References and Resources
Wider list of references and resources used in the course (please also find the list attached as a downloadable pdf)
Teaching strategies and curriculum implementation
Strategies for using peer-assisted learning effectively in an undergraduate bioinformatics course https://pubmed.ncbi.nlm.nih.gov/23382123/
Evidence That Personal Genome Testing Enhances Student Learning in a Course on Genomics and Personalized Medicine https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068853
Elective 8-week course on genomics and personalized medicine, Genetics 210; http://gene210.stanford.edu /
An educational guide for nanopore sequencing in the classroom https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007314#sec003
Active learning strategies for Bioinformatics teaching https://flxlexblog.wordpress.com/2015/08/31/active-learning-strategies-for-bioinformatics-teaching-2/
Evaluating the effectiveness of a practical inquiry‐based learning bioinformatics module on undergraduate student engagement and applied skills https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20954
Early Requirement for Bioinformatics in Undergraduate Biology Curricula https://www.frontiersin.org/articles/10.3389/fbinf.2021.656531/full
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data https://www.frontiersin.org/articles/10.3389/fgene.2017.00023/full
Bionformatics Education and Training Collection https://f1000research.com/collections/bioinformaticsedu
Preparing the next generation of genomicists: a laboratory-style course in medical genomics https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-015-0124-y
“On the Job” Learning: A Bioinformatics Course Incorporating Undergraduates in Actual Research Projects and Manuscript Submissions https://iubmb.onlinelibrary.wiley.com/doi/pdf/10.1002/bmb.20848
Designing and running an advanced Bioinformatics and genome analyses course in Tunisia https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006373
Bioinformatics for Undergraduates Steps towards a quantitative bioscience curriculum https://iubmb.onlinelibrary.wiley.com/doi/pdf/10.1002/bmb.2006.49403403180
Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597031/ doi: 10.1371/journal.pcbi.1006746
Establishing a computational biology flipped classroom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532840/
Integrating PCR Theory and Bioinformatics into a Research-oriented Primer Design Exercise https://www.lifescied.org/doi/10.1187/cbe.07-07-0051 https://doi.org/10.1187/cbe.07-07-0051
Introduction to genomics and bioinformatics lab course https://www.biograd.co.uk/introduction-to-geomics-and-bioinformatics.php
Applying service design in competency‐based curriculum development https://onlinelibrary.wiley.com/doi/full/10.1002/cbe2.1171
The application of project-based learning in bioinformatics training https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005620 https://doi.org/10.1371/journal.pcbi.1005620
OncoSim and OncoWiki: an authentic learning approach to teaching cancer genomics https://bmcmededuc.biomedcentral.com/articles/10.1186/s12909-019-1812-7
The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa https://doi.org/10.3389/fgene.2019.01209
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action https://f1000research.com/articles/6-1040
Preparing teachers for the global citizenship education https://unesdoc.unesco.org/ark:/48223/pf0000265452.locale=en
Universal Design for Learning principles:https://udlguidelines.cast.org https://youtu.be/shgJYEmD1_A
Magana, A. J., M. Taleyarkhan, D. R. Alvarado, M. Kane, J. Springer and K. Clase (2014). “A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research.” CBE Life Sci Educ 13(4): 607-623. https://www.lifescied.org/doi/10.1187/cbe.13-10-0193
FAIR training materials: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854
The FAIR Guiding Principles for scientific data management and stewardship https://www.nature.com/articles/sdata201618
Building Machine Learning Models for Predicting Antibiotic Resistance https://towardsdatascience.com/building-machine-learning-models-for-predicting-antibiotic-resistance-7640046a91b6
Kaggle tutorial used in Dr. Nicole Wheeler’s course https://www.kaggle.com/nwheeler443/gono-unitigs
