fun", and "Sex-Linked Traits" offered by Khan Academy. (CC BY NC SA) https://www.khanacademy.org/science/biology/classical-genetics/mendelian--genetics/v/introduction-to-heredity https://www.khanacademy.org/science/biology/classical-genetics/mendelian--genetics/v/punnett-square-fun https://www.youtube.com/watch?v=-ROhfKyxgCo • The resources used in the third lecture were from: 1- Open Learning Initiative (OLI) “Modern Biology” offered by Carnegie Mellon University. Unit 4: Basis of Molecular Biology (CC BY NC SA 3.0) https://oli.cmu.edu/jcourse/workbook/activity/page?context=df459f350a0001dc0ba0da35eb68f1a4&view=frameset 2- Open Textbook “Concepts of Biology” offered by OpenStax College, Rice University. http://cnx.org/content/col11487/1.9 (CC BY 4.0) Chapter 9: Molecular Biology, pp: 199-224 3- Open Podcasts and Video Content “DNA” offered by Khan Academy. (CC BY NC SA) https://www.khanacademy.org/science/biology/classical-genetics/molecular-basis-of-genetics-tutorial/v/dna-deoxyribonucleic-acid • The resources used in the fourth lecture were from: 1- Open Podcasts and Video Content “Genetics 101 (Part 1 of 5): What are genes?” offered by 23andMe and Khan Academy. (CC BY NC SA 2.0) https://dobmovies.com/watch/genetics-101-part-1-of-5-what-are-genes-/ubq4eu_TDFc.html 2- OpenCourseWare (OCW) Isaac Kohane, Leonid Mirny, Robert Berwick, and Alvin Kho. HST.508 Quantitative Genomics. Fall 2005. Massachusetts Institute of Technology: MIT, Module 2: Comparative Genomics, “Human Variations: Genes, Genotypes and Generations” by Marco F. Ramoni (CC BY NC SA 2.0) https://ocw.mit.edu/courses/health-sciences-and-technology/hst-508-quantitative-genomics-fall-2005/ 3- Open Podcasts and Video Content “Biology – Evolution and the Tree of Life – Population Genetics”, “Hardy-Weinberg equation”, “Applying the Hardy-Weinberg equation” offered by Khan Academy. (CC BY NC SA) https://www.khanacademy.org/science/biology/her/heredity-and-genetics/v/allele-frequency https://www.khanacademy.org/science/biology/her/heredity-and-genetics/v/hardy-weinberg https://www.khanacademy.org/science/biology/her/heredity-and-genetics/v/applying-hardy-weinberg 4- Saylor Academy's Flexbook: Jill Schmidlkofer's Advanced Probability and Statistics: "Section 10.1: The Goodness-of-Fit Test”; partially adapted from David Lane's Online Statistics Education: A Multimedia Course of Study and CK-12: Advanced Probability and Statistics. (CC BY NC SA 4.0) https://www.saylor.org/site/wp-content/uploads/2013/07/Statistics-FlexBook-20130714-FINAL.pdf 5- “Statistics and Probability - Inference for Categorical Data (Chi-square Tests) - Chi-square goodness-of-fit tests” offered by Khan Academy. (CC BY NC SA) https://www.khanacademy.org/math/statistics-probability/inference-categorical-data-chi-square-tests/chi-square-goodness-of-fit-tests/v/pearson-s-chi-square-test-goodness-of-fit 6- Zhang X, Huang S, Zhang Z, Wang W (2012) Chapter 10: Mining Genome-Wide Genetic Markers. PLoS Comput Biol 8(12): e1002828. (CC BY 4.0) http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002828 • The resources used in the fifth lecture were from: 1- Mary L. McHugh. The odds ratio: calculation, usage, and interpretation. Biochemia Medica 2009;19(2):120-6. (CC BY) http://www.biochemia-medica.com/content/odds-ratio-calculation-usage-and-interpretation 2- Saad MN, Mabrouk MS, Eldeib AM, Shaker OG (2015) Genetic Case-Control Study for Eight Polymorphisms Associated with Rheumatoid Arthritis. PLoS ONE 10(7): e0131960. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131960 (CC BY) 3- Bush WS, Moore JH (2012) Chapter 11: Genome-Wide Association Studies. PLoS Comput Biol 8(12): e1002822. (CC BY 4.0) http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002822 4- OpenCourseWare (OCW) Isaac Kohane, Leonid Mirny, Robert Berwick, and Alvin Kho. HST.508 Quantitative Genomics. Fall 2005. Massachusetts Institute of Technology: MIT, Module 2: Comparative Genomics, “Human Variations: Genes, Genotypes and Generations” by Marco F. Ramoni (CC BY NC SA 2.0) https://ocw.mit.edu/courses/health-sciences-and-technology/hst-508-quantitative-genomics-fall-2005/