The bioinformatics experts at the Core Facilities center their tasks around the construction and testing of reproducible analysis workflows for the most common types of experiments performed at the Core Facilities, the initial analysis following a sequencing experiment and delivery of results to the researchers with project-specific annotations for interpretation, mainly in the field of NGS-based transcriptomics and bioimage analysis.
Analyses are run on a local workstation, a Linux virtual machine at MUV ITSC and on the Meduni Scientific Cluster (MSC, link: https://msc.hpc.meduniwien.ac.at).
We aspire to bridge the gap between wet lab experiment and data processing, with the aim to extract as much biomedically relevant information as possible from precious samples and costly experiments.
The bioinformatic services offered at the Core Facilities include:
- contact for