Course description

Informatics for zoologist tentative course outline 2024./2025. 1^st semester

 

Description

The aim of the course to provide essential hard skills for reasonable use of various software that can support a researcher’s work. The course provides three modules: 1) data organization, management and short analyses in Excel and R; 2) creating and managing text documents, reports and presentations in MS Office and other environment such as HTML  and Rmarkdown; 3) Other important IT skills for researchers such as scientific databases, scientometrics and daily management of a computer and files.

Attendance

It is mandatory to attend both lectures and practicals. Signature is subject to no more than 3 absences from lectures. In case of more than 3 absences, signatures will be rejected and the course has to be retaken regardless of the results.

• All practicals begin on the 2nd week. The practical teachers will only allow students to participate who have registered to the given group in Neptun. You may be absent from 3 practicals, however you may not attend other practicals to make up for an absence. Absence from midterms or tests is only accepted upon a medical certificate is provided.

 

Grades and scores

Total number of collectable points is 100 (excluding bonus points). Score thresholds:

• 0 – 54.49%: 1
• 54.5 – 62.99%: 2
• 63 – 74.99%: 3
• 75 – 87.99%: 4
• 88 – 100%: 5

 

Course outline by modules

Module 1 – Data management

1. Excel intro, data in Excel (Broman and Woo 2018. Data organization on spreadsheets)
2. R & Rstudio intro (open data, view data in R)
3. Excel tasks 1. /Rtask 1. (practicals only)
4. Excel tasks 2. /Rtask 2. (practicals only)

 

Module 2 – Text documents, reports and presentations

1. Essentials for HTML and CSS (ATZS)
2. Intro to Rmarkdown for text documents
3. Word part #1 – basics of text editing in MS word (ATZS)
4. Making formulas and equations in Rmarkdown
5. Word part #2 – long documents – using styles, table of contents, tables and figures (ATZS)
6. Presentation in PowerPoint (ATZS)

 

Module 3 –  Other important IT skills for researchers

1. Reference managers (Mendeley, Zotero), scientific databases and essentials for scientometrics (WOS, Scopus, github, publons)
2. Managing files locally (explorer, vs. total commander) and globally (free cloud services for science with pros and cons), Window OS daily management + (best of )hotkeys

 

 

Time schedule

Lecture → Thursday 12.15-13.00 (N3)

Practicals → Monday 14.15-16.00 (group #1, H1), Thursday 08.15-10.00 (group #2, H2)

 

1. Week 02.09 – 06.09 – no education
2. Week 09.09 – 13.09 – Course overview, introduction to univet IT
3.  Week 16.09 – 20.09 – Excel intro, data in Excel, data organization on spreadsheets
4. Week 23.09 – 27.09 – Advanced functions and graphics in Excel
5. Week 30.09 – 04.10 – R & Rstudio intro (open data, view data in R)
6. –Week 07.10 – 11.10 – (Estimate) Diversity in R, essential analyses for biological data
7. Week 14.10 – 18.10 – Rmarkdown I. – create/edit your first reports with RMarkdown
8. Week 21.10 – 25.10 –  Rmarkdown II. – create/edit reports (with formulas/equations) with RMarkdown
9. Week 28.10 – 01.11 – Midterm I. (excel, R, Rmarkdown assignment open)
10. Week 04.11 – 08.11 – Presentation in PowerPoint (ATZS)
11. Week 11.11 – 15.11 Word part #1 – basics of text editing in MS word (ATZS)
12. Week 18.11-22.11 – Word part #2 – basics of text editing in MS word (ATZS)
13. Week 25.11 – 29.11 – Word part #3 – basics of text editing in MS word (ATZS)
14. Week 02.11 – 06.11 –  Reference manager (Mendeley, Zotero) + scientific databases and essentials for scientometrics (WOS, Scopus, github, publons)
15. Week 15 09.12 – 13.12 – (Midterm II./Test on word?), Deadline Rmarkdown report assignment

 

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