Blog

Technical articles from the Data Intuitive team on bioinformatics workflows, Viash, Nextflow, single-cell and spatial omics, reproducibility and data infrastructure.

Blog

Blog

Field notes from our team on bioinformatics, workflow engineering and the software side of science.

Interoperable single-cell pipelines with anndataR and Viash

Single-cell transcriptomics analysis is split across two language ecosystems.

A Deep Dive into Nextflow’s Asset Caching

At Data Intuitive, we deploy data workflows at scale using Viash, a framework that allows us to build reusable Nextflow modules and an accompanying Docker container from…

Dries Schaumont

European Infrastructure for Secure Drug Discovery R&D

Modern drug discovery R&D depends on large, sensitive, and strategically critical datasets-multi-omics, imaging, formulation data, PK/PD models, and advanced analytics.

Making Sense of Multiomics Data

The use of multiomics technologies and analysis for research continues to expand in academia and across industry.

J.P. Morgan 2026: From AI Hype to ROI

It wasn’t foggy, but sunny.

2025: from one-off analyses to workflows that last

As 2025 comes to an end, many teams working in computational biology are noticing a shift.

Turning R&D Into Scalable, Reproducible Solutions

At this year’s NextGen omics conference in London, we explored one of the most persistent challenges in bioinformatics: how to transform fast-moving R&D work into…

Single-Cell: Where Machine Learning Meets Biology

Single-cell analysis stands at the intersection of machine learning (ML) and biology, with advances in microfluidic technology generating massive datasets that are ideal…

Re-thinking user-friendly computational workflows

Modern-day computational workflows often combine tens to a hundred different computational steps.

End-to-End Workflows for Spatial Omics Data Processing

viash catalogue

OpenPipeline Spatial delivers technology-agnostic, end-to-end workflows for spatial omics data processing, supporting platforms like 10X Xenium, NanoString CosMx, and…

Easy H5AD access in R with anndataR

A best practices approach to single-cell analysis requires combining methods from the three major ecosystems: scverse for Python and Bioconductor or Seurat for R.

Automated Demultiplexing and Processing of High-Throughput Transcriptomics

A fully automated high-throughput RNA-seq workflow built with Viash and Nextflow for a top-10 pharma R&D client, featuring CSV-driven automation and modular subworkflows.

How to Avoid the GitHub Graveyard?

Each summer a familiar scene repeats itself across research groups and R&D units: students graduate, postdocs move on, contractors wrap up.

Webinar: Mastering Bioinformatics Data Workflows

On May 15, we hosted a free webinar that brought together deep technical insights and real world experience on how to build robust, sustainable and efficient…

Mastering Bioinformatics Tool & Workflow Management with Viash

Are you a bioinformatician tired of spending hours configuring environments, debugging container arguments, or struggling with complex workflow maintenance?

Why modern omics data projects need better workflow tools

In today’s fast-paced research and development environments, the ability to build, maintain and scale data processing workflows efficiently isn’t just a technical…

10 Common pitfalls in omics data processing

In today’s data-driven world, efficiently processing and analyzing large volumes of biological data is crucial for organizations to maintain a competitive edge and…

Data Intuitive fuels Tabula Sapiens v2

We’re thrilled to share the exciting news of the Tabula Sapiens v2 preprint launch on bioRxiv!

Navigating the use of LLMs for Code Generation

Data Intuitive is committed to streamlining bioinformatics workflow development processes.

Standardizing Benchmarks in Spatial Omics with OpenProblems

Spatial omics is an emerging field that is allowing researchers to unravel the complexities of cellular organization and function within their native tissue context.

Sai Nirmayi Yasa

Technical overview: how Viash works in practice

Viash is a command-line tool that transforms scripts into self-contained, reusable and reproducible components.

Running OpenPipeline on public data

Effortlessly execute Openpipeline workflows from its open-source repo using a straightforward, user-friendly process on nf-tower

Explainer animation Viash

1 minute explainer video about the possibilities of Viash

Why use Nextflow and Viash?

Nextflow is a leading workflow manager in computational biology, known for its portability, scalability, and reproducibility.

Viash Basics Demo

Watch our screencast demonstration to see the getting started script of Viash.io in action.

ComPass: Connectivity Map Data Analysis

ComPass is an open-source application for querying and analyzing Connectivity Map (L1000) data, developed by Data Intuitive with customization capabilities for pharma…

Phylotrees for Virusbank

Data Intuitive developed the computational toolbox for the VirusBank Platform, a KU Leuven initiative creating a strategic collection of viruses for pandemic preparedness…

anndata: annotated data in R

anndata is a commonly used Python package for keeping track of data and learned annotations, and can be used to read from and write to the h5ad file format.

Processing Single-Cell Data at Scale

viash catalogue

OpenPipelines delivers best-practice, modular Viash and Nextflow workflows for single-cell single- and multi-omics data analysis, developed in collaboration with a leading…

A Practical Approach to Model Error - Part 2

It’s been a while since I first wrote about tackling model error using a simple model.

Bring us the question you keep re-answering.

In 45 minutes we listen to what you need, mark what already runs for your instrument and kit and think through how we would solve the rest with you.