Building institutional and regional capacity in genomics through train the trainer programmes
TtT course page: Train the Trainer: Capacity building for genomic surveillance of AMR in low- and middle-income countries https://coursesandconferences.wellcomeconnectingscience.org/event/train-the-trainer-capacity-building-genomic-surveillance-of-amr-2019/
Video presenting the TtT https://www.youtube.com/watch?v=EdPM5oibKiA
Project presentation page: Train the trainer courses in pathogen genomics and surveillance: t3connect.org
Paper: Train-the-trainer as an effective approach to building global networks of experts in genomic surveillance of AMR http://tttmanuscript.cgps.group
From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006923
Teaching approaches used in Train the Trainer: Capacity building for genomic surveillance of AMR in low- and middle-income countries course https://ugc.futurelearn.com/uploads/files/19/fc/19fc7fbe-431c-4c15-9c6d-1bc69bfb474f/TtT_Teaching_approaches.pdf
EMBL-EBI Train the Trainer https://www.ebi.ac.uk/training/trainer-support/expand-your-training-skills
About peer reviewing:
David Nicola, Avril Thomson & Caroline Breslin: Rethinking feedback practices in higher education: a peer review perspective. Assessment and Evaluation in Higher Education, volume 39 issue 1, Published online 10 May 2013 http://l2l.ie/documents/feedback.pdf
Peer Feedback Marking: Developing Peer Assessment Nancy Falchikov Pages 175-187 | Published online: 09 Jul 2006 https://www.tandfonline.com/doi/abs/10.1080/1355800950320212
Rubrics
A Mastery Rubric: guiding curriculum design, admissions and development of course objectives https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664514/
A comprehensive rubric for instructional design in e-learning https://www.emerald.com/insight/content/doi/10.1108/IJILT-09-2017-0092/full/pdf
Evaluating the effectiveness of a laboratory-based professional development program for science educators https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669365/
Design of assessment rubrics http://johnsonongcheebin.blogspot.com/2015/11/
Curriculum development guide and rubric http://winbev.pbworks.com/f/Curriculum_Development_Guide_2008.pdf
Appropriate Criteria: Key to Effective Rubrics Susan M. Brookhart, Department of Educational Foundations and Leadership, Duquesne University, Pittsburgh, PA, United States https://www.frontiersin.org/articles/10.3389/feduc.2018.00022/full
Using Rubrics To Promote Thinking and Learning, Heidi Goodrich Andrade https://www.semanticscholar.org/paper/Using-Rubrics-To-Promote-Thinking-and-Learning.-Andrade/8ea5836dc2c3b476d2fbc7eafc541a03f5b8060d
Further reading on rubrics https://facultyinnovate.utexas.edu/sites/default/files/build-rubric.pdf
Curriculum development and Instructional design
Khalil MK, Elkhider IA. Applying learning theories and instructional design models for effective instruction. Adv Physiol Educ. 2016 Jun;40(2):147-56. https://journals.physiology.org/doi/full/10.1152/advan.00138.2015
Wee Hong Woo: Applying ADDIE Model to Ideate Precision Medicine in a Polytechnic Biomedical Science Programme, Journal of Biomedical Education, vol. 2018, Article ID 4268517, 5 pages, 2018. https://doi.org/10.1155/2018/4268517
Tractenberg, Rochelle & Lindvall, Jessica & Attwood, Teresa & Via, Allegra. (2020). Guidelines for curriculum and course development in higher education and training https://osf.io/preprints/socarxiv/7qeht/
Via et al (2020) Course design: Considerations for trainers – a Professional Guide https://f1000research.com/documents/9-1377
McCartthy Nine quick tips for efficient bioinformatics curriculum development and training https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008007
https://www.shiftelearning.com/blog/top-instructional-design-models-explained
https://www.dashe.com/blog/instructional-design-models-comparing-addie-bloom-gagne-merrill
Instructional design https://www.umt.edu/umonline/services-and-support/instructional-design/default.php
Instructional Design in Blended Learning: Theoretical Foundations and Guidelines for Practice https://link.springer.com/chapter/10.1007/978-3-030-45781-5_6
