When using pixi to manage bioinformatics analysis environments, we often encounter issues where some Bioconductor R packages show missing dependencies after installation. The exact cause of this problem is currently unclear. After using pixi for a year, this issue still hasn’t been fixed (as of October 2025). This article introduces how to use pixi’s tasks feature to resolve such problems.

In our current single-cell analysis pipeline based on scanpy, there’s a step that requires saving AnnData objects in loom format. However, unlike saving to h5ad format, when we write an AnnData object to a loom file without any special handling and then read it back, we find that the index information of obs and var (typically cell barcodes and gene names) is lost, and these indices become ordinary numeric identifiers.

Milo is a differential abundance analysis method for single-cell RNA sequencing data that can detect compositional changes in cell neighborhoods across different conditions.

DevPod is an open-source development environment management tool that allows you to create development environments similar to GitHub Codespaces on any Kubernetes cluster or Docker host. This article will introduce how to use the DevPod CLI to create workspaces and provide a detailed explanation of writing DevContainer configuration files.

As my classmate said, I’m currently experiencing a situation of “being forced to code”… The several websites I maintain each have their own frontend, backend databases, and some even have test code and migration code, involving languages ranging from Python commonly used in bioinformatics to JS, TS, HTML, C#, which I rarely used before. In actual work, there isn’t much time to systematically learn each language from scratch, so mastering the most basic debugging methods is crucial. Among them, I find the debugging methods for JavaScript and TypeScript particularly worth recording, as they do have some unique aspects compared to other languages.

Uptime Kuma is an extremely user-friendly open-source monitoring tool that makes monitoring various network services simple and efficient. It supports multiple protocol monitoring including HTTP(s), TCP, Ping, DNS queries, and even simulates real user access through Chrome engine mode to more accurately monitor service stability. Additionally, it supports dozens of notification methods for alerts and can integrate with various applications we use daily. It also offers a unique Push monitoring method, allowing users to extend monitoring functionality through custom code (such as monitoring SSH service availability).

In cancer research, comparing genomic features between tumor samples and organoid models is crucial for validating model reliability. Circos plots provide an intuitive way to visualize detected mutations across the genome, making them commonly used for representing overall detection results of representative samples. While reading the circlize documentation, I came across an example demonstrating paired samples, which I found suitable for showcasing paired primary samples and organoids. I’ve adapted it to create a plot for displaying paired samples. The code is primarily based on the official documentation’s 9.5 Concatenating two genomes

Last year, I actually used Fydetab Duo to compress videos from my travels. At that time, I found a pre-built library on GitHub, but now I can’t find that repository anymore… So this time, I tried to compile it myself…

There are really many modules for rapidly developing data or AI-related applications in Python. I’ve already used Dash, Streamlit, Gradio, NiceGUI, and recently I discovered two more. Just when I needed to develop a simple data dashboard to display company data, I once again recklessly decided to use a new framework - Taipy.

Picking up from where we left off, after successfully compiling the code in the libapp project, the next steps are: modifying the libapp code and applying the changes to the image.