General course information
Schedule
| Day | Date | Time | Room | Topic | Lecturer |
|---|---|---|---|---|---|
| Mon | 14.10.2024 | 12:00-14:00 | S09 | Introduction to course | Schmid |
| Tue | 15.10.2024 | 10:00-12:00 | S09 | Working with scientific literature - 1 | Schmid |
| Mon | 21.10.2024 | 12:00-14:00 | PC Room 3 | Introduction to data science and R (Part I) | Thorwarth |
| Tue | 22.10.2024 | 10:00-12:00 | S09 | Working with scientific literature - 2 | Daware |
| Mon | 28.10.2024 | 12:00-14:00 | PC Room 3 | Introduction to R (Part 2) | Thorwarth |
| Tue | 29.10.2024 | 10:00-12:00 | S09 | Scientific measurements and estimation | Daware |
| Mon | 04.11.2024 | 12:00-14:00 | PC Room 3 | Tools for reproducible research | Daware |
| Tue | 05.11.2024 | 10:00-12:00 | S09 | Visualization of scientific data | Daware |
| Mon | 11.11.2024 | 12:00-14:00 | PC Room 3 | Cleaning and processing of scientific data | Daware |
| Tue | 12.11.2024 | 10:00-12:00 | S09 | What is science? | Schmid |
| Mon | 18.11.2024 | 12:00-14:00 | S09 | The scientific method | Schmid |
| Tue | 19.11.2024 | 10:00-12:00 | S09 | Scientific reasoning: General rules | Schmid |
| Mon | 25.11.2024 | 12:00-14:00 | S09 | Scientific reasoning: Common errors | Schmid |
| Tue | 26.11.2024 | 10:00-12:00 | S09 | Limits of science and pseudoscience | Schmid |
| Mon | 02.12.2024 | 12:00-14:00 | S09 | Experimental design 1: Hypotheses and designs | Thorwarth |
| Tue | 03.12.2024 | 10:00-12:00 | S09 | Experimental design 2: Variation and pseudoreplication | Thorwarth |
| Mon | 09.12.2024 | 12:00-14:00 | S09 | Experimental design 3: Types of experimental designs | Thorwarth |
| Tue | 10.12.2024 | 10:00-12:00 | S09 | Experimental design 4: Blocking and other considerations | Thorwarth |
| Mon | 16.12.2024 | 12:00-14:00 | S09 | Scientific reasoning with probabilities | Schmid |
| Tue | 17.12.2024 | 10:00-12:00 | S09 | Bayes’ theorem in scientific analysis | Schmid |
| End of year break | |||||
| Mon | 06.01.2025 | 12:00-14:00 | No class (Epiphany) | ||
| Tue | 07.01.2025 | 10:00-12:00 | S09 | Statistical testing | Schmid |
| Mon | 13.01.2025 | 12:00-14:00 | S09 | Models and model selection | Schmid |
| Tue | 14.01.2025 | 10:00-12:00 | S09 | Publishing and patenting in science | Schmid |
| Mon | 20.01.2025 | 12:00-14:00 | S09 | Ethics in scientific research and Rules for good research practice | Schmid |
| Tue | 21.01.2025 | 10:00-12:00 | S09 | Science and the public | Schmid |
| Mon | 27.01.2025 | 12:00-14:00 | S09 | Final presentations 1 | Schmid |
| Tue | 28.01.2025 | 10:00-12:00 | S09 | Final presentations 2 | Schmid |
Course lecturers
Karl Schmid
Professor of Crop Biodiversity and Breeding Informatics
Office hours: Wednesday, 14:00 - 16:00 or by appointment
Contact: karl.schmid@uni-hohenheim.de
Research: Population Genetics of Wild and Crop Plants
Webpage: http://evoplant.uni-hohenheim.de
Patrick Thorwarth
Anurag Daware
Clemens Hacke
Course organisation
Coursework
- You need to submit one declaration of plagiarism that covers both courseworks. You can find the form here
- Due date: Sunday, 26.01.2025 23:55
- All documents are to be uploaded on ILIAS here
Coursework 1: Summary of a review paper or book chapter
- Guidelines for coursework 1: Link
- List of texts to be reviewed for coursework 1: Link (Will be expanded depending on the number of students)
- Assignment of literature to students: PDF
- Due date for upload of handout: 12 January 2025, 23:55 | Upload link
- Due date for upload of presentation slides: 26 January 2025, 23:55 | Upload link
Coursework 2: Small data analysis project
- Guidelines for coursework 2: Link
- List of assignment of data sets to students: PDF
- Due date for upload of report: 26 January 2024, 23:55 | Upload link
Course topics and material
Introduction to course
Teaching guide
In class
- Welcome to Crop Science Master Program (Ivan Guzman and Karl Schmid)
- Photoshooting
- Introduction to course: Organisation and topics (Notes
Working with scientific literature 1: Outlining, citing, plagiarism
Prepare for class
In class
- Short lecture on outlining, citing and plagiarism (Lecture notes)
- Short demonstration of Zotero reference manager
- Outlining exercise on the opinion article by Stam and McDonald (See lecture notes for this class)
Introduction to data science and R (Part 1)
Prepare for class
Installation R, R Studio and Quarto on your own computer:
- Download and install R: http://cran.r-project.org
- Download and install RStudio: http://www.rstudio.com/products/rstudio/download/
- Download and install Quarto: https://quarto.org/docs/download/index.html
If you encounter problems with your installation, please post questions (including error messages or screenshots) to the forum!
