Find below a wider list of references and resources used in the T3Connect course.

Use the drop-down list below to select a category: course design, curriculum, evaluation, data visualisation, competencies, Ethics, building institutional capacity.

The list can also be browsed using the Search bar on the right.

The training materials designed specifically for the T3Connect courses will be published on a GitHub repository soon.

WebsiteMicrobe – Measuring Infectious Causes and Resistance Outcomes for Burden EstimationInstitute for Health Metrics and Evaluation (IHME)data-visualisation
WebsiteOur World in DataOur World in Datadata-visualisation
WebsiteInteractive data visualsInstitute for Health Metrics and Evaluation (IHME)data-visualisation
WebsiteShipMapUCL Energy Institutedata-visualisation
BookFundamentals of Data VisualizationClaus O. Wilkedata-visualisation
WebsiteVisualising DataAndy Kirkdata-visualisation
ArticleWHO Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance.WHOMycobacterium tuberculosisgenomic-epidemiology
ReportWHO report on The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guideWHOMycobacterium tuberculosisgenomic-epidemiology
GuidanceUS CDC Guide to the Application of Genotyping to Tuberculosis Prevention and ControlCDCMycobacterium tuberculosisgenomic-epidemiology
GuidanceUKHSA guidance on Mycobacterium tuberculosis whole-genome sequencing and cluster investigation handbookUKHSAMycobacterium tuberculosisgenomic-epidemiology
ReportPHE Expert opinion on whole genome sequencing for public health surveillancePHG FoundationAMR; surveillance; whole genome sequencing; WGSgenomic-epidemiology
ReportPHG foundation report Pathogen Genomics Into PracticePHG FoundationAMR; surveillance; whole genome sequencing; WGSgenomic-epidemiology
ReportFIND report on Sequencing for antimicrobial resistance surveillancePHG Foundation for FINDAMR; surveillancegenomic-epidemiology
ProtocolUse of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United StatesFDAAMR; whole genome sequencing; WGSgenomic-epidemiology
ReportGLASS 2020 report on Whole-genome sequencing for surveillance of antimicrobial resistanceWHOwhole genome sequencing; WGSgenomic-epidemiology
ProtocolISO on Microbiology of the food chain — Whole genome sequencing for typing and genomic characterization of bacteria — General requirements and guidanceISOwhole genome sequencing; WGSgenomic-epidemiology
ProtocolThe use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guideWHOAMR; whole genome sequencing; WGSgenomic-epidemiology
General presentationGlobal Microbial IdentifierGMI - Global Microbial Identifiergenomic-epidemiology
ArticleWhole Genome Sequencing Reveals Potential Spread of Clostridium Difficile between Humans and Farm Animals in the Netherlands; 2002 to 2011.Knetsch; C. W.; et al.whole genome sequencing; WGSgenomic-epidemiology
ArticleTowards a global antibiotic resistance surveillance system: A primer for a roadmap.Grundmann; H. (2014).AMRgenomic-epidemiology
ArticleMicroreact: Visualizing and sharing data for genomic epidemiology and phylogeography.Argimón; S.; Abudahab; K.; Goater; R. J. E.; Fedosejev; A.; Bhai; J.; Glasner; C.; Feil; E. J.; Holden; M. T. G.; Yeats; C. A.; Grundmann; H.; Spratt; B. G.; & Aanensen; D. M.microreact; data visualisationgenomic-epidemiology
ArticleLong read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over six years.Roberts; L.; Enoch; D. A.; Khokhar; F.; Blackwell; G. A.; Wilson; H.; Warne; B.; Gouliouris; T.; Iqbal; Z.; & Torok; M. E.plasmidgenomic-epidemiology
ProtocolTransport and storage of samples: Best Practice Guideline for Primary CareNHS Oxford University; collectiongenomic-epidemiology
ArticleInternational Charter of principles for sharing bio-specimens and data.Mascalzoni; D.; Dove; E. S.; Rubinstein; Y.; Dawkins; H. J. S.; Kole; A.; McCormack; P.; Woods; S.; Riess; O.; Schaefer; F.; Lochmüller; H.; Knoppers; B. M.; & Hansson; Mspecimen collection; sample handlinggenomic-epidemiology
ArticleThe use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak.Lalor; M. K.; Casali; N.; Walker; T. M.; Anderson; L. F.; Davidson; J. A.; Ratna; N.; Mullarkey; C.; Gent; M.; Foster; K.; Brown; T.; Magee; J.; Barrett; A.; Crook; D. W.; Drobniewski; F.; Thomas; H. L.; & Abubakar; I. (2018).whole genome sequencing; WGSgenomic-epidemiology
ArticleFundamental principle of clinical specimen collection.Kumar; V.specimen collection; sample handlinggenomic-epidemiology
