Sections

When What
Aug 21 Day 1: Computers in General, BASH, Git and GitHub, and markdown
Aug 22 Day 2: R practice, frequentists statisics and machine learning basics

Purpose

  • Warm-up
  • Get everyone on the same page

Day 1: Computers in general, review of R

Schedule for day 1 - Warm up

From To What
9:00 09:30 General introduction
9:30 10:15 Discussion on scientific activities, computers and tools
10:15 10:30 Coffee
10:30 11:30 Presentation on FAIR and open data, install git
11:45 13:15 Lunch
13:15 13:30 Project and file management principles
13:30 - Installing Git, Terminal and BASH, Directories, Git basics, GitHub, Markdown
- 17:30 Markdown - the dinosaur example, GitHub Pages
17:30 -> Pizza and beer in the Pal Garden

Papers

Slides

Schedule for day 2

From To What
09:00 09:50 Finishing git-related, markdown, websites
12:00 13:30 Lunch
13:00 15:30 R: Quiz and solutions (by Michal Kowalewski)
15:30 17:15 Example code and stas

R

Notes from earlier

Academic activities

  • grant writing,
  • emails
  • teaching
  • supervision and mentoring
  • committees
  • Writing papers
  • University service
  • Programming, Data analysis
  • Programming, software development
  • Outreach and non-profit
  • Field Work
  • EDI (Equity, Diversity, Inclusion)
  • Graphic design
  • Networking and conferences
  • Reading
  • Coordinating and management
  • Scientific meetings
  • Reviewing papers and grants
  • Logisitics, management of lab space
  • Lab work
  • Rock fossil preparation
  • Imaging (photograph, SEM, CT, surface scanning)
  • Databasing (entry, curation, management, architecture)
  • E-learning - web design

Text processor

  • MS Word
  • Google Doc
  • Latex/Overleaf
  • (Word Perfect)
  • Quarto

Bibiliography

  • Zotero
  • Mendeley
  • Endnote
  • Jabref (bibtex)
  • Readcube

Email

  • Web client
  • Outlook
  • Thunderbird
  • Maildir

Graphics

  • Adobe CS (Illustrator, Photoshop)
  • GIMP
  • Inkscape
  • Krita

3d modelling

  • Blender

GIS

  • QGIS
  • ArcGIS
  • GPlates
  • programming tools

Programming

  • R, Python, Matlab, Julia
  • C, C++, Fortran
  • SQL

Some GNU tools that were mentioned

  • wget
  • pandoc
  • ffmpeg
  • imagemagick

Making a website with academicpages

  • Go to Acadmic pages (example jekyll), and fork the repository!
  • Go to your forked version of the repository. Go to Settings, and then to Pages (currently under the section Code and automation).
  • Under Build and deployment select the source: Build from a branch. And in Branch select master, and /root and hit save.
  • The page will take some time to build. If you go on the repository’s main page, there will be an orange dot next to the commit hash. When the page is ready, this will change to a green checkmark.
  • If you go the settings page where you set up the things above, you should see the URL to the webpage. This URL will typicall be: https://<yourgithubname>.github.io/<reponame, i.e. academicpages>/.
  • If you want to make a webpage with the URL https://<yourgithubname>.github.io/, you have to create a repository called <yourgithubname>.github.io.
  • You can also set up a custom domain for this page. See this article to find out how.