The blog of a juvenile Geekus biologicus

Query a BioPAX ontology with DuckDB

Mon, 28 Sep 2026 19:09:00 +0200

Install DuckDB

pipx install duckdb

Download PathBank BioPAX files

Throughout this blog post, we will work with example BioPAX files from the pathbank database. I downloaded the BioPAX files from https://pathbank.org/downloads on <2026-09-28 Mon>, the announced date of generation is September 13, 2019.

Load the DuckDB `rdf` extension

duckdb

INSTALL rdf FROM community;
LOAD rdf;

How to load the content of a BioPAX file with DuckDB rdf extension?

I extracted the zip archive in ~/data/pathbank/pathbank_all_biopax/pathbank_all_biopax/.

How to load the PathwayCommons OWL file into a local QLever instance?

Sun, 12 Jul 2026 10:07:00 +0200

What are we talking about?

QLever (pronounced “clever”) is a graph database for RDF triplets supporting the SPARQL query language.

PathwayCommons is an initiative to gather multiple sources of metabolic pathways, from multiple databases, and merge them in a single entrypoint, using the standard BioPAX ontology. Pathway-Commons provides a compressed OWL file for each release, as well as an API.

What do we want to do?

The objective of this tutorial is to show how one can load the Pathway-Commons OWL file in a local QLever instance, for unlimited local SPARQL queries.

How to interface TidalCycle with LMMS via MIDI ?

Sun, 07 Jun 2026 13:55:00 +0200

TidalCycle is a livecoding environment enabling live performance of code-generated music. LMMS is a digital audio workstation software. Both are free-libre opensource softwares. TidalCycle typically use SuperCollider to generate audio based on the patterns of Tidal. We can also use any device that can handle MIDI input to generate sound from Tidal patterns.

Procedure

On SuperCollider window, open startup file (File > Open startup file), then add the following code:

MIDIClient.init;

In the section where SuperDirt server starts, add the following before the ~dirt.start command:

ob-exec

Thu, 14 May 2026 10:03:00 +0200

I created a generic Org-babel mode, named ob-exec. This emacs-lisp script enable to execute any executable on a code fragment within Org-mode.

How it works

ob-exec simply execute the code sample with the provided command-line

For example, suppose you want to use the command line glpsol of the GNU Linear Programming Kit on a Linear program encoded in MathProg. To the best of my knowledge, there is no org-babel mode for GLPK. It wouln’t be too difficult to build one, but suppose further that you feel lazy and want to execute GLPK solver directly. Then, you can insert the following source code in emacs:

Tent Game in Answer Set Programming

Mon, 29 Dec 2025 18:40:00 +0100

The Tent game is a logic puzzle on a square or rectangular grid. Each grid cell can have a tree, a tent or stay empty. <Nourry (2024)>

The following rules must be respected:

Tent can be placed on empty cells.

Each tent is attached to a tree placed on an adjacent cell.

A tree cannot be attached to more than one tent.

Two tents cannot be placed on adjacent, nor diagonal cells.

The number of tents on each row and column is specified.

Some cells are not accessible, no tent can be pitched there. <“Fiche: Jeux de Réflexion - Tentes” (n.d.);Nourry (2024)>

The aim of this article is to propose a implementation of the Tent game in Answer Set Programming.

News

Sun, 14 Apr 2024 00:00:00 +0000

<2025-10-01 Wed>

Je commence une thèse au Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme au Génoscope (LABGeM). Je vais travailler sur une méthode de reconstruction de réseaux métaboliques à l'échelle des pangénomes de bactéries et d'archées.

<2025-01-01 Wed>

Je commence un stage de Master 2 au LaMME, sous la direction de Carène Rizzon, Marie Szafranski et Franck Samson du LaMME et de Emmanuelle Lerat du LBBE (CNRS / Lyon). Il porte sur la prédiction de la redondance fonctionelle de paire de gènes dupliqués chez Arabidopsis thaliana avec des approches de machine learning.

How to render pseudocode in Hugo with pseudocode.js

Sat, 09 Mar 2024 00:00:00 +0000

To render pseudocode in Hugo, you can use the pseudocode.js library.

Here is what I did to make this working on my blog.

Theme configuration

In your theme files, you will first need to add link to the library CDN.

<!-- in themes/<theme>/layouts/partials/pseucodode.html -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js"
        integrity="sha512-EKW5YvKU3hpyyOcN6jQnAxO/L8gts+YdYV6Yymtl8pk9YlYFtqJgihORuRoBXK8/cOIlappdU6Ms8KdK6yBCgA=="
        crossorigin="anonymous" referrerpolicy="no-referrer">
</script>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/pseudocode@latest/build/pseudocode.min.css">
<script src="https://cdn.jsdelivr.net/npm/pseudocode@latest/build/pseudocode.min.js"></script>

And render all element with pseudocode HTMl class.

<!-- in themes/<theme>layouts/partials/pseudocode-render.html -->
<script>
    let pseudocodeElements = document.getElementsByClassName("pseudocode");
    for (let element of pseudocodeElements) {
        pseudocode.renderElement(element);
    }
</script>

<!-- in themes/<theme>/layouts/_default/baseof.html -->
<head>

    ...

    {{ if .Param "pseudocode" }}
      {{ partialCached "pseudocode" . }}
    {{ end }}
</head>

<body>
    
    ...