ProtocolICH E18 Guideline on genomic sampling and management of data.European Medicines Agencygenomic samplinggenomic-epidemiology
ProtocolCommunity Infection Prevention and Control Policy for Care Home settings.Harrogate and District NHS Foundation Trust.genomic-epidemiology
ProtocolCollection and presevation.WHOsample handlinggenomic-epidemiology
ArticleMycobacterium tuberculosis transmission in Birmingham; UK; 2009–19: An observational studyTimothy M. Walker; Marc Choisy; Martin Dedicoat; Philip G. Drennan; David Wyllie; Fan Yang-Turner; Derrick W. Crook; Esther R. Robinson; A. Sarah Walker; E. Grace Smith; Timothy E.A. PetoMycobacterium tuberculosis; sample handlinggenomic-epidemiology
ArticleLuheshi; L. R.; Sobia; Moorthie; Sowmiya. (2015). Pathogen Genomics Into Practice. PHG Foundation.Leila Luheshi; Sobia Raza; Sowmiya Moorthie; Alison Hall; Laura Blackburn; Chris Rands; Gurdeep Sagoo; Susmita Chowdhury; Mark Kroese and Hilary Burtonpathogen-genomics-into-practice
ArticleImplementing pathogen genomics: A case study. (n.d.). GOV.UK.Kathie Grant; Claire Jenkins; Cath Arnold; Jonathan Green; Maria Zambonpublic-health
ArticleTen recommendations for supporting open pathogen genomic analysis in public healthAllison Blackpublic-health
ArticleEthical challenges in pathogen sequencing: a systematic scoping reviewStephanie Johnsonethics-legal-social-challenges-of-pathogen-genomics
ArticleEthical Challenges Associated with Pathogen and Host Genetics in Infectious DiseaseRichard Milneethics-legal-social-challenges-of-pathogen-genomics
ArticleThe ethics of sequencing infectious disease pathogens for clinical and public healthStephanie B. Johnsonethics-legal-social-challenges-of-pathogen-genomics
Blog articleA case study for taking your short bioinformatics courses online: The Ensembl browser webinar seriesBen Mooremoving-to-virtual
Blog articleOU guide to good practice for online collaborationThe Open Universitymoving-to-virtual
ArticleEvaluating Learning DesignerDiana Laurillardmoving-to-virtual
Blog articleBlog on learning technologyALTmoving-to-virtual
ArticleLessons learned when moving SIB Training courses from in-person to online – anything in bioinformatics can be taught online; but not anyhowPatricia M. Palagimoving-to-virtual
ArticleCore competencies in genetics for healthcare professionals: results from a literature review and a Delphi methodAlessia Tognettocompetencies
ArticleMethods of Genomic Competency Integration in PracticeJean Jenkinscompetencies
ArticleThe African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in AfricaAGMTcompetencies
ArticleThe Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and trainingRochelle E. Tractenbergrubrics
ReportNHS Report: Developing Clinical Bioinformatics Training in the NHS – a timeline for action;NHScompetencies
ArticleDesign of a Genomics Curriculum: Competencies for Practicing PathologistsJennifer Laudadiocompetencies
ArticleThe development and application of bioinformatics core competencies to improve bioinformatics training and educationNicola Muldercompetencies
WebsiteISCB V3 Bioinformatics Competency FrameworkISCBcompetencies
MOOCOnline teaching: Evaluating and improving courses.Perryman; L.; Ferguson; R.; Weller; M.; Sargent; J.; Papathoma; T. and Rees; T.evaluation
HandbookW.K. Kellogg Foundation Evaluation HandbookKellogg Foundationevaluation
BookEvaluating Training Programs: The Four LevelsDonald Kirkpatrick; James Kirkpatrick Berrett-Koehlerevaluation
ArticleTalk about walkabout: evaluation of a flexible learning initiativeevaluation
ArticleEvaluation of a TtT programme – Developing sustainable capacity-building in mental health research: implementation outcomes of training of trainers in systematic reviewingevaluation
ProtocolMassive Open Online Courses (MOOC) Evaluation Methods: Protocol for a Systematic Reviewevaluation
ArticleData Collection Approaches to Enable Evaluation of a Massive Open Online Course About Data Science for Continuing Education in Health Care: Case Studyevaluation
WebsiteMetrics for Evaluating Effectiveness of Genomics Education and Training Programsevaluation
WebsiteBenefits and Cons of using virtual labs – Why Are Virtual Labs Crucial for the New Normal?teaching-strategies
WebsiteTeaching strategies – 10 effective teaching strategiesteaching-strategies
WebsiteA positive learning experiencelearning-environments
WebsiteA Personal Experience Of Positive And Negative Learning Strategieslearning-environments
ArticlePositive and negative learning experienceslearning-environments
