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Programming formalisms for life scientists and bioinformaticians

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Main page: https://github.com/UPPMAX/programming_formalisms Rendered page: https://uppmax.github.io/programming_formalisms/

Zoom meetings will be called when needed most issues shall be resolved through github issues if meeting is requested i will be posted in the slack chanell and the below meeting id will be used

https://uu-se.zoom.us/j/63272190301 (Passcode: 880630)

Course certificates

Course certificates fall 2023

Certificates

Text for course certificate use https://rshiny.nbis.se/shiny-server-apps/shiny-certificate/ to create certificate change the dates in brackets

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has participated in the NBIS workshop Programming Formalisms held in Online during [[April 22 – 26 2024]] The workshop consisted of 40 hours of lectures and computer exercises. This full 5-day workshop aims to g an understanding of the underlying principles of software development, design, and programming.

This included the following topics:

Introduction to programming formalism
Source control and GitHub
Introduction to UML using plantUML
Introduction to Algorithms
Data types and data structures
Introduction to Software Development Lifecycle
common models
planning
source/version control
documentation
reproducibility and sharing
collaboration
testing
Introduction to Modular programming and the modular programming paradigm
Introduction to Social Coding
Pair Programming
Introduction to Object orientation and Object oriented design
Introduction to Test Driven Design and Testing (TDD)
including to GitHub Actions
automated testing
Introduction Software re-usability through component based and Modular programming
Optimization, measuring and common pitfalls

Course Leader | Lars Eklund, PhD Applications Expert UPPMAX/NBIS NBIS | Uppsala University

Course spring 2024

Dates and info

  • Onboarding takes place Thursday 18th April 11:00-(max)12:00
    • [Lars, Richel] Available 11:00-11:20
    • [Lars] Write welcome letter to participants today must be done 14:30
      • Encourage strongly to have a good Zoom setup :-)
      • Monday April 22nd to and including Friday April 26th
      • Each day from 9:00-16:00
      • R volunteers to (help) write the letter if needed!

Meeting after course

  • [Richel, discuss] How many things at the same time should our learners do?
    • B: ceil(\pi - e)
    • L:
    • R: 1
  • [Richel, discuss] What should the learners do in the break?
    • B: break or technical issues if OK with them
    • L:
    • R: do nothing, take a break
  • [Richel, discuss] How long should a monologue be? What should happen when this duration has been crossed?
    • B: aim to 10 minutes
      • is a demo where they can choose to do a type-along a monologue?
      • with demo it can be up to 20 I guess
    • L:
    • R: 20 minutes max, a helper should remind the teacher by voice