[AI] How to effectively use AI agents: a lesson learned from paper summary skills
Like many scientists and engineers, I have been working hard to leverage AI to boost my productivity by automating routine tasks—such as writing LinkedIn posts to summarize research papers—and generating code so that I don’t have to memorize every syntax.
However, I have mixed feelings about the power of AI tools like Claude Code, Gemini CLI, or Qwen-code. On one hand, they are incredibly effective at generating ideas I hadn’t considered, such as finding the perfect word to refine my meaning.
[VS code] How to use Google Colab in VS Code
Recently I found that I can use Google Colab in VS Code, which is very convenient. In this post, I will show how to do it.
Install Google Colab extension First, you need to install the Google Colab extension for VS Code.
You can find the extension by searching the Extensions view in VS Code for “Google Colab” and then install it, as below:
Collect to Colab Restart VS Code after installing the extension, and then open a Jupyter notebook file (.
[Python] Install quarto in Windows
Quarto is a popular tool for creating dynamic documents, reports, presentations, and websites using markdown and code. It supports multiple programming languages, including Python, R, and Julia.
When I installed it in my Windows, I found some challenges to make it find correct python in different environments, so I would like to share my experience here to help you.
Installation You can download the installer for Windows from the official Quarto website: https://quarto.
[R] Setting Up an Interactive R Shiny Plotting App
I have an ieda of creating a shiny app to create all kinds of plots interactively, so that users can choose their color, symbols, etc, which is very useful for data exploration and make a publication-quality figure.
Today, I make it and published it at https://fortune9.shinyapps.io/interactive_plot/. The source code is at github https://github.com/fortune9/interactive_plot.
This guide focuses on the infrastructure setup for creating and deploying an interactive plotting application using R Shiny.
[Python] How to install pyenv-win?
If you have used pyenv on Linux or Mac, you may want to use pyenv-win on Windows.
Basically, these tools allow one to easily switch between multiple versions of Python.
There is already a good document for how to install pyenv-win in windows at https://github.com/pyenv-win/pyenv-win?tab=readme-ov-file#installation. In this post, I would like to share my experience and share some tips/tricks you may need in your setup.
Installation I started with the git method, so what I did were as follows:
[R] Use new_scale_xxx() function to add the same scale type in different ggplot layers
In one ggplot figure, normally you can only use one scale for each aesthetic mapping. For example, if you use scale_color_manual() to set the color scale for a layer, you cannot use another scale_color_manual() for another layer, or set the color scale more then once in the function aes(). However, you can use the new_scale_color() function from the ggnewscale package to add a new scale for the same aesthetic mapping in different layers.
[Linux] How to escape single quote in 'sh -c'
Sometimes, you need to run a command in ‘sh -c’ and to avoid its subshell expression is evaluated in parent shell, you need to put the command string into a single quote, like:
1 sh -c 'a="hello world"; echo $a' However, for some commands in the command string, you need to use single quote such as awk, and how do you escape the single quote in the command string?
[R] How to create errorbars with overlaid points using ggplot
library(ggplot2) library(dplyr) Sometimes you may want to create a plot with the following features:
a point to indicate the mean of a group error bars to indicate the standard deviation of the group and each group may have subgroups, which are represented by different colors. In this post, I will show you how to create such a plot using the ggplot2 package in R.
We will use the builtin mtcars dataset as an example.
[git] Exclude a path when staging files
Occasionally, you may want to exclude a specific path when staging files in Git. This can be useful when you have a directory with many files, but you only want to stage some of them. Today I will show how to do it.
Preparation First, let’s clone a git repository and create some files to demonstrate the process.
The repository used here is one of my own, which contains some bioinformatics tools.
[Linux] How to set limit on memory usage in a shell?
Occasionally, my computer crashed when I ran a program which ate up all the memory. To prevent this from happening again, I want to set a limit on the memory usage in a shell, so any command run in that shell will be limited to set memory usage.
My system OS: Ubuntu 22.04 Solution not working I searched Google and many suggested to use
1 ulimit -m <value> to set memory usage, but it did not work – no restriction on memory at all.