Blog articleCharacteristics of positive learning environmentlearning-environments
ArticleStudents’ reflections on the relationships between safe learning environments; learning challenge and positive experiences of learning in a simulated GP cliniclearning-environments
Resources websiteH3ABioNet training pages and resourcesH3ABioNetcourse-design
GuidelineH3ABioNet training guide/training support packH3ABioNetcourse-design
ArticleUsing a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in AfricaVerena Rascourse-design
ArticleDesigning a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experienceH3ABioNetcourse-design
ProtocolProtocol for Bacterial Whole Genome SequencingThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolProtocol for Normalisation & Pooling of Multiplexed Libraries for WGSThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolProtocol for Bacterial DNA Library QCThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolProtocol for Bacterial DNA Library Construction for WGS:The Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolGenomic DNA Quantification using a Qubit FluorometerThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolGenomic DNA Purity Measurement using a Nanodrop SpectrophotometerThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolProtocols for Bacterial Genomic DNA isolationThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
ProtocolProtocol for DNA transportThe Centre for Genomic Pathogen Surveillance; Oxford; United Kingdomexamples-of-protocols-used-in-training-courses-on-laboratory-methods-for-genomics
Training materialsTraining materials for the online seminar on the Ensembl Genome browserEMBL-EBItraining-materials
WebsiteAuthorAID Training of Trainers ToolkitINASPtoolkits-and-training-materials
WebsiteTrain the trainer: administering and facilitating effective training eventsINASPtoolkits-and-training-materials
WebsiteA tailor-made toolkit for trainers and practitionersINASPtoolkits-and-training-materials
BookRevised Bloom’s taxonomyL. W. Anderson and David R. Krathwohllearning-theories
BookBlooms taxonomyPatricia Armstrong; Vanderbilt University Center for Teachinglearning-theories
WebinarConversational frameworkDiana Laurillardlearning-theories
BookHow People learnlearning-theories
ArticleAMEE Guide No 20: The good teacher is more than a lecturer – the twelve roles of the teacherR.M. Harden; Joy Crosbylearning-theories
ArticleNeeds Assessment for Informing Extension Professional Development Trainings on Teaching Adult LearnersNathan W. Connerlearning-theories
ArticleAdult learning theories: Implications for learning and teaching in medical education:David C. M. Taylorlearning-theories
ArticleBest practices in summative assessmentKibble JDassessment
ArticleBeyond formative: assessments to enrich student learningKulamakan Kulasegaram; Patangi K. Rangachariassessment
ArticleImpacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course yearsMichael D. Linderman; Saskia C. Sanderson; Ali Bashir; George A. Diaz; Andrew Kasarskis; Randi Zinberg; Milind Mahajan; Sabrina A. Suckiel; Micol Zweig & Eric E. Schadtcourse-design
ArticleA Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using RAnne E. KruchtenMetagenomics; R; undergraduatescourse-design
ArticleApplication of Kern’s Six-step approach to curriculum development by global health residentsLeigh R Sweet; Debra L Palazzicurriculum-development-and-instructional-design
University resourceModels of course design and steps for course developmentUniversity of Torontocurriculum-development-and-instructional-design
ArticleThe Phoenix Rising: Emergent models of instructional designSonja Irlbeckcurriculum-development-and-instructional-design
ArticleA Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using RAnne E. Kruchtencurriculum-development-and-instructional-design
ArticleApplication of Kern’s Six-step approach to curriculum development by global health residents.Leigh R Sweet; Debra L Palazzicurriculum-development-and-instructional-design
ArticleInstructional Design in Blended Learning: Theoretical Foundations and Guidelines for PracticeJesús Valverde-Berrocoso; María Rosa Fernández-Sánchezcurriculum-development-and-instructional-design
WebsiteInstructional Design Models: Comparing ADDIE; Bloom; Gagne; & Merrillcurriculum-development-and-instructional-design
Blog articleA Quick Guide to Four Instructional Design Modelscurriculum-development-and-instructional-design
