Plotly Hangout featuring Thomas Weber, Research Fellow of Molecular Biology
Meet the Speaker
Adam Schroeder
Adam Schroeder is a Community Manager at Plotly.
Thomas Weber
Thomas Weber is a research fellow at the Data Science Center of the European Molecular Biology Laboratory in Heidelberg and part of the ARISE program.
The video is a Plotly Hangout with Thomas Weber, a research fellow at the Data Science Center of the European Molecular Biology Laboratory in Heidelberg and part of the ARISE program. Thomas shares how he moved from environmental engineering into bioinformatics, using machine learning to study pathogenic variants and rare diseases, which led him into data science, Plotly, and Dash.
He presents Depicto, a platform that turns complex bioinformatics pipeline outputs into interactive Dash dashboards and web applications. Built for workflows based on Nextflow and nf-core, Depicto lets researchers browse apps, duplicate templates, and edit their own versions using a drag and drop grid layout. Users can add figures, metric cards, tables, and text, either through a no code UI powered by Plotly Express or a code mode that runs restricted Python with Polars for preprocessing and Plotly Express for visualization.
Thomas shows microbiome dashboards that combine quality control and diversity analysis using components such as taxonomic composition plots, MultiQC based metrics, alpha rarefaction curves, summary cards, and filters by habitat and collection date. Under the hood, Depicto uses Polars, Delta Lake on top of Apache Parquet, FastAPI, MongoDB, S3 storage, Dash pattern matching callbacks, and deployment options with Docker, Kubernetes, and SciLifeLab infrastructure, with future work around Celery background callbacks and DuckDB joins for large datasets.
He closes with career advice on bioinformatics and a key engineering lesson to keep systems as simple as possible before adding complexity.
