A selection of projects that Scientific IT Services (SIS) have worked on.

Genomics Facility Basel

The Genomics Facility Basel gives researchers of the life science community in Basel and at ETH Zurich direct access to next generation sequencing (NGS) and complementary genomics technologies. We assisted them and developed software to manage and track sequencing data. Read about our work for the Genomics Facility Basel.

Data Management for High-Throughput Metabolomics

The Sauer and Zamboni Labs pursue a strongly data-driven research approach largely based on mass spectrometry and fluorescent microscopy running several hundreds of experiments and > 100’000 mass spectrometry runs per year. We provide the High-Throughput Metabolomics data management solution to the labs.

Single Cell Force Spectroscopy Analyzer

Atomic Force Microscopy (AFM) allows imaging, measuring, and manipulating matter at the nanoscale level. SIS developed the Single Cell Force Spectroscopy Analyzer to support researchers in using AFM for measuring the force between two living cells.

envipy software for EAWAG

EAWAG researchers use LCMS to track water quality, for example in swiss lakes and rivers. We took over existing algorithms developed in R and integrated them into a versatile application with a graphical user interface for end users. See envipy Software for EAWAG.


Big data analysis often exceeds the capabilities of researchers own desktop computers or institutes computing servers. Using the ETH HPC infrastructure we implemented algorithms for finding patterns in large text corpuses: Sparkgram.

OpenSWATH Proteomics Workflow

The Aebersold Lab at the Institute of Molecular Systems Biology is developing and using the new SWATH technology to analyze protein compositions of diverse biological samples. We established a data analysis workflow in close collaboration with members of the Aebersold Lab: OpenSWATH Proteomics Workflow.

Multi-view Reconstruction for Light-sheet Microscopy

We implemented an existing workflow for automated reconstruction of multi-view image data acquired with a light-sheet microscope. The workflow enables researchers to offload this time consuming analysis from their local desktop machines to the ETH cluster computing infrastructure. It was implemented in close collaboration with members of the group of Dagmar Iber. Read more

Image Background Correction Workflow

We implemented a workflow for background correction of microscopy images for the Cell Systems Dynamics group of Timm Schröder to analyze their images on a compute cluster and to track this process for enabling reproducibility of their results. Read more about the Image Background Correction Workflow.

Mass-Spec Software Environment emzed

The software application Mass Spec Software environment emzed was developed to facilitate development of individual analysis workflows for liquid chromatography-mass spectroscopy (LCMS) data.

MediaWiki plug-in for annotating parts of pages​

YATA (Yet Another Text Annotation) is a plug-in for MediaWiki developed for the Wagner group in D-GESS. A requirement was to be able to search on categories and display the context of the matches. Read more

Utility and Ecoval​

The R packages ecoval and utility are tools to assess natural morphology of surface waters, or of plants in rivers from EAWAG SIAM. EcoVal UI is a stand-alone installer and user-friendly graphical interface for these packages such that cantonal administration offices can easily interact with the R packages.​Read more

Biomechanical Analyzer​

The Biomechanical Analyzer is a web-based analysis and visualisation tool to upload, process, store and analyze curves from an atomic force microscope developed for the Nash Group at the University of Basel and BSSE. Read more