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The Linux terminal for health researchers in a hurry
Find a file, read a dataset, and run a script on a Linux server. Eight short lessons for people who already have a login and need to get to the data.
8 lessons · about 45 minutes · Health researchers, data staff, and students who can log in to a server and have not used the terminal for real work.
- 1. The prompt
- 2. Video · Move around
- 3. Read a file
- 4. Video · Folders and copies
- 5. Find a file
- 6. Video · Permission denied
- 7. Keep the output
- 8. Video · Shared-server habits
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A tidy dataset a statistician can use
Hand over a table that can be analysed: one row per person, stable IDs, real dates, and missing values that mean missing.
5 lessons · about 44 minutes · Field teams, data clerks, and students who prepare spreadsheets for a study statistician.
- 1. One row, one person
- 2. Video · Names a program can read
- 3. Dates, zeros, and gaps
- 4. Video · The ID that must not change
- 5. The file you hand over
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What the IRB is looking for
Prepare an application the BRTI Institutional Review Board can review: consent a participant can follow, risks in plain language, and documents that match.
5 lessons · about 45 minutes · Fellows, interns, and investigators submitting a study to the BRTI Institutional Review Board.
- 1. What the board is for
- 2. Video · Consent someone can follow
- 3. Risks in plain language
- 4. Video · Why an application comes back
- 5. A difficult application
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A study day on a clinical trial
Orientation for a trial visit: the protocol for today, consent, source documents, deviations, and an adverse event. This is not an accredited Good Clinical Practice certificate.
5 lessons · about 44 minutes · New trial staff who need the rules of a study day before a formal Good Clinical Practice course.
- 1. The protocol for today
- 2. Video · Consent before the procedure
- 3. Where it was written first
- 4. Video · When the day leaves the script
- 5. An adverse event before the coordinator arrives
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Read the result before you report it
Viral load, GeneXpert, culture, and drug-sensitivity results: what the words mean, and what must not go on a report.
5 lessons · about 45 minutes · Laboratory staff, clinicians, and data officers who record or release HIV and TB results.
- 1. Whose result this is
- 2. Video · A viral load
- 3. A GeneXpert result
- 4. Video · Culture and drug sensitivity
- 5. The report you send
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A specimen that can still be found
Labels, aliquots, and freezer logs so a tube still matches the form months later.
5 lessons · about 44 minutes · Interns, laboratory staff, and research-support teams who handle study specimens.
- 1. The ID on the tube
- 2. Video · A label that still sticks
- 3. Aliquots
- 4. Video · The freezer log
- 5. A tube that does not match
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One table, one abstract
Turn a small results table into a 250-word abstract: who was studied, the number from the table, and the claim you will not make.
5 lessons · about 44 minutes · CREATE fellows, postgraduate students, and staff writing a conference abstract.
- 1. What the abstract is for
- 2. Video · Who was studied
- 3. The number in the sentence
- 4. Video · The claim you will not make
- 5. Two hundred and fifty words
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A sequencing file, explained
A short primer before a genomics workshop: what a FASTQ file is, what a quality score is saying, and when to stop and ask a bioinformatician.
5 lessons · about 44 minutes · Researchers and laboratory scientists preparing for sequencing work or the Advanced Genomics Technologies workshop.
- 1. What the machine hands you
- 2. Video · Four lines
- 3. The quality string
- 4. Video · Files that belong together
- 5. When to stop and ask
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The statistic you need before you call a statistician
Mean and median, what a confidence interval is saying, and why a p-value is not the result. Enough to ask a useful question.
5 lessons · about 45 minutes · Fellows and research staff who read a results table before they meet a statistician.
- 1. Mean and median
- 2. Video · A confidence interval
- 3. A p-value
- 4. Video · The comparison
- 5. A table that misleads
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Troubleshooting a computer when you are not in IT
What to try when a work computer will not start, freezes, loses the internet, or will not print, and when to stop and call for help.
5 lessons · about 44 minutes · Office, laboratory, and research staff who use a computer for work and are not the IT person.
- 1. What changed
- 2. Video · Power and the screen
- 3. A frozen program and a missing file
- 4. Video · Internet, email, and the printer
- 5. The note you send
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