A selection of projects that Scientific IT Services (SIS) have worked on.
Genomics Facility Basel
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
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:
OpenSWATH Proteomics Workflow
The Aebersold Lab at the
Institute of Molecular Systems Biology
is developing and using
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
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)
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
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