Scientific workflows: Tools and tips / Lecture series by Dr. Selina Baldauf
Early-career researchers understand the importance of digital tools for processing data, managing workflows, and enhancing efficiency. However, they often lack time to discover new tools and improve their workflows. In this lecture series we will explore a diverse range of topics, including R code quality and efficiency, reproducible document creation, version control with Git, literature management, and academic notetaking. You'll learn practical tips and tricks that can help you optimize your research workflow and increase your productivity.
We will meet online on the third Thursday of every month during the lecture period for one hour and you are welcome to join.
If you don't want to miss any future meetings, subscribe to the mailing list. You can find the lecture slides, recordings and additional material here.
If you would like to receive a certificate of attendance (with ECTS), please contact Dr. Alette Winter via graduate-center@bcp.fu-berlin.de
Title: An introduction to the tidyverse
Description: Discover the power of the tidyverse, an integrated suite of R packages designed for streamlined data analysis. In this lecture, we'll explore the cohesive design philosophy that makes the tidyverse efficient and intuitive, covering popular packages like ggplot2 and dplyr, as well as less familiar ones such as purrr and stringr. Ideal for those new to the tidyverse or familiar with only a few of its components, this session will introduce you to a comprehensive range of user-friendly tools.
Meeting info: February 15th, 4-5 pm
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m7ab678971aa8b2dc48ef001f23af09b5
Meeting number:
2787 870 7932
Meeting password:
cGBFpGZE434
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Dial 27878707932@fu-berlin.webex.com
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+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27878707932
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https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=ma835b9b36a40c2cb9fbbebca0ed3eec9
Title: AI tools for programming
Description: AI tools promise to make our programming workflows faster and more efficient. If applied correctly, such tools help us write better code, be more productive and learn new techniques easily. In this lecture, I will present some AI tools for programming (mainly GitHub Copilot and ChatGPT) and show examples of how they can be integrated into our daily workflows for different purposes. I will also briefly talk about the problems and ethical concerns that come with such tools in science. Join me if you are interested!
Meeting Info:
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m4724bc747dc6b563394c30a17d15ee94
Meeting number:
2784 020 2015
Meeting password:
4rXHhRgW383
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Dial 27840202015@fu-berlin.webex.com
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Join by phone
+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27840202015
Global call-in numbers
https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=m9303975ffca17977fe8c7251f9f7c205
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For most data analysis and statistical computing, R is efficient enough. However, there are times when we encounter bottlenecks in our code that slow it down significantly. In this lecture, I'll teach you techniques to identify those bottlenecks and write more efficient code. You'll learn the fundamental principles of faster R code and discover efficient packages for data analysis. We'll also touch on advanced optimization methods like parallelization and integrating C++ code. If you have previous experience with R programming and looking to make your R code run faster, this lecture is for you. If you are an R beginner, you'll still benefit from learning the principles and patterns but the more advanced techniques won't be relevant for you yet.
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m9c03c7cf0e63f2375ee5b6cd7072b305
Meeting number:
2787 868 2233
Meeting password:
GXwkJaMN698
Join from a video or application
Dial 27878682233@fu-berlin.webex.com
You can also dial 62.109.219.4 and enter your meeting number.
Join by phone
+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27878682233
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https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=m8c290979afd7cf28f7318b93fa98534c
Effective digital note taking with Obsidian - Create your second brain
Effective note taking is crucial for both students and scientist. It's useful to manage tasks, capture key insights from papers, and write down new ideas. In this lecture, I will introduce you to my note taking software of choice. Obsidian is a highly customizable, markdown-based tool that lets you organize your notes efficiently and create interconnected webs of thoughts and ideas (also called "second brain" or "Zettelkasten"). Join me if you want to streamline your note taking process and keep organized records of your tasks, readings and ideas.
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m28c1650aeb60ee7e36490ba396859564
Meeting number:
2731 265 3753
Meeting password:
huYCGJ9nA42
Join from a video or application
Dial 27312653753@fu-berlin.webex.com
You can also dial 62.109.219.4 and enter your meeting number.
Join by phone
+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27312653753
Global call-in numbers
https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=m5f86c3056c3dd68e4c383eeab3e692fa
Description: A research compendium is a collection of all the digital parts of your research project (data, code, documents) which is often required to be published alongside a scientific paper.
The structure and tools of R packages provide a standard workflow for building such reproducible research compendia. In this lecture, you will learn how to build, test and publish your research compendia in the form of an R package. This lecture is mainly aimed at people that have some experience with R, R-Studio and Git. But even if you are new to these topics, you will still get a valuable overview of key concepts for reproducible research compendia and tools to build them.
When? Thursday July 20th, 1-2 pm
Where? Online on Webex
Description: Git is an essential skill if you use any programming language. It allows you to keep track of changes to your project over time, collaborate with others, and maintain a clear and organized project structure. This can save time, improve research efficiency, and also makes it easy to publish your code via platforms such as Github. In this lecture, I will introduce the basic concepts of Git and how to use it for you own projects. The lecture is for Git beginners but also for people who use basic Git for their own projects and want to know a bit more about the concepts behind the workflow.
When? Thursday June 15th, 4-5 pm
Where? Online on Webex
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m6e3c9e53d5f27f25773cb4d5747e08d7
Meeting number:
2734 873 2317
Meeting password:
Y6UpBC3Aep9
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Dial 27348732317@fu-berlin.webex.com
You can also dial 62.109.219.4 and enter your meeting number.
Join by phone
+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27348732317
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https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=m4a56a70edb5a39b6b945c2aee379f363
Description: Quarto (the successor of rmarkdown) is a powerful tool that enables the seamless integration of code (R, Python, and more) and its output into a variety of formats such as reports, research papers, presentations, and more. This tool streamlines the process of creating reproducible workflows by eliminating the need to copy and paste figures, tables, or numbers. During this lecture, you'll learn the fundamentals of Quarto and explore practical use cases that you can implement in your data analysis workflow.
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=m685a25fabee8a6b0af94f6bb7f14ee1b
Meeting number:
2731 360 6501
Meeting password:
gqCZr67X2n8
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Dial 27313606501@fu-berlin.webex.com
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20230420_Lecture_Series_1
Description: Do you use R in your daily work and research but you still feel your workflow isn't as smooth as it could be? In this lecture, I will share with you my best tips from 8 years experience with R. We will cover those concepts and tricks that are often overlooked but can make a big difference. Whether you're a beginner or more experienced R programmer, this lecture will enhance your workflow and help you write clean, reproducible and reusable code in R.
When? Thursday April 20th, 4-5 pm
Where? Online on Webex
Meeting link:
https://fu-berlin.webex.com/fu-berlin-en/j.php?MTID=mb1c11e727797625c65c3346e614ea571
Meeting number:
2732 425 9948
Meeting password:
FkNfEby2p53
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Dial 27324259948@fu-berlin.webex.com
You can also dial 62.109.219.4 and enter your meeting number.
Join by phone
+49-619-6781-9736 Germany Toll
+49-89-95467578 Germany Toll 2
Access code: 27324259948
Global call-in numbers
https://fu-berlin.webex.com/fu-berlin/globalcallin.php?MTID=m8502415529031778b6a28a837ef89ac5