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Hello, I'm Thomas Weber! 👋

I'm an ARISE fellow hosted in the Data Science Centre of the European Molecular Biology Laboratory (EMBL) in Heidelberg. I have a PhD in bioinformatics and I'm passionate about combining advanced data science workflows and technologies to drive research and innovation.

👨‍💻 Technologies & Interests

  • Bioinformatics Workflows: Snakemake, Nextflow, and Galaxy
  • Containerization & Orchestration: Docker and Kubernetes
  • Data Visualization: Expertise in Plotly Dash for creating interactive data visualizations
  • Home Automation & DIY Tech: Enthusiast of Home Assistant, Zigbee, ESPhome, and 3D printing
  • Self-Hosted Tools: Managing personal server with Plex, Immich, Bitwarden, OctoPi, NPM, Glances, Authentik, ...
  • Exploring New Technologies: Currently diving into no-code tools like n8n, and LLM technologies including LangChain and Ollama

🌟 Highlighted Projects

  • Depictio - My main ongoing project.
  • Mosaicator Pipeline v2 - Recently updated and published the version 2. Structural variant calling from single-cell Strand-seq data using Snakemake.

📫 How to Reach Me

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Thomas Weber's Projects

ampliseq icon ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

chat-gpt-starter icon chat-gpt-starter

This is a Python Flask starter pack for a ChatGPT project that uses OpenAI API to create a ChatGPT chatbox.

mosaicatcher icon mosaicatcher

Processing of raw Strand-seq data as part of the SV calling pipeline

multiqc icon multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

nahrwhals icon nahrwhals

R package and wrapper functions for identifying serial structural variations from genome assemblies

pipeline icon pipeline

Integrated workflow for SV calling from single-cell Strand-seq data

sapporo-service icon sapporo-service

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification.

sapporo-web icon sapporo-web

A web application for managing and executing WES services.

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