Resource	Who publishes it	Why read it
★ PubMed User Guide and PubMed online training (Help pages), pubmed.ncbi.nlm.nih.gov	US National Library of Medicine	How to build a search with MeSH, Boolean operators and filters. It repeats the live demo at your own pace.
MeSH Browser, meshb.nlm.nih.gov	US National Library of Medicine	Find the official MeSH term for your topic and see its narrower and broader terms.
Cochrane Handbook for Systematic Reviews of Interventions, Chapters 1–4 (starting a review; scope and questions; eligibility criteria; searching for studies), training.cochrane.org/handbook	Cochrane	The gold standard on turning a question into PICO and searching systematically. Read the “Key points” box at the start of each chapter.
Oxford CEBM Levels of Evidence, cebm.ox.ac.uk	Centre for Evidence-Based Medicine, University of Oxford	A one-page table of which study type answers which kind of question best.
“How to read a paper” series, BMJ 1997 (first article: “Getting your bearings”)	T. Greenhalgh, BMJ	Classic short articles on reading research critically. The first ones help with framing questions.
Designing Clinical Research, chapters on the research question (not free; check your library)	S.B. Hulley and colleagues	The book that introduced the FINER criteria.
Zotero (free reference manager), zotero.org	Corporation for Digital Scholarship (open source)	Store references, insert citations and switch to Vancouver style with one click. Its documentation has short start-up guides.
“Misrepresentation and distortion of research in biomedical literature”, PNAS 2018;115(11):2613–2619 (open access)	I. Boutron and P. Ravaud	What spin is, how common it is, and how to spot it in abstracts.
“Reporting and interpretation of randomized controlled trials with statistically nonsignificant results for primary outcomes”, JAMA 2010;303(20):2058–2064	I. Boutron and colleagues	The classic study of spin in trial reports, and useful background for segment 1.4.
SQUIRE 2.0 guidelines (Standards for QUality Improvement Reporting Excellence), squire-statement.org	SQUIRE group (via EQUATOR)	How quality-improvement work is reported; it helps separate QI from research and audit.

Weeks 3–4 (Sessions 3–4): Design, bias and measures of effect

Resource	Who publishes it	Why read it
★ *Epidemiology for the Uninitiated* (online book)	D. Coggon, G. Rose, D.J.P. Barker, BMJ	Short, plain-language chapters on measuring disease, comparing rates, case-control and cohort studies.
Catalogue of Bias, catalogofbias.org	Centre for Evidence-Based Medicine, University of Oxford	One page per type of bias, each with a clinical example and how to prevent it. Look up “confounding by indication” and “recall bias”.
*Statistics at Square One*, chapter on study design and choosing a statistical test (online book)	T.D.V. Swinscow and M.J. Campbell, BMJ	Links study design to the analysis that follows.
CEBM study design pages, cebm.ox.ac.uk	Centre for Evidence-Based Medicine, University of Oxford	Brief descriptions and a flow chart for identifying study designs (useful for “Name that design”).
“The environment and disease: association or causation?”, Proceedings of the Royal Society of Medicine 1965;58:295–300 (free online)	A. Bradford Hill	The original nine “viewpoints” for judging causation. Short and very readable.
CONSORT extensions for cluster, non-inferiority and crossover trials (via equator-network.org)	CONSORT group	What is different about reporting these trial variants.
Risk-of-bias tools: RoB 2 and ROBINS-I, riskofbias.info	Developers of the Cochrane risk-of-bias tools	The official tools, guidance documents and templates for randomised (RoB 2) and non-randomised (ROBINS-I) studies of interventions.
QUADAS-2 (diagnostic accuracy studies), University of Bristol, Annals of Internal Medicine 2011;155:529–536	P. Whiting and colleagues	The standard tool for appraising diagnostic accuracy studies.
AMSTAR 2 (systematic reviews), amstar.ca; BMJ 2017;358:j4008	B. Shea and colleagues	A 16-item tool for judging how far a systematic review can be trusted.
Newcastle–Ottawa Scale (cohort and case-control studies), Ottawa Hospital Research Institute website	G. Wells and colleagues	A short star-based checklist widely used in systematic reviews of observational studies.
PRISMA 2020 statement, checklist and flow diagram, prisma-statement.org	PRISMA group	How systematic reviews are reported; Use the flow-diagram template when reading a review.
STARD 2015 (diagnostic accuracy studies), via equator-network.org	STARD group	What a diagnostic accuracy paper must report (sensitivity, specificity, flow of participants).
Cochrane Handbook, chapter on undertaking meta-analyses (forest plots, heterogeneity, I²), training.cochrane.org/handbook	Cochrane	Plain explanation of pooled estimates and heterogeneity. Read the key-points box.

