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/