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Meeting 7 Feb 11-12

  • Teachers: Björn, Lars, Richel (Marcus)
  • Date:
    • Monday April 22nd to and including Friday April 26th
    • NOT Monday May 6th ..., because 3 days
    • NOT Monday May 13nd because conference Lars
    • NOT Monday May 20nd because conference Lars
    • NOT Monday May 27th to and including Friday May 31st, due to some reason
    • NOT Monday June 3rd - Friday ..., due to Nationaldagen
    • NOT Monday June 10th ..., due to summer holiday
    • [x] Björn and Lars will double-check if that works
    • [ ] Lars will advertise this
    • [ ] Richel will notify Marucus
  • Format:
    • Fully virtual
  • Do we need more helpers?
    • Yes/No
  • Social coding, as taught by Jon goes to Richel, if noone else wants it
  • Next iteration dreams:
    • Richel: start with social coding
    • Lars: Start introducing project from Day 1
  • TODO for next meeting:
    • Suggest a course schedule
      • ALL OF US
    • Lars: Vote between mermaid and PlantUML
      • Pro mermaid: works out of the box
      • Con mermaid: does not do all types of diagrams: maybe Lars needs one!
      • Pro PlantUML: has all types of diagrams
      • Con PlantUML: learners need to install things
      • VOTE NEXT WEEK
    • Björn: Think about how to do the git section.
      • Lars idea:
        • as long as they use the course repo with the folder structure, I am happy
        • Björn is boss!
      • Richel:
        • as long as I've seen all learners have made a commit on the course repo, I am happy
        • Björn is boss!
    • Lars: Think about how to do the design document
      • Richel:
        • as long as a class diagram ended up in the repo, I am happy
        • Lars is boss!

Sections

Course certificates fall 2023

Certificates

Text for course certificate use https://rshiny.nbis.se/shiny-server-apps/shiny-certificate/ to create certificate

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has participated in the NBIS workshop Programming Formalisms held in Online during 27 November -- 1 December 2023. The workshop consisted of 40 hours of lectures and computer exercises. This full 5-day workshop aims to give scientists, bioinformaticians and other research engineers with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The workshop aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance. 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

November course zoom

Lars Eklund is inviting you to a scheduled Zoom meeting.

Topic: Programming Formalism Course Meeting Time: Nov 24, 2023 08:30 AM Stockholm Every day, until Dec 1, 2023, 8 occurrence(s) Nov 24, 2023 08:30 AM Nov 25, 2023 08:30 AM Nov 26, 2023 08:30 AM Nov 27, 2023 08:30 AM Nov 28, 2023 08:30 AM Nov 29, 2023 08:30 AM Nov 30, 2023 08:30 AM Dec 1, 2023 08:30 AM Please download and import the following iCalendar (.ics) files to your calendar system. Daily: https://uu-se.zoom.us/meeting/u5Ipd-CvrjIiHd0mA7LZEoc8tehKfAe9R5oi/ics?icsToken=98tyKu-uqjsjHdScuB6OR_MABoigXe3ziFhHgqcNkT6yLxp2bQCuIudKGbReFYHi

Join Zoom Meeting https://uu-se.zoom.us/j/66409709879

Meeting ID: 664 0970 9879 Passcode: 583470 One tap mobile +46850539728,,66409709879# Sweden +46844682488,,66409709879# Sweden

Dial by your location +46 850 539 728 Sweden +46 8 4468 2488 Sweden +45 89 88 37 88 Denmark +45 47 37 25 75 Denmark +49 69 7104 9922 Germany +49 695 050 2596 Germany +33 1 8699 5831 France +33 1 7095 0350 France +44 131 460 1196 United Kingdom Meeting ID: 664 0970 9879 Find your local number: https://uu-se.zoom.us/u/cb33F9G1YH

Join by SIP 66409709879@109.105.112.236 66409709879@109.105.112.235

Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 664 0970 9879 Passcode: 583470

Meeting Notes

Current Teachers/TA

Assistants

  • [See schedule at https://github.com/UPPMAX/programming_formalisms#schedule]

NEXT COURSE DATE Nov 27-1 Dec 2023

Online ONBOARDING Session Friday Nov 24 10:00-11:00

make deadline Oct 31 ~~Dec~~

Course project

[students] R: simulating bacterial movement in 2D space [selves!] M: N-body simulation, e.g. galaxy sim or predator-prey Marcus and Richel will write a project breef that Lars Formalises. The [selves!] project has a Requierments modeleling and a first usecasemodel done, Next step is to create modules and classes to solve the structure problem. as well as describing the testcases in more detail for each use case-requierment.