Weeks 5–6 (Sessions 5–6): Data and analysis (with the FLUID-ICU course dataset)

Resource	Who publishes it	Why read it
★ *Statistics at Square One* (online book), chapters on data display and summary, confidence intervals, t-tests and the chi-squared test	T.D.V. Swinscow and M.J. Campbell, BMJ	The clearest free introduction to the statistics in this course, with medical examples.
Statistics Notes series, BMJ (1994 onwards)	J.M. Bland and D.G. Altman	One-page notes on single ideas; start with “Absence of evidence is not evidence of absence” (BMJ 1995).
“Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations”, European Journal of Epidemiology 2016;31:337–350 (open access)	S. Greenland, S.J. Senn, K.J. Rothman and colleagues	A list of common misreadings of p-values and CIs, and the source behind “5 common misinterpretations”. Read the numbered list and skip the technical parts.
“The ASA statement on p-values: context, process, and purpose”, The American Statistician 2016;70:129–133 (open access)	R.L. Wasserstein and N.A. Lazar, American Statistical Association	Six short principles on what a p-value can and cannot tell you.
OpenEpi, openepi.com	Open-source project (Emory University and partners)	Free online calculators for 2×2 tables and sample size, the kind of tool used in the live demo.
REDCap, project-redcap.org; KoBoToolbox, kobotoolbox.org	Vanderbilt University (REDCap consortium); KoBoToolbox (non-profit)	Free electronic data capture tools with validation and audit trails. REDCap is free for non-profit institutions that join the consortium.
“Beyond bar and line graphs: time for a new data presentation paradigm”, PLoS Biology 2015;13(4):e1002128 (open access)	T.L. Weissgerber and colleagues	Why “dynamite plots” hide data and what to use instead.
Statistics Notes: “Multiple significance tests: the Bonferroni method” (BMJ 1995;310:170) and “Survival probabilities (the Kaplan-Meier method)” (BMJ 1998;317:1572)	J.M. Bland and D.G. Altman	One-page explanations of multiple comparisons and Kaplan–Meier curves.
“Multiple imputation for missing data in epidemiological and clinical research: potential and pitfalls”, BMJ 2009;338:b2393	J.A.C. Sterne and colleagues	MCAR, MAR and MNAR, complete-case analysis and multiple imputation, with reporting advice.
“Guidelines for the content of statistical analysis plans in clinical trials”, JAMA 2017;318(23):2337–2343	C. Gamble and colleagues	What a statistical analysis plan (SAP) should contain. Use it as a checklist alongside the SAP template.
TRIPOD+AI statement, BMJ 2024;385:e078378, tripod-statement.org	G.S. Collins and colleagues	How prediction models, including machine-learning models, should be reported. It also works as a checklist for judging them.
“Calculating the sample size required for developing a clinical prediction model”, BMJ 2020;368:m441	R.D. Riley and colleagues	Why overfitting happens and why “10 events per variable” is only a rough guide.
*Clinical Data Analysis in R* (free online course)	Neudata	Learn to clean, describe and analyse a clinical dataset yourself. It is the prerequisite for reproducing the FLUID-ICU analyses with the course R scripts, and the entry requirement for Level 2 (hands-on analysis).

Weeks 7–8 (Sessions 7–8): Protect, write and publish (with your own manuscript and the individual peer review)

Ethics and good practice

Resource	Who publishes it	Why read it
★ Declaration of Helsinki (2024 revision), wma.net	World Medical Association	The core ethical principles for research involving people, short enough to read in 20 minutes.
ICH E6(R3) Guideline for Good Clinical Practice (2025), ich.org	International Council for Harmonisation	The international GCP standard. Read the “Principles of ICH GCP” section first.
International Ethical Guidelines for Health-related Research Involving Humans (2016), cioms.ch	Council for International Organizations of Medical Sciences (CIOMS) with WHO	Detailed guidance, including research with people who cannot consent and research in emergencies.
Free GCP e-learning, globalhealthtrainingcentre.tghn.org	The Global Health Network	Free online Good Clinical Practice courses. Check which version of ICH E6 a course covers.
ClinicalTrials.gov, clinicaltrials.gov; WHO International Clinical Trials Registry Platform (ICTRP), who.int/clinical-trials-registry-platform	US National Library of Medicine; World Health Organization	Where trials are registered and searched. ICTRP links the WHO-recognised primary registries.
PROSPERO, crd.york.ac.uk/prospero	Centre for Reviews and Dissemination, University of York	International register for systematic review protocols.
SPIRIT 2025 statement (trial protocols), via equator-network.org	SPIRIT group	Checklist of what a trial protocol must contain. Use it with the protocol template.

