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docs/meeting_notes/20230419.md

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+# Meeting 6 (April 19 2023)
+
+### Participaton List
+
+- Lars
+- Björn
+- Richèl
+- Marcus
+- Diana
+
+### Tentative schedule
+
+- Monday: Intro
+    - Björn?
+- Tuesday: SDLC + social coding
+    - Lars
+    - Jon? (social and pair)
+- Wednesday: Modular programming + TDD (etc)
+    - Lars
+    - Richél?
+    - Matias?
+- Thursday: Algorithms
+    - Marcus
+- Friday: Optimization
+    - Marcus

docs/meeting_notes/20230426.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting 7 (April 26 2023)
+
+### Participaton List
+
+- Lars
+- Björn
+- Richèl
+
+### Things to check
+
+- PlantUML vs mermaid
+    - [name=Lars]
+    - [name=Björn]
+
+- Change formalism to formalisms everywhere
+-

docs/meeting_notes/20230510.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting 8 (May 10 2023)
+
+### Participaton List
+
+- Lars
+- Björn
+- Richèl
+- Jon
+

docs/meeting_notes/20230524.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting 9 (May 24 2023)
+
+### Participaton List
+
+- Lars
+- Björn
+- Richèl
+- Jon
+
+
+### Agenda
+
+- status 5 min each
+- There will be c. 1-2 hrs OO
+- Question to each:
+    - which Python testing framework, according to you, is best practice to use today?
+    - [x] unittest
+    - [ ] PyTest (CodeRefinery has material already)
+    - [ ] nose (Links)
+    - Bonus points if you have a reference to the literature
+
+### Intro day
+
+- Restructure again
+- Idea
+    - Intro to programming and state problem
+        - example matlab script without modularity
+    - Intro to SDLC and the tools (theory)
+        - models
+        - planning
+        - source/version control
+        - documentation
+        - reproducibility and sharing
+        - collaboration
+        - testing
+    - Hands-on
+        - planning
+            - pseudocode of example matlab script
+            - uml of modular
+        - startup of coding (first iteration)
+            - coding (python) (copy-paste)
+            - in-code documentation
+            - isolated environment (python)
+            - working dir
+            - license
+        - git and iterations
+            - git init
+            - branching
+            - modular
+            - no testing
+            - "backup on github"
+        - collaboration
+            - centralized
+        - deploy
+            - short
+        - documentation part 2
+            - wiki
+    - Extra-reading
+        - Rather important stuff but due to time limitations...
+        -

docs/meeting_notes/20230526.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting 10 (May 26 2023) 9.00
+
+## Participation List
+
+- Observers
+    - Richel will not observe all, but will try to do:
+        - Monday 11:00-12:00 @ Björn
+        - Tuesday 11:00-12:00 @ Lars
+        - Wednesday 11:00-12:00 @ Jon
+        - Thursday 11:00-12:00 @ Lars
+Björn
+    -

docs/meeting_notes/20230913.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# 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
+-------
+
+**<<name>>**
+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
+
+- [name=Lars Eklund], <[email protected]>
+- [name= Björn Claremar], <[email protected]>
+- [name=Marcus Lundberg],<[email protected]> (Can't give the current course)
+- [name= Matias Piqueras],<[email protected]>
+- [name=Richèl Biderbeek],<[email protected]>
+- [name=Jon Ander Novella],<[email protected]>
+
+## Assistants
+
+- [See schedule at https://github.com/UPPMAX/programming_formalisms#schedule]
+
+
+## Participation List
+
+- Diana Iusan, <[email protected]>
+-
+
+## 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]`

docs/meeting_notes/20230920.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting 20/9
+
+## Agenda
+
+   **When?**
+
+- suggested time Nov 20-24 (+2) Marcus can't
+- new suggestion is  Nov 27-1 (+3)
+- or having two weeks???
+
+- Pre-session week before
+
+-
+
+- **Where?**
+- Online or in uppsala
+   (contact NGI, om på plats om hela gänget kommer)
+- Current insights and experieces from last course.
+    - Reflections and learning 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

docs/meeting_notes/20230925.md

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+---
+tags:
+  - meeting
+  - notes
+---
+
+# Meeting at 2023-09-25 11:00
+
+Suggested agenda points:
+
+- Next course date is at Monday Nov 27 to and including Friday 1 Dec (+5)
+- [R, 0 mins, L needs to fill in :-) ] Who intends to teach/assist in the next course? Björn, Jon, Lars, Marcus, Richel
+- [R, 2 mins, vote] R: I suggest to work on a non-biological project. Vote yes/no
+    - Jon suggests to move the November 1st
+    - [R, 2 mins, vote] R: if we have a biological project, I suggest to schedule the time to explain the problem properly. Vote yes/no
+- Course is a NBIS hosted course with UPPMAX being main contributor for teaching
+    - Should be on the certificate
+- R: suggest to make 'Planning' session shorter, more tuned to scientists, e.g. 'Write down what you want to do in English first' or writing a draft of a paper/preregistration. R feels that current ISO things are overkill for this course. No vote
+- We work together on a example project, so the students have one good example how it should be done.
+- [R, 17 mins total] R: suggest one/two project topics (1 for students, maybe 1 for teachers)
+    - [10 mins, collect] All suggest the topics for a general project individually, in silence [R asked in Slack to do this before meeting]
+        - [0 votes] R: beat all <https://projecteuler.net/> problems
+        - [4 votes][students] R: simulating bacterial movement in 2D space +:t-rex::t-rex: x
+        - [1 votes] R: a chess game :t-rex:
+        - [2 votes] R: a tic-tac-toe game :t-rex: +
+        - [0 votes] R: a chat-bot without memory of earlier questions
+        - [2 votes] R: a maze creator and solver +:t-rex:
+        - [1 votes] J: Morse Code Translator: Build a program that can translate text to Morse code and vice versa. This can be a fun and educational project. :t-rex:
+        - [3 votes] J: Simple Web Scraper: Develop a web scraper that extracts specific information from a website and displays it in the console. You can use libraries like requests and BeautifulSoup. +:t-rex:x
+        - [5 votes][selves!] M: N-body simulation, e.g. galaxy sim or predator-prey + :t-rex:+:t-rex:x
+        - [2 votes] M: crystal growing simulation: generate snowflakes :t-rex:x
+        - [1 votes] L: 2D brownian motion :t-rex:project /can be branded as bacterial movemnt x
+        - [3 votes] L: Trait selection simulation :+1::t-rex:x
+    - [5 mins, present] Each presents his/her suggested topics
+    - [2 mins, vote] Each does :+1: per topic. Two topics with most :+1:s wins
+    - Result, obtained by vote:
+        - For us: N-body simulation, e.g. galaxy sim or predator-prey
+        - For students: simulating bacterial movement in 2D space
+
+## TODOs
+
+- [x] M and R will down more detailed exact description about their projects and send to L
+    - [x] M: The program should visually display a number of particles on a field. Particles are initialised with a certain position and speed. Each particle interacts with all the other particles in a simple way, e.g. gravitational attraction, Lennard-Jones potential, direction alignment (implementing a flocking behaviour), or something else, the group chooses which. Decide on a boundary condition (e.g. bounce or wrap or eliminate the particle). The simulation is then stepped forward, drawing each step, until stopped. The goal is to create a stable simulation capable of the maximum number of particles at an acceptable framerate.
+    - [x] R: `https://github.com/UPPMAX/programming_formalisms/blob/richel/projects/student_project.md`