Sweet LR, Palazzi DL. Application of Kern’s Six-step approach to curriculum development by global health residents. Educ Health [serial online] 2015 [cited 2021 May 11];28:138-41. Available from: https://www.educationforhealth.net/text.asp?2015/28/2/138/170124
Course Design Considerations for trainers; Learning experiences https://f1000research.com/documents/9-1377
A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R https://www.frontiersin.org/articles/10.3389/fmicb.2020.578600/full
Curriculum for Clinical Genetics Training
The Phoenix Rising: Emergent models of instructional design https://doi.org/10.1080/01587910600789514
Curriculum Development and Evaluation Guide https://appd.s3.amazonaws.com/docs/meetings/2013SpringPresentations/PCWS1Handout.pdf
Models of course design and steps for course development https://www.cpd.utoronto.ca/wp-content/uploads/2016/07/P02-Models-of-course-design-and-steps-for-course-development-1.pdf
Application of Kern’s Six-step approach to curriculum development by global health residents PMID: 26609014 DOI: 10.4103/1357-6283.170124
Course design https://f1000research.com/documents/9-1377
Mrunal Mahajan and and Manvender Kaur Sarjit Singh: Importance and Benefits of Learning Outcomes. IOSR Journal Of Humanities And Social Science (IOSR-JHSS) Volume 22, Issue 3, Ver. V (March. 2017) PP 65-67 http://www.iosrjournals.org/iosr-jhss/papers/Vol.%2022%20Issue3/Version-5/J2203056567.pdf
Kapur, Radhika. (2018), Formulation of Objectives in Curriculum Development https://www.researchgate.net/publication/323694981_Formulation_of_Objectives_in_Curriculum_Development
Krutchen, AE, A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R, Frontiers in Microbiology 2020;11 pp 2135 https://www.frontiersin.org/articles/10.3389/fmicb.2020.578600/full
Tractenberg, Rochelle & Lindvall, Jessica & Attwood, Teresa & Via, Allegra. (2020). Guidelines for curriculum and course development in higher education and training https://osf.io/preprints/socarxiv/7qeht/
Linderman, M.D., Sanderson, S.C., Bashir, A. et al, Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years, BMC Med Genomics 11, 5 (2018) https://doi.org/10.1186/s12920-018-0319-0
Weitzel KW, McDonough CW, Elsey AR, Burkley B, Cavallari LH, Johnson JA., Effects of Using Personal Genotype Data on Student Learning and Attitudes in a Pharmacogenomics Course https://www.ajpe.org/content/80/7/122) Am J Pharm Educ. 2016;80(7):122
Salari K, Karczewski KJ, Hudgins L, Ormond KE., Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine, PLoS One. 2013;8(7):e68853. Published 2013 Jul 23 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068853
Miller, G E The assessment of clinical skills/competence/performance, Academic Medicine: September 1990 – Volume 65 – Issue 9 – p S63-7
Cheung JJH, Kulasegaram KM, Woods NN, Moulton CA, Ringsted CV, Brydges R. Knowing how and knowing why: testing the effect of instruction designed for cognitive integration on procedural skills transfer. Adv Health Sci Educ Theory Pract. Brown S. Assessment for learning. Learn Teach Higher Educ 1: 81–89, 2005
Kulasegaram K, Rangachari PK., Beyond “formative”: assessments to enrich student learning](https://journals.physiology.org/doi/full/10.1152/advan.00122.2017) Adv Physiol Educ. 2018 Mar 1;42(1):5-14
Kibble JD. Best practices in summative assessment https://journals.physiology.org/doi/full/10.1152/advan.00116.2016) Adv Physiol Educ. 2017 Mar 1;41(1):110-119
Flexible Approaches for Teaching Computational Genomics in a Health Information Management Program: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709875/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709875/
Learning Theories
Adult learning theories: Implications for learning and teaching in medical education: AMEE Guide No. 83 https://doi.org/10.3109/0142159X.2013.828153
Needs Assessment for Informing Extension Professional Development Trainings on Teaching Adult Learners https://archives.joe.org/joe/2018june/a1.php
About learning types: Laurillard, D. (2012). Teaching as a Design Science: Building Pedagogical Paterns for Learning and Technology. New York and London: Routledge.Chapters 6-11