Integrity, authorship and AI

Resource	Who publishes it	Why read it
★ Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals, icmje.org	International Committee of Medical Journal Editors (ICMJE)	The four authorship criteria, conflicts of interest and the current position on AI-assisted work. Read “Defining the Role of Authors and Contributors”.
COPE guidance, flowcharts and position statement “Authorship and AI tools”, publicationethics.org	Committee on Publication Ethics (COPE)	What to do about plagiarism, duplicate publication or authorship disputes, step by step.
CRediT (Contributor Role Taxonomy), credit.niso.org	NISO (National Information Standards Organization)	The 14 contributor roles to use in your publication plan and author statement.
ORCID, orcid.org	ORCID (non-profit)	Get a free researcher identifier before your first submission.
ICMJE disclosure form (conflicts of interest), icmje.org	ICMJE	The standard form most journals use for declaring competing interests.

Reporting, publishing and appraisal

Resource	Who publishes it	Why read it
★ EQUATOR Network, equator-network.org	EQUATOR Network	The library of reporting guidelines. Use its “Toolkits” and the guideline finder to pick the right checklist.
CONSORT 2025 statement and checklist (randomised trials)	CONSORT group (via EQUATOR)	What a trial report must contain. Used to appraise Paper 1.
STROBE statement and checklists (cohort, case-control, cross-sectional), strobe-statement.org	STROBE initiative	What an observational study report must contain. Used to appraise Paper 2.
SPIRIT 2025 (trial protocols), STARD 2015 (diagnostic accuracy), PRISMA 2020 (systematic reviews), prisma-statement.org	Respective groups (via EQUATOR)	The other guidelines named in the course. Open only the one that fits your design.
Think. Check. Submit., thinkchecksubmit.org	Cross-industry initiative of publishers and library organisations	A short checklist to decide whether a journal is trustworthy before you submit.
Directory of Open Access Journals (DOAJ), doaj.org	DOAJ	Check whether an open-access journal is listed and what it charges.
CASP checklists, casp-uk.net	Critical Appraisal Skills Programme	Free one-page appraisal checklists for each design, and a natural next step after the course’s 10-question checklist.
ICMJE Recommendations, section “Manuscript Preparation and Submission”, icmje.org	ICMJE	What goes in each part of a manuscript (title page, abstract, IMRaD sections, references) and in the submission package.
EQUATOR Network toolkits (“Writing research”, “Using reporting guidelines”), equator-network.org	EQUATOR Network	Practical guidance on writing each section and on using checklists at submission.
AuthorAID, authoraid.info	INASP	Free online courses and mentoring in research writing and publishing for researchers in low- and middle-income countries.
medRxiv, medrxiv.org	Cold Spring Harbor Laboratory, BMJ and Yale University	The main preprint server for health research. Check your target journal’s preprint policy first.
COPE “Ethical guidelines for peer reviewers”, publicationethics.org	Committee on Publication Ethics	What reviewers are expected to do. Useful when writing a response to reviewers and for the “Be the reviewer” exercise.

Going further: Level 2 (hands-on) and Level 3 (advanced)

This course is Level 1. The next steps are described in Course_Levels/.

Level 2: Doing the analysis (hands-on R). The free Neudata course Clinical Data Analysis in R is the entry requirement. Statistics at Square One (regression and survival chapters) supports the modelling sessions (linear, logistic, count and Cox models), the Sterne BMJ 2009 paper on multiple imputation supports the missing-data basics in Session 1, and the EQUATOR toolkits support the final Results section.
Level 3: Advanced topics. For reproducible research, version control and journal-ready figures, see the Level 3 outline (Module G). For meta-analysis, the Cochrane Handbook and PRISMA 2020. For prediction models and ML, TRIPOD+AI and the Riley BMJ 2020 sample-size paper. For diagnostic accuracy, STARD 2015 and QUADAS-2. For advanced survival analysis, Statistics at Square One and the Bland–Altman Statistics Notes on survival. For clustered and multicentre data, the CONSORT extension for cluster trials.

All resources were selected for being free, stable and from recognised organisations. Versions change (e.g. CONSORT, ICMJE): always use the current version on the publisher’s site.

Further reading

Foundations of Clinical Research · Level 1: From Clinical Question to Publication

Weeks 1–2 (Sessions 1–2): Ask, find and read