ArticleNine quick tips for efficient bioinformatics curriculum development and trainingSusan McClatchy; Kristin M. Bass; Daniel M. Gatti; Adam Moylan; Gary Churchillcurriculum-development-and-instructional-design
ArticleCourse design: Considerations for trainers – a Professional GuideAllegra Via; Patricia M. Palagi; Jessica M. Lindvall; Rochelle E. Tractenberg; Teresa K. Attwood; The GOBLET Foundationcurriculum-development-and-instructional-design
ArticleGuidelines for curriculum and course development in higher education and trainingRochelle E. Tractenberg; Jessica M. Lindvall; Teresa Attwood; Allegra Viacurriculum-development-and-instructional-design
ArticleApplying ADDIE Model to Ideate Precision Medicine in a Polytechnic Biomedical Science ProgrammeWee Hong Woocurriculum-development-and-instructional-design
ArticleApplying learning theories and instructional design models for effective instructionKhalil MK; Elkhider IAcurriculum-development-and-instructional-design
University resourceWhat is a rubricThe University of Texas at Austinrubric definitionrubrics
ArticleUsing Rubrics To Promote Thinking and LearningHeidi Goodrich Andradeinstruction; assessmentrubrics
ArticleAppropriate Criteria: Key to Effective Rubrics Susan M. Brookhart; Department of Educational Foundations and Leadership; Duquesne University; Pittsburgh; PA; United StatesSusan M. Brookhartrating-scale language versus qualityrubrics
ArticleA Mastery Rubric: guiding curriculum design; admissions and development of course objectivesRochelle E. Tractenberg; Jason G. Umans; Robert J. McCarterphysicians; clinical research; reflection; cognitive self-monitoringrubrics
ArticlePeer Feedback Marking: Developing Peer AssessmentNancy Falchikovpeer assessment; critical feedback; Peer Feedback Markingpeer-review
ArticleRethinking feedback practices in higher education: a peer review perspective.David Nicola; Avril Thomson & Caroline Breslinfeedback reviews; higher educationpeer-review
Course pageEMBL-EBI Train the TrainerEMBL-EBITrain-the-trainerbuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
Course pageTeaching approaches used in Train the Trainer: Capacity building for genomic surveillance of AMR in low- and middle-income countries courseWellcome Connecting ScienceTrain-the-trainer; MOOC; FutureLearnbuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
ArticleFrom trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics trainingAnnette McGrath; Katherine Champ; Catherine A. Shang; Ellen van Dam ;Cath Brooksbank; Sarah L. MorganTrain-the-trainer; bioinformatics; Australiabuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
ArticleTrain-the-trainer as an effective approach to building global networks of experts in genomic surveillance of AMRMonica Abrudan; Alice Matimba; Dusanka Nikolic; Darren Hughes; Silvia Argimón; Mihir Kekre; Anthony Underwood; David M AanensenTrain-the-trainer; LMICS; antimicrobial resistancebuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
Promo videoVideo presenting the TtTWellcome Connecting ScienceTrain-the-trainer; LMICS; antimicrobial resistancebuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
Course announcementTtT course page: Train the Trainer: Capacity building for genomic surveillance of AMR in low- and middle-income countriesWellcome Connecting ScienceTrain-the-trainer; LMICS; antimicrobial resistancebuilding-institutional-and-regional-capacity-in-genomics-through-train-the-trainer-programmes
Blog articleBuilding Machine Learning Models for Predicting Antibiotic ResistanceNicole Wheelermachine learningteaching-strategies-and-curriculum-implementation
ArticleThe FAIR Guiding Principles for scientific data management and stewardshipMark D. Wilkinson; Barend Monsfindable; reusable; exemplar implementationsteaching-strategies-and-curriculum-implementation
ArticleFAIR training materialsLeyla Garcia; Patricia M. Palagishare; description; identity; registration; Interoperability; Reusabilityteaching-strategies-and-curriculum-implementation
WebsiteUniversal Design for Learning principlesCenter for Applied Special Technology (CAST)Engagement; Representation; Action; Expressionteaching-strategies-and-curriculum-implementation
ArticleDeveloping a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot actionAleksandra Pawlik; Celia W.G. van Gelder; Aleksandra Nenadic ; Patricia M. Palagi; Eija Korpelainen; Philip Lijnzaad; Diana Marek; Susanna-Assunta Sansone; John Hancock; Carole GobleLife sciences; bioinformatics; training; IT and computational skills; data analysis; capacity building; software carpentry; data carpentryteaching-strategies-and-curriculum-implementation