AMEE Guide No 20: The good teacher is more than a lecturer – the twelve roles of the teacher https://www.tandfonline.com/doi/pdf/10.1080/014215900409429?needAccess=true
How People learn https://www.nap.edu/catalog/9853/how-people-learn-brain-mind-experience-and-school-expanded-edition
Conversational framework https://mediacentral.ucl.ac.uk/Player/CG6hD928
M.S. Knowles, E.F. Holton III, R. A. Swanson, The Adult Learner, Routledge 2015
R. G. Brockett, R. Hiemstra, Self-direction in Adult Learning, Routledge 1991
Blooms taxonomy by Patricia Armstrong, Vanderbilt University Center for Teaching https://cft.vanderbilt.edu/guides-sub-pages/blooms-taxonomy/
Revised Bloom’s taxonomy https://www.uky.edu/~rsand1/china2018/texts/Anderson-Krathwohl%20-%20A%20taxonomy%20for%20learning%20teaching%20and%20assessing.pdf
Toolkits and training materials
A tailor-made toolkit for trainers and practitioners https://www.researchtoaction.org/2016/05/tailor-made-toolkit-trainers-practitioners/
Train the trainer: administering and facilitating effective training events https://www.inasp.org.uk/training/train-the-trainer/index.html
AuthorAID Training of Trainers Toolkit https://www.inasp.info/publications/authoraid-training-trainers-toolkit
Training materials for the online seminar on the Ensembl Genome browser https://training.ensembl.org/events/2020/2020-11-04-RoBioinfo
Examples of protocols used in training courses on Laboratory Methods for Genomics:
Protocol for DNA transport https://www.protocols.io/view/c-sop-901-preparation-of-dna-isolates-for-domestic-bqzdmx26
Protocols for Bacterial Genomic DNA isolation: https://www.protocols.io/view/c-sop-101-bacterial-genomic-dna-isolation-using-th-bq3ymypw
https://www.protocols.io/view/c-sop-202-genomic-dna-purity-measurement-using-a-n-bq2tmyen
https://www.protocols.io/view/c-sop-201-genomic-dna-quantification-using-a-qubit-bq2bmyan
Protocol for Bacterial DNA Library Construction for WGS: https://www.protocols.io/view/c-sop-301-dna-library-preparation-using-the-nebnex-bq4cmysw
Protocol for Bacterial DNA Library QC https://www.protocols.io/view/c-sop-401-quality-control-qc-of-dna-libraries-for-bq56my9e
Protocol for Normalisation & Pooling of Multiplexed Libraries for WGS https://www.protocols.io/view/c-sop-501-normalisation-and-pooling-of-dna-librari-bq7vmzn6
Protocol for Bacterial Whole Genome Sequencing (https://www.protocols.io/view/c-sop-601-operation-of-the-illumina-miseq-for-whol-bq5hmy36
Resources
WCS resources: https://coursesandconferences.wellcomeconnectingscience.org
EMBL-EBI support for trainers https://www.ebi.ac.uk/training/trainer-support
GOBLET https://www.mygoblet.org
Elixir https://elixir-europe.org
H3ABioNet resources: H3ABioNet website with useful information regarding training:https://www.h3abionet.org/
Relevant papers:
Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005715
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008640
H3ABioNet training guide/training support pack https://doi.org/10.25375/uct.14337806.v1
H3ABioNet training pages and resources https://www.h3abionet.org/training
Learning environments
Students’ reflections on the relationships between safe learning environments, learning challenge and positive experiences of learning in a simulated GP clinic Adv in Health Sci Educ (2016) 21:63–77 DOI 10.1007/s10459-015-9611-3
Characteristics of positive learning environment https://us.humankinetics.com/blogs/excerpt/characteristics-of-a-positive-learning-environment
Positive and negative learning experiences http://sheilaokane.weebly.com/uploads/2/6/1/8/26183300/positive_and_negative_learning_experiences_paper.pdf
A Personal Experience Of Positive And Negative Learning Strategies https://www.tutorhunt.com/resource/15730/
A positive learning experience https://www.etprofessional.com/media/2684/bress.pdf 36 Issue 103 March 2016 ENGLISH TEACHING professional www.etprofessional.com
Teaching strategies – 10 effective teaching strategies https://www.clickview.co.uk/teaching-strategies/
Benefits and Cons of using virtual labs – Why Are Virtual Labs Crucial for the “New Normal”? https://www.enago.com/academy/why-are-virtual-labs-crucial-for-the-new-normal/?utm_source=TrendMD&utm_medium=cpc&utm_campaign=Enago_Academy_TrendMD_1
