Basel, Basel, Switzerland
Degree in Medical Informatics with long experience in Bioinformatics and data management in research environments
- Spatial RNASeq: 10x Visium HD - scRNAseq - Kubernetes - MongoDB -Angular, React - Rancher - besca/scanpy/squidpy - Github Actions - Gitlab CI/CD - Python: Jupyter lab, Sphinx, poetry - FastAPI - Illumina InterOP - Streamlit - marimo.io -LangChain
• Data Management for SARS-COV2 strains / MF 2 - Genome Sequencing and Genomic Epidemiology / Robert Koch Institut (RKI) Data management with FAIR principles Data upload, GISAID & ENA • Full Stack Developer / Library Information Science (LIS) team / AbbVie Knowledge and data extraction, ontology-enabled text and data mining from scientific literature, patents, and other information resources, as well as semantic enrichment, visualization and library information search services New features and bug fixing of a Flask-based web application including D3js-based visualizations • Software Engineer and Architect / Web app / University Hospital Basel, Neurology React.js based front end app for eEDSS Score Assessment (Multiple sclerosis) Bug fixing of Java based back end • Software Engineer / Build process automation / Internal Migration from make files to Gradle for Argus Dissolution software • Application specialist / Confluence and Jira / Internal Installation, configuration and maintenance of Confluence and Jira. Based on Docker • Software Engineer / Web app for mobiles / University Hospital Basel Node.js based web app which queries the internal LDAP/AD for phone numbers, email addresses, etc. • Data Scientist / Audit Trail Review / Carbogen Audit Trail Analysis using pandas, altair and Jupyter lab • Business Analyst / Decision support / Roche Business Analysis and Data Science Analysis for Roche pREDi, Basel in the field of compound logistics • Software Engineer / Source Version Control / Internal Responsible for the migration from svn to Gitlab based on Docker at wega Informatik, including the operation • Software Architect / Database modeling / SBP Database modeling for the Swiss Biobanking Platform, Lausanne
• Built up the Genomics Facility Basel on the IT side to serve more than 80 research groups in the academic field Coordinated, implemented and managed: data dissemination, billing, automatic email notification, fully automated demultiplexing, single cell worflow analysis, reporting, assessment of scientific software for data analysis • Project lead in introducing openBIS as a Meta Data Management system for NGS sites at NIBR (Basel & Cambridge, US) • DevOps of production instances (>20) of our own developed Data Management Software called openBIS including the ELN/LIMS extension • Integration of big data amount from technical devices, especially Illumina/PacBio sequencers and 10x Genomics. The distribution of data for our collaborators is a crucial part of this and is highly automated • Established pipelines for automatic analysis of NGS (Next Generation Sequencing) data, due to the emerging technology a constant adoption is needed • Experience in several pipelining SW like snakemake, Nextflow, Galaxy and Big Data Script • PostgreSQL administration that includes minor and major upgrades of production databases. Analysis and implementation of performance issues; reliability and disaster recovery • Visualization of sequencing results based on JavaScript (jQuery & D3.js) • Grid integration of openBIS with OGE and the ETHZ Euler cluster (LSF) • Responsible for the availability and updates for the data share application called CIFEX which is exposed ETH wide • BA tasks for scientists and cross functional teams and implementing solutions for them, regarding data management and/or NGS analysis • Contribution to an open source project called illuminate (https://bitbucket.org/ilmn8/illuminate) • Close collaboration on data sharing and data exchange with University of Basel (sciCORE) and the FMI • Basic knowledge about Apache Spark • Experience in RNA-Seq, DNA-Seq and ChIP-Seq data analysis and the complete software stack
- Maintenance, Monitoring (EM Grid Control) - Backup (RMAN) and Patching of 9i, 10g and 11g Oracle DB - Consulting of Oracle specific questions inside and outside of the company - Maintenance of Active Directory - MSI-Deployment - General system administration and IT support - Administration and Backup Concept for OTRS and the underlying MySQL DB - Maintenance of an ERP system: ]Project open[ and the underlying PostgreSQL DB