In class
- Lecture notes: Introduction to data science
- R introduction tutorial: Link
Additional material:
- Introduction to the Quarto publishing system:
- Wickham and Grolemund: R for Data Science, 2nd edition
Working with scientific literature 2: Quality and searching
Prepare for class
- Watch lecture videos: Plagiarism (8 min), Searching for literature (5 min) Impact-1 (19 min) Impact-2 (19 min) (Slides)
- Or read the lecture notes (more up to date)
In class
- Plagiarism exercise: PDF
- Discussion of outlining exercise: Outlines Outlines with Plagiarism-Check
- Short demonstration of Google Scholar and Research Rabbit
- Group discussion: How to identify and evaluate good research papers? PDF
Introduction to R - Part 2
In class
- R introduction tutorial: Link
Scientific measurements and estimation
Prepare for class
- Lecture notes on measurements
In class
Tools for reproducible research
Prepare for class
- Read this paper by Sandve et al. (2013): PDF
In class
Visualization of scientific data
Prepare for class
- Lecture: Slides | Lecture videos: Visualization-1 (15 min) Visualization-2 (22 min) Visualization-3 (18 min) | Lecture notes
In class
Cleaning and processing of scientific data
Prepare for class
In class (Computer lab):
What is science?
Prepare for class
In class
- Short lecture on the history of science philosophy Lecture notes
- Group discussion of Okasha, Philosopy of Science, Chapter 1
The scientific method
Prepare for class
In class
- Short lecture on the scientific method. Lecture notes
- Discuss questions on Okasha, Philosopy of Science, Chapter 2
Scientific reasoning: General rules
Prepare for class
No preparation for this class!
In class
- Lecture on scientific reasoning Lecture notes: HTML
Scientific reasoning: Common errors
Prepare for class
- Videos: Fallacies in deductive reasoning (17 min) Inductive reasoning (Total 30 min; start at minute 22:00)
- Slides: PDF
- Lecture notes: HTML
In class
- Short repetition of errors in scientific reasoning
- Group discussion on key fallacies and errors in scientific reasoning: PDF
Limits of science and pseudoscience
Prepare for class
In class
- Lecture on limits of science and pseudoscience | Lecture notes
- Discussion of paper on eurythmic treatment of apples?: Good science, bad science or pseudoscience? Questions for discussion are here
Additional material:
Experimental design 1: Hypotheses and designs
Prepare for class
- Watch introductory videos: Introduction (9 min) | History and basic principles (18 min) | Design and planning (17 min) | Slides: PDF
- Or, read the lecture notes on experimental design: Link
- Or, read the chapter about selecting the broad design of a study in Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 3
In class
- Short lecture with discussions on topics related to hypotheses
- Group discussion of use cases on experimental design: Link
Experimental design 2: Variation and pseudoreplication
Prepare for class
- Read Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 4
In class
- Short lecture with discussions on variation and pseudoreplication
- Group discussion of use cases on experimental design: Link
Experimental design 3: Types of experimental designs
Prepare for class
In class
- Short review of experimental designs based on the assigned literature
- Group discussion of use cases on experimental design: Link
Experimental design 4: Blocking and other considerations
Prepare for class
- Read about the concept of blocking in Ruxton and Colgreave: Experimental Design for the Life Sciences (4th Ed) 2016, Chapter 9 (9.1 and 9.2)
In class
- Short lecture on topics related to blocking
- Group discussion of use cases on experimental design: Link
Scientific reasoning with probabilities
Prepare for class
- Slides | Videos: Introduction (19 min) | Formal definition (16 min) | Bayes’ Theorem (18 min)
- Lecture notes
In class
- Recapitulation and discussion of key concepts
- In class discussion exercises: HTML
Statistical testing
Prepare for class
- Statistical testing: Slides | No video | Lecture notes
In class
Models and model selection
Prepare for class
In class
- Recapitulation of key concepts
- In class discussion of exercises
Publishing and patenting in science
Prepare for class
- Scientific publishing: Slides | Videos: Publishing-1 (17 min) Publishing-2 (9 min) Publishing-3 (20 min) | Lecture notes
- Patenting : Slides | Videos: Patents-1 (26 min) Patents-2 (15 min) Patents-3 (9 min) | Lecture notes
In class
- Scientific publishing: Discussion questions
- Patenting: Discussion questions
Additional reading
- Scientific writing: Mensh and Kording (2017) PLOS Comp. Biol: Ten simple rules for structuring papers (PDF)
- Patenting: Lab Times: Patented Outgrowths (2017) PDF
Ethics in scientific research
Prepare for classs
- Ethics in scientific research:
- Slides | No video! | Lecture notes
- TED talk on the dignity of plants (YouTube) (15 min) - Will discuss in class
- Discussion questions for the TED talk: Link
In class
- Short introductory lectures on ethics
- Discussion questions on ethics in science and dignity of plants based on the TED video
Rules for good research practice
Prepare for class
- Good research practice: Slides | No video! | Lecture notes
- DFG code of conduct for good research practice: Link
In class
- Short introductory lecture on good research practice
- Discussion of DFG Rules for research practice
- Discussions of problems related to good research practice: PDF
Science and the public
Prepare for class:
- Slides | Video (22 min) | Lecture notes
- TED Talk on the engineering of our food (YouTube) (18 min)
In class
- Short lecture
- Discussion of TED talk: Questions as PDF