What we’re about
A meetup for Bioinformatics students, researchers, academics and curious people about how Python can be used to solve biological problems related with DNA and Protein sequences.
There will be 2 talks:
1- Python for Bioinformatics book presentation (a book will be drawn among the attendants).
2- From Legacy to the Future, a tale on how we help our clients to build flexible and scalable data models
A 2 day course on Docker for bioinformatics.
In today’s data-driven life sciences landscape, reproducibility, scalability, and environment consistency are critical. This intensive, hands-on course is designed to quickly equip researchers, bioinformaticians, and data scientists with the practical Docker skills needed to run reproducible scientific workflows. While the examples and hands-on labs focus on bioinformatics, the principles and skills you will learn are universally applicable to any data science, machine learning, or software development project. Participants will learn how to containerize bioinformatics tools, manage dependencies, and deploy reproducible pipelines.
Day 1 (Saturday, August 16):
Core Concepts: Virtual machines vs. Containers What is containerization? Key differences between a Virtual Machine and a Container. Docker's architecture: Docker Engine (Client, Daemon) and Docker Hub Alternatives to Docker: Podman
Essential Docker Skills Images: Finding and fetching images from Docker Hub (docker search, docker pull).
Containers: Running a container from an image (docker run). Running modes.
Management: Listing, stopping, and removing containers (docker ps, docker stop, docker rm). Mounting volumes to access files outside the container. Using Docker with GPU Access for AI Workloads.
Hands-On Lab: Pull and run bioinformatic workloads with Docker or Podman Running docker in Interactive, Foreground and Detached mode.
Day 2 (Saturday, August 23):
Building Your Own Images
Introduction to the Dockerfile. Core instructions: FROM, WORKDIR, COPY, RUN, and CMD.
Building a custom image using docker build. Building strategies: deb, conda, source code, binaries and others
Multiplatform support: AMD64 (x86_64) and ARM64 (aarch64)
Tagging images for versioning.
Pushing to Dockerhub and to ECR (AWS) Best practices.
Hands-On Lab: Build a new image using an existing Dockerfile Modify an existing Dockerfile and build the new image Dockerize a bioinformatic program Push the new image to Dockerhub or ECR
Requirements for Participants:
- Laptop: Participants must bring their own laptop for the hands-on lab sessions.
- Software: Please have either Docker Desktop or Podman pre-installed on your laptop.
- Command Line: Participants will use the command line. We will teach all the necessary commands to successfully complete the labs, but a basic familiarity with the terminal is recommended.
Where to register: https://lu.ma/docker-life-science
## About us: Toyoko is the main author of OmicsContainers, a project that features a curated collection of containers for bioinformatics (https://github.com/DNALinux/OmicsContainers)
Upcoming events (1)
See all- Accelerated Docker Skills for Life Sciences ResearchFrontier Tower - Biotech Lab, San Francisco, CA
A 2 day course on Docker for bioinformatics.
In today’s data-driven life sciences landscape, reproducibility, scalability, and environment consistency are critical. This intensive, hands-on course is designed to quickly equip researchers, bioinformaticians, and data scientists with the practical Docker skills needed to run reproducible scientific workflows. While the examples and hands-on labs focus on bioinformatics, the principles and skills you will learn are universally applicable to any data science, machine learning, or software development project. Participants will learn how to containerize bioinformatics tools, manage dependencies, and deploy reproducible pipelines.
Day 1 (Saturday, August 16):
Core Concepts: Virtual machines vs. Containers What is containerization? Key differences between a Virtual Machine and a Container. Docker's architecture: Docker Engine (Client, Daemon) and Docker Hub Alternatives to Docker: Podman
Essential Docker Skills Images: Finding and fetching images from Docker Hub (docker search, docker pull).
Containers: Running a container from an image (docker run). Running modes.
Management: Listing, stopping, and removing containers (docker ps, docker stop, docker rm). Mounting volumes to access files outside the container. Using Docker with GPU Access for AI Workloads.Hands-On Lab: Pull and run bioinformatic workloads with Docker or Podman Running docker in Interactive, Foreground and Detached mode.
Day 2 (Saturday, August 23):
Building Your Own Images
Introduction to the Dockerfile. Core instructions: FROM, WORKDIR, COPY, RUN, and CMD.
Building a custom image using docker build. Building strategies: deb, conda, source code, binaries and others
Multiplatform support: AMD64 (x86_64) and ARM64 (aarch64)
Tagging images for versioning.
Pushing to Dockerhub and to ECR (AWS) Best practices.Hands-On Lab: Build a new image using an existing Dockerfile Modify an existing Dockerfile and build the new image Dockerize a bioinformatic program Push the new image to Dockerhub or ECR
Requirements for Participants:
- Laptop: Participants must bring their own laptop for the hands-on lab sessions.
- Software: Please have either Docker Desktop or Podman pre-installed on your laptop.
- Command Line: Participants will use the command line. We will teach all the necessary commands to successfully complete the labs, but a basic familiarity with the terminal is recommended.
Where to register: https://lu.ma/docker-life-science
## About us: Toyoko is the main author of OmicsContainers, a project that features a curated collection of containers for bioinformatics (https://github.com/DNALinux/OmicsContainers)
