A modern platform that allows to create dashboards from bioinformatics workflows outputs.

Build dashboards from production workflow results like:

Interactive Dashboards

Create customizable dashboards with real-time data interaction

Cloud-Ready

Designed for cloud environments with Kubernetes support

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Project Overview

In the field of bioinformatics, researchers often face significant challenges when working with frequently executed production workflows, especially in managing and analyzing large-scale datasets. Despite the availability of numerous bioinformatics tools, there is a notable absence of platforms specifically designed for seamless integration with production workflows, which include standardized data ingestion, QC monitoring, and results exploration.

Depictio addresses this gap, offering a generic and centralized platform that allows to integrate workflows output data in order to build interactive dashboards, facilitating downstream analysis and QC metrics monitoring into a cohesive system. Depictio provides a scalable, flexible, and open-source solution tailored to meet needs of researchers handling large datasets generated by production workflows, agnostically of their execution engine (nextflow, snakemake, galaxy, R …).

Key Features

Data Ingestion

• Manual or Automated: Data ingestion can be triggered manually or through a watcher system
• Client-side scan & processing: Depictio-CLI (using typer python package) allows to scan and process data locally, pushing to the S3 bucket the resulting data format ready to be used by the dashboard
• Data Types: Support for tabular data formats (Parquet, CSV, JSON, TSV, compressed/uncompressed) using Polars and Delta Lake format

Frontend

• Customizable Dashboards: Design and customise dashboards easily
• Interactivity: Explore data dynamically with instant updates in response to selections and inputs applied to the dashboards components
• Project-based Organization: Organize dashboards according projects, allowing easier management and sharing

System

• Scalable and Cloud-Oriented: Built for cloud environments with Kubernetes and Docker-Compose support
• Open-Source and Shareable: Community-driven development model with transparent deployment

Getting Started

Ready to get started with Depictio? Check out our installation guides:

• Docker Compose Installation - Quickest way to get started
• Kubernetes Installation - For production environments
• CLI Installation - For data ingestion and management

Funding

Marie Skłodowska-Curie Grant

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945405

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ARISE Programme

ARISE is a postdoctoral research programme for technology developers, hosted at EMBL.

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EMBL

The European Molecular Biology Laboratory is Europe's flagship laboratory for the life sciences.

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Academic Partners

SciLifeLab Data Centre

SciLifeLab Data Centre provides data-driven life science research infrastructure and expertise to accelerate open science in Sweden and beyond.

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