    <main>
        {{ block "main" . }}{{ end }}
        {{ if .Param "pseudocode" }}
            {{ partialCached "pseudocode-render" . }}
        {{ end }}
    <main>
</body>

Writing

Then, in your Markdown article, add the following in your frontmatter:

Unixfu

Sun, 14 Jan 2024 00:00:00 +0000

A bean for some useful UNIX command snippets.

Add two hours

This could be useful for nocmig fan, to ease the hour computation of a bird contact.

hour() {
    start=$1
    duration=$2
    IFS=":" read -r duration_hour duration_minute <<< $duration
    date -d "$start $(($duration_hour * 60 + $duration_minute)) minutes" +"%H:%M"
}
hour 17:00 5:43

22:43

WAV creation datetime

Here is a small snippet that demonstrates how to get the creation date-time of a WAV file with ffprobe

Analyze projects programming languages using github-linguist

Wed, 29 Mar 2023 00:00:00 +0000

github-linguist is a Ruby library and command line tool for detecting the programming languages used in a project. It is used by GitHub to detect the language of a project and to generate language statistics.

We can use it through the command line, in order to analyze the programming languages used in a project.

During my application to bioinformatics master degree, I had to say which programming languages I commend. So here is some quick tips to use github-linguist as I learned to do for this purpose.

Astuce: Copier du texte dans le presse-papier depuis un terminal Linux

Sun, 05 Feb 2023 00:00:00 +0000

Il suffit d’installer xclip:

sudo dnf install xclip # sur fedora par exemple

Puis, c’est tout simple:

echo "Coucou !" | xclip -selection c

Un exemple d’utilisation: copier une clé publique ssh dans le presse papier depuis le terminal:

cat ~/.ssh/id_ecdsa.pub | xclip -selection c

Générer le code LaTeX/chemfig d'une réaction chimique avec Zyme

Sun, 02 Oct 2022 00:00:00 +0000

Durant les trois années de licence bioinformatique, nous avons des cours de biochimie, et ceux ci viennent avec leur lots de structure chimiques à connaître.

En L1, j’avais réalisé un document pdf avec LaTeX/chemfig des acides aminées protéinogènes en représentation de FISCHER, et j’avais trouvé ça plutôt sympa, bien que ça m’avait pris pas mal de temps à rédiger.

Ajourd’hui, j’améliore ma méthode: fini le code de la structure en chemfig (extension LaTeX) a la mano, vive le code généré par du code !

Arduino Camera Trap

Sun, 18 Sep 2022 18:15:49 +0200

Some years ago, I had the opportunity to create a camera trap based on an Arduino board. The goal of this project was to capture photos of wild animals, and to have fun with electronics and programming.

At the time, I created a website in html, to present the project; but I can’t find the source code anymore… That’s a shame.

I will try to present this old project again, hoping that it may interest someone.

How to mount a shared folder between Linux KVM Host and Guests

Tue, 21 Jun 2022 00:00:00 +0000

Sharing folder between KVM virtual machines and host, may be useful. Here is a way found in fedora forum.

Quickstart

Change vm to your vm hostname.

sudo mkdir -p /mnt/shared
sudo chmod -R a+rwX /mnt/shared
sudo semanage fcontext -a -t svirt_home_t "/mnt/shared(/.*)?"
sudo restorecon -R /mnt/shared
tee fs.xml << EOF > /dev/null
<filesystem type='mount' accessmode='mapped'>
<source dir='/mnt/shared'/>
<target dir='shared'/>
</filesystem>
EOF
virsh shutdown vm
virsh attach-device vm fs.xml --config
virsh start vm
ssh vm
sudo mkdir -p /mnt/shared
sudo tee -a /etc/fstab << EOF > /dev/null
shared /mnt/shared 9p trans=virtio 0 0
EOF
sudo mount -a

References

Virt-manager and shared folder host/guest permission issue?

How to use virtual environments

Sun, 19 Jun 2022 00:00:00 +0000

To not interfere with your os configuration and keep your project reproducible, you should use a virtual environment as long as possible.

Virtual environment are a way to isolate your project from the rest of the system, and to avoid dependencies conflicts.

Python Virtualenv

Lets start by installing the virtualenv package.

sudo apt install python3-venv

And now you can create venvs for your project:

python3 -m venv .venv/myproject

It is a good practice not to create a virtualenv with name “venv”, but to use a name that reflects the project you are working on, in order to see directly in which venv you are working.

How to make automatic documentation using Doxygen, breathe and Sphinx

Wed, 15 Jun 2022 00:00:00 +0000

Doing documentation is required, to allow people to use your project. Here I present a rather easy solution.

Analyze Ultrasound on GNU/Linux using Wine

Thu, 25 Mar 2021 00:00:00 +0000

After recording bats, orthoptera or birds sounds, it is often necessary to have a look at the spectrograms of the sounds, for instance while analyzing Vigie-Chiro Program bat records.

The software needed to do so are often developed only for Windows. In this article, we will learn how to install these softwares (e.g., Kaleidoscope, Syrinx, Batsound 4, 7-zip and Lupas-Rename).

Install Wine

Wine is a software that enable .exe software to run on UNIX systems such as Linux or Mac OS.

Mon, 01 Jan 0001 00:00:00 +0000