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Meeting 13/9

Agenda

When?

  • suggested time Nov 20-24 (+2) Marcus can't

(contact NGI, om på plats) Where?

  • Online or in uppsala

Current learnings and experieces from last course.

How?

  • larger more fully scoped excerise do we want and in which areas does that need to expand and be worked at

  • Under vilken verksamhet ska vi hålla kursen Uppmax eller NBIS

  • Hur många studenter kommer från NBIS sidan UPPMAX profiling på kursen/certifikat

  • Contact Jonas Söderberg for design of common course certificate. And also Nina and the other NBIS training, contact Roy about the RShiny thingiy.

  • Reflections and learning from last course

Certificates

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

<> has participated in the NBIS workshop Programming Formalisms held in Online during 29 May -- 2 June 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
  • Datatypes 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 and 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 to Design Patterns and Software reusability

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

Fall course in December

we will start the first course meeting in August wednesday last week in august with resrvation for UPPMAX intro course.

Weekly Zoom meeting Wednesdays 11.00

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

course Zoom

Topic: Programming Formalisms Time: May 29, 2023 8:30 AM Stockholm

Join Zoom Meeting https://uu-se.zoom.us/j/65052228138

Meeting ID: 650 5222 8138 Passcode: 595312

QA hackmd

[Broken link to a HackMD document]

Current Teachers/TA

Assistants

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

Participation List

- Diana Iusan, diana.iusan@uppmax.uu.se

Course two

  • Course time?
    • 9.00-16.00?
  • Course Date?
    • 29 May -- 2 June
  • Course Projects
    • first day: planetary app (broader audience than life scientists!)

    • second-fifth day EasyBlast? Yes that is the plan, the reason is that the EasyBlast or Reduced blast is complicated enough to make a good project but easy enough to finish somthing in 4 days.

At the end of day use (Scrum/Sprint)reflections as a feedback method for each day. First day may need to use other ways of gathering feedback. https://hackmd.io/hh9xENMvRrWWm-STsNCeJQ https://hackmd.io/YX32lWjSS5qu1r29zrbyig https://hackmd.io/--Qgp344TdOxC5uX-UWNQA https://hackmd.io/EUQ5PY10SeWj_JR5kTUNTA https://hackmd.io/naC4mOulSOSWv74YYf7xRg

The registration link works but the landing page needs to be changed. I have downloaded the old responses and cleared the respones for new participants

Advertising text for the SNIC training newsletter Course 2

Programming Formalisms Course - May 29- june 2 (online)

This full 5-day course 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 course 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.

We will cover an introduction to Algorithms and Data structures, Programming Paradigms especially structured and object oriented programming, and to give an overview of other paradigms like functional programming. Modular development and (code) reusability, testing and optimisation.

We will cover theory with bridging practical examples and applications to enhance the theoretical understanding of the principles.

For more information and registration, please visit: [broken link to Programming Formalisms course at UPPMAX website]