ArticleThe African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in AfricaVictoria Nembaware; Nicola Mulderhealthcare professionals; blended learningteaching-strategies-and-curriculum-implementation
ArticleOncoSim and OncoWiki: an authentic learning approach to teaching cancer genomicsPriska Schoenborn; Richard Osborne; Nick Toms; Karen Johnstone; Chlöe Milsom; Reema Muneer; Michael A. Jarvis; Robert Belshawcancer genomics; case study; precision oncologyteaching-strategies-and-curriculum-implementation
ArticleThe application of project-based learning in bioinformatics trainingLaura R. Emery; Sarah L. Morganproject-based learning; bioinformatics summer schoolteaching-strategies-and-curriculum-implementation
ArticleApplying service design in competency‐based curriculum developmentJon Scoresby; Mary Tkatchov; Erin Hugus; Haley Marshallcompetency-based educationteaching-strategies-and-curriculum-implementation
ArticleIntegrating PCR Theory and Bioinformatics into a Research-oriented Primer Design ExerciseAmber L. Robertson; Allison R. PhillipsDNA primers; PCR; Pseudomonas putidateaching-strategies-and-curriculum-implementation
ArticleEstablishing a computational biology flipped classroomPhillip Compeauflipped classroom teaching-strategies-and-curriculum-implementation
ArticleProblem-based learning in clinical bioinformatics education: Does it help to create communities of practice?Angela C. Davies; Diane Harris; Amanda Banks-Gatenby; Andy Brassmedicine; group-centred problem-based learning; case studiesteaching-strategies-and-curriculum-implementation
ArticleDesigning and running an advanced Bioinformatics and genome analyses course in TunisiaFatma Z. Guerfali;Dhafer Laouini;Abdellatif Boudabous;Fredj TekaiaBioinformatics; Genome Analysesteaching-strategies-and-curriculum-implementation
ArticleOn the Job Learning: A Bioinformatics Course Incorporating Undergraduates in Actual Research Projects and Manuscript SubmissionsJason T. Smith; Justine C. Harris; Oscar J. Lopez; Laura Valverde; Glen M. Borchertcollaborative research; computational geneticsteaching-strategies-and-curriculum-implementation
ArticlePreparing the next generation of genomicists: a laboratory-style course in medical genomicsMichael D. Linderman; Ali Bashir; George A. Diaz; Andrew Kasarskis; Saskia C. Sanderson; Randi E. Zinberg; Milind Mahajan; Hardik Shah; Sabrina Suckiel; Micol Zweig & Eric E. Schadtpersonal genome sequencingteaching-strategies-and-curriculum-implementation
ArticleEvaluating the effectiveness of a practical inquiry‐based learning bioinformatics module on undergraduate student engagement and applied skillsJames A. L. BrownBioinformatics; Qualitative assessment; peer-assisted learningteaching-strategies-and-curriculum-implementation
Blog articleActive learning strategies for Bioinformatics teachingLex NederbragtLive coding; Jupyter notebook; peer learning; carpentriesteaching-strategies-and-curriculum-implementation
ArticleAn educational guide for nanopore sequencing in the classroomAlex N. Salazar; Franklin L. Nobrega ;Christine Anyansi;Cristian Aparicio-Maldonado; Ana Rita Costa; Anna C. Haagsma; Anwar Hiralal; Ahmed Mahfouz; Rebecca E. McKenzie;Teunke van Rossum; Stan J. J. Brouns; Thomas AbeelOxford Nanopore Technologies; sequencing; bacteria; bacteriophage; genometeaching-strategies-and-curriculum-implementation
Course descriptionElective 8-week course on genomics and personalized medicine; Genetics 210Stanford Universitygenetic variants; disease susceptibility; risk factors; complex genetic disorders; pharmacogenetics; population structure; genetic ancestry; ethics; clinical medicineteaching-strategies-and-curriculum-implementation
ArticleEvidence That Personal Genome Testing Enhances Student Learning in a Course on Genomics and Personalized MedicineKeyan Salari; Konrad J. Karczewski; Louanne Hudgins; Kelly E. Ormondhands-on genomics; clinical genomic testingteaching-strategies-and-curriculum-implementation
ArticleStrategies for using peer-assisted learning effectively in an undergraduate bioinformatics courseCasey Shapiro; Carlos Ayon; Jordan Moberg-Parker; Marc Levis-Fitzgerald; Erin R Sanderspeer learning; tutorial training; genome annotation; bioinformaticsteaching-strategies-and-curriculum-implementation
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