The TPACK framework considers integration of technology into teaching https://en.wikipedia.org/wiki/Technological_pedagogical_content_knowledge
Evaluation
Metrics for Evaluating Effectiveness of Genomics Education and Training Programs https://www.genome.gov/Multimedia/Slides/IntlGenomicsEducation/JenkinsJ_metrics.pdf
Data Collection Approaches to Enable Evaluation of a Massive Open Online Course About Data Science for Continuing Education in Health Care: Case Study https://mededu.jmir.org/2019/1/e10982/ doi: 10.2196/10982
Massive Open Online Courses (MOOC) Evaluation Methods: Protocol for a Systematic Review https://www.researchprotocols.org/2019/3/e12087?utm_source=TrendMD&utm_medium=cpc&utm_campaign=JMIR_TrendMD_0 doi: 10.2196/12087
Evaluation of a TtT programme – Developing sustainable capacity-building in mental health research: implementation outcomes of training of trainers in systematic reviewing https://www.tandfonline.com/doi/full/10.1080/16549716.2020.1715325 https://doi.org/10.1080/16549716.2020.1715325
Talk about walkabout: evaluation of a flexible learning initiative https://www.worldscientific.com/doi/epdf/10.1142/9789812772725_0002
Evaluating Training Programs: The Four Levels Donald Kirkpatrick, James Kirkpatrick Berrett-Koehler Publishers, 1 Jan 2006
W.K. Kellogg Foundation Evaluation Handbook https://www.wkkf.org
Perryman, L., Ferguson, R., Weller, M., Sargent, J., Papathoma, T. and Rees, T. (2021): Online teaching: Evaluating and improving courses. Available at: /courses/online-teaching-evaluating-what-works/1/steps/966785
Likert scales https://www.sheffield.ac.uk/polopoly_fs/1.597637!/file/likertfactsheet.pdf
Tips for designing questionnaires https://psr.iq.harvard.edu/files/psr/files/PSRQuestionnaireTipSheet_0.pdf
Competencies
Competency frameworks:
ISCB V3 Bioinformatics Competency Framework https://competency.ebi.ac.uk/framework/iscb/3.0
The development and application of bioinformatics core competencies to improve bioinformatics training and education https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005772
Design of a Genomics Curriculum: Competencies for Practicing Pathologists https://www.researchgate.net/publication/279628889_Design_of_a_Genomics_Curriculum_Competencies_for_Practicing_Pathologists
NHS Report: Developing Clinical Bioinformatics Training in the NHS – a timeline for action, https://www.genomicseducation.hee.nhs.uk/wp-content/uploads/2019/06/Clinical_Bioinformatics_Training.pdf
The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225256
The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa https://www.frontiersin.org/articles/10.3389/fgene.2019.01209/full
Methods of Genomic Competency Integration in Practice https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413944/
Core competencies in genetics for healthcare professionals: results from a literature review and a Delphi method https://bmcmededuc.biomedcentral.com/articles/10.1186/s12909-019-1456-7
The development and application of bioinformatics core competencies to improve bioinformatics training and education https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005772
On teachers’ competency frameworks https://ec.europa.eu/assets/eac/education/experts-groups/2011-2013/teacher/teachercomp_en.pdf
Moving to virtual
Lessons learned when moving SIB Training courses from in-person to online – anything in bioinformatics can be taught online, but not anyhow https://f1000research.com/documents/9-1148
On learning in virtual environments (nice definitions of terms too) https://firstmonday.org/ojs/index.php/fm/article/view/3496/3133
Blog on learning technology https://altc.alt.ac.uk/blog/
Evaluating Learning Designer https://bera-journals.onlinelibrary.wiley.com/doi/full/10.1111/bjet.12697
OU guide to good practice for online collaboration https://www.open.ac.uk/blogs/learning-design/wp-content/uploads/2020/04/Collaborative-activities-booklet-V2.5.pdf
A case study for taking your short bioinformatics courses online: The Ensembl browser webinar series https://lifescitrainers.org/2020/06/02/a-case-study-for-taking-your-short-bioinformatics-courses-online-the-ensembl-browser-webinar-series/
Train the Trainer: Design Genomics and Bioinformatics Training

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