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Articles about data science and science in general, open source and other free DIY solutions, and personal stuff.
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Loading and saving files in Google Colab
Enable I/O support in your notebooks running in Google Colab with just a few additional commands.
How to get an RSS feed of your Mastodon bookmarks
The third-party service Mastodon Bookmark RSS allows you to subscribe to your Mastodon bookmarks via RSS, so you don’t forget to make use out of them. You can even integrate the feed into your favorite Zettelkasten apps such as DEVONthink and Obsidian.
Problems with large vaults in Obsidian
In the past few days I played a bit with Obsidian. Turns out that its iOS app has some serious problems with large vaults.
DEVONthink and privacy
One thing I really love about DEVONthink, is its high security and privacy measures regarding the synchronization of my notes across different devices. No other app that I have so far used offered such high standards.
Bio-image registration with Python
Which method works best for which registration problem? In this tutorial we compare different methods for the registration of bio-images using Python.
Using VS Code as LaTeX editor
It doesn’t take much to convert Visual Studio Code into a powerful LaTeX editor. Here are the necessary steps that enable full LaTeX support.
Moving a Mastodon account to another server
I recently moved my Mastodon account to a new server, including all my followers. I was surprised, how easy and seamless it worked. Here is a how-to, summarizing the migration steps.
I’m on Mastodon
Mastodon is not just a Twitter alternative. It’s a free and open-source social media platform of its own kind. Here is my story how I got there.
How to run PyTorch on the M1 Mac GPU
As for TensorFlow, it takes only a few steps to enable a Mac with M1 chip (Apple silicon) for machine learning tasks in Python with PyTorch.
How to run TensorFlow on the M1 Mac GPU
In just a few steps you can enable a Mac with M1 chip (Apple silicon) for machine learning tasks in Python with TensorFlow.
Is there a difference between miniconda and miniforge?
Simply said: not really. Miniconda is the company driven minimal conda installer, while miniforge is its community driven variant. In the end, you’ll get the same minimal conda installation on your machine – with a minor difference.
Hacks and extensions to improve your coding with Visual Studio Code
This curated list contains useful hacks and extensions to improve the overall coding performance with Visual Studio Code (VS Code).
Setting up Visual Studio Code for Python
In just a few steps you can turn Visual Studio Code (VS Code) into a powerful Python editor for both pure Python code and Jupyter Notebooks.
Laying off thousands of employees: Not okay! How to delete a Twitter account
Putting thousands of people on the street is anything else than cool. Here is how to fix it.
Enable interactive plots and other plot modes in Jupyter notebooks
Learn how to enable interactive, static and stand-alone window plots in Jupyter notebooks with the magic command
%matplotlib.
Enable code folding in JupyterLab
Learn how to enable code folding in JupyterLab for both, Jupyter Notebooks and pure Python scripts.
How to create and apply a requirements.txt file in Python
Learn how to install Python packages with a requirements.txt file and how to create one yourself.
Virtual environments with venv
In addition to conda’s
create command, Python’s built-in venv command offers another way for creating virtual environments.
Using pip to install Python packages
pip is another package installer for Python. Learn how to use it for installing and managing Python packages in your projects.
How to install and run Python code from GitHub
Learn how to install code from GitHub, that is, e.g., not (yet) available via conda or pip.
A minimal Python installation with miniconda
Learn how to install miniconda to have a quick and minimal Python installation on any operating system. Also learn how to use conda to create and manage virtual environments, install packages, run Python scripts and run Jupyter Notebooks and JupyterLab.
Stable installation of Napari on a M1 Mac
In case you’re having problems installing Napari on your M1 Mac, try to install it from conda instead of pip.
Using Zarr for images – The OME-ZARR standard
As for any other NumPy array, we can use the Zarr file format to store image files. In this post we additionally explore the NGFF (next-generation file format) OME-ZARR standard.
Zarr – or: How to save NumPy arrays
What is Zarr and why is it probably the most suitable file format for saving NumPy arrays?
How to read patch clamp recordings in WaveMetrics IGOR binary files (ibw) in Python
This is a mini tutorial on how to read patch clamp recordings in WaveMetrics IGOR binary files (*.ibw) in Python using the neo and igor packages.
How to add statistical annotations to matplotlib plots
This mini tutorial shows, how to add statistical annotations to matplotlib plots with just a few commands.
The Feynman method as an effective learning tool
The Feynman method can help you not only to remember new knowledge, but also to really and deeply understand it.
Variable Explorer in Jupyter Notebooks
Extend your Jupyter environment with Notebook Extensions and enable, e.g., the option to explore your currently defined variables in a running Jupyter session.
How DEVONthink’s auto-WikiLink feature changed my Zettelkasten workflow
DEVONthink’s automatic WikiLinks function is a powerful tool, both for discovering connections between notes – expected and unexpected ones – and for the automatized linking of these notes. In this post I briefly explain, how this feature has impacted my Zettelkasten workflow.
DEVONthink Markdown Table-of-Contents generator
I wrote a custom AppleScript for DEVONthink Markdown files, that bypasses the problem of broken links in the auto-generated Table-of-Contents (TOC) of MultiMarkdown (MMD).
Floating Back-to-top button for Markdown documents
You can quickly add a floating Back-to-top button to your Markdown documents in just two steps.
Use your Zettelkasten as a research, thinking and learning tool – Personal knowledge management as a system
In the last part of the series about personal knowledge management, we dive deeper into the Zettelkasten method and demonstrate, how to integrate all parts as an overall system into our research workflow.
Take smart notes with the Zettelkasten method
With the Zettelkasten method by Niklas Luhmann, we give the previously presented personal knowledge network a concrete shape and practical implementation. This is the second of three parts of the series about personal knowledge management.
Don’t take isolated notes, connect them! Vannevar Bush on building a self-organizing network of knowledge
In 1945, Vannevar Bush presented his concept of a self-organizing personal knowledge network by linking informational units with each other. This concept, that would later be known as the Hypertext concept or Hypertext theory, provides the theoretical base of the personal knowledge management system presented in the short series on that topic. This is the first of three parts of that series.
Boost your research with a smart personal knowledge management system
My next posts will be a short series about personal knowledge management and how it can be integrated as a holistic system into our overall research workflow. The system is based on the Hypertext Theory and the Zettelkasten method, and its core element is the personal note-taking process. We go step by step through all parts and see, how we can practically implement them into our daily research work.
Clean Thesis: A simple and elegant LaTeX thesis template
If you’re looking for some inspiration for your thesis, I just came across Clean Thesis by Ricardo Langner, a simple and elegant LaTeX template for thesis documents.
Using Markdown for note-taking
It might be a bit difficult to learn at the beginning, but there are several benefits of taking personal notes in Markdown. Here is why I switched.
The quickest way to find help for Python commands: The help() command
Python’s built-in help system is probably the fastest way, to quickly look up Python commands and their syntax. It works without leaving your Python environment and is fully offline available.
On teaching
I strongly believe that teaching is not a unidirectional thing, but both sides, the participants and the teacher benefit from it. This is a personal comment on teaching.
My website is now completely cookie-free
I made several changes to my website to further increase the privacy protection. As a result, it runs now completely without cookies.
New Teaching Material: Python Cheat Sheets
I’ve started a collection of various Python cheat sheets that contain some useful and commonly used commands and usage examples.
New Teaching Material: Statistical data analysis and basic time series analysis with Python
I’ve added two new tutorials in the teaching section on statistical data analysis and basic time series analysis with Python.
New Teaching Material: Analyzing IGOR binary files of patch clamp recordings
I’ve added a new tutorial in the teaching section on how to read and process IGOR binary files (ibw) of patch clamp recordings.
Create fancy text styles with Unicode
I found an online font generator to create fancy text styles, simply by using Unicode letters.
New Teaching Material: Fiji short course
There is a new tutorial in the Teaching Material. It’s a short Fiji tutorial on analyzing biomedical image data.
On website subscriptions via RSS and Atom feeds
Personal opinion on how to create and maintain personal news feeds beyond the dependence on big social media and tech companies.
strftime Cheat Sheet
Cheat Sheet on formatted date and time strings used, e.g., in Python, C/C++ or even on Jekyll websites by using Liquid tags.
Liquid Cheat Sheet
This Cheat Sheet gives an overview of Liquid syntax commands one might encounter while developing a Jekyll website.
Minimal Mistakes Cheat Sheet
A quick overview of available commands for creating content with the Minimal Mistakes Jekyll theme.
New Teaching Material: LaTeX Guide
I’ve added a LaTeX guide to the General Teaching Materials in the teaching section. It serves as a Getting started with LaTeX guide and as a LaTeX glossary.
Building New Universes
Lost&found: In the wake of the redesign of my website, I’ve rediscovered an old project from 2016, where I created imaginative sceneries by using water, oil, transparency film and a camera.
About my MINIDISKO project
MINIDISKO is a series of kitschy postcards, that I create from time to time. It’s a charity project, all profits will be donated to a non-profit, charitable organization.
About Weekend Stories
Weekend Stories is my on-going photographic diary project, where I collect everyday stories (mostly) occurring on the weekends.
I switched to Jekyll websites
I have redesigned my website and moved it to a new host as well: I’m running it as Jekyll website hosted on GitHub now.
I’m moving to a new web host
I’m currently transferring the content from my former website hosting service to a new one. This transfer is not yet completed (as of mid of July, 2021). Please stand by, I give my best to finish the transfer as soon as possible.
IDAHOT (International Day Against Homophobia, Transphobia and Biphobia, May 17)
Today is the International Day Against Homophobia, Transphobia and Biphobia ꜛ. As a small contribution to the fight for equal rights, I’ve redesigned my “heart” graphic and I will share it on my social media accounts. Feel free to re-share it anytime.
Material Design
In 2014, Google introduced its new design language Material Design ꜛ. I was fascinated by its design concept:
Study with Colored Pencils
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Searching for a new desktop wallpaper, I took some photographs with colored pencils. For the first time, I worked with my little improvised studio. You can download all images as desktop-wallpapers (16:9, mid-res: ~3MB, hi-res: ~70 MB) for your personal use, they are running under Creative Common license CC BY-NC-ND 4.0 ꜛ.
Original articles on this blog are CC BY-NC-SA licensed unless otherwise stated.