Cifonauta 2.0 went live last week! It’s been almost two years of work since our project to modernize the image database was approved. Link: https://cifonauta.cebimar.usp.br The site now has a responsive interface for mobile devices and a new administrative dashboard for users and curators of the database. Yes! We will gradually open up the database […]
Category: code
Posts about software that I wrote myself or that I use often. From small commands to scripts to full-stack applications.
The botsin.space community, a popular Mastodon server for automated accounts (bots), will be retiring soon. They have been kindly hosting EvoDevo Papers for the past couple of years. To avoid any downtime, I recently migrated the account to a new server, the biologists.social community managed by The Company of Biologists. I think it’s a great match, […]
Djot is the potential successor to Markdown (the popular lightweight markup format for plain text files). It provides better-defined standards compared to the original Markdown, which make parsing easier while still keeping the sample principles of readability (see Beyond Markdown). It is being developed by John MacFarlane, the creator of CommonMark (the main Markdown specification) and Pandoc (the universal file type converter). Here’s […]
Summary To add data from a ManyToManyField to a SearchVectorField, you can join the related values in a string and pass this string as a Value() expression to the SearchVector object: Cifonauta’s full-text search During the past year, we’ve been working on several updates for modernizing the Cifonauta database. The website now has a fully […]
EvoDevo Papers is a bot that shares research articles in the field of evolutionary developmental biology (or evo-devo). Originally, I created it as a Twitter bot, and everything was going well for years… until Twitter’s takeover. The new policies and API restrictions made it unsustainable to continue posting there. In response to that, I decided […]
I’m refactoring the image processing functions of the Cifonauta database and wondering if there’s any Python library with native video processing capabilities. For the past years, I used a subprocess.call() to run a FFmpeg command to scale down and convert video files for the Cifonauta website (which is Django-powered). The ffmpeg command has some niceties […]
Blog posts are an invitation to interact. This usually happens in the comments section down below. But, posting public comments isn’t for everyone and it’s not the best option for every type of conversation. Often, a more direct and private response works better. As an alternative to regular comments, I added a reply by email […]
After posting the first version of our cephalic furrow pre-print, I received an email asking for further technical details about using the CARE upsampling module to restore the Z-resolution of lightsheet datasets: I am curious about some details of your “Pre-patterned epithelial invagination prevents mechanical instability during fly gastrulation” paper. You mention that you trained […]
This blog is now connected to the Fediverse. If you have a Mastodon account, you can see the new posts in your timeline. To follow, login to your Mastodon instance and search for @blog@brunovellutini. You should see something like this: The feature is still experimental. It works via the ActivityPub plugin from WordPress. In fact, […]
Zim Desktop Wiki is my primary note-making software. I use it to take notes, organize my projects, manage daily and long-term tasks, grow a digital garden, keep a journal, and more. Zim is great for the desktop, but it lacks a mobile app. So I’ve been using Simplenote for saving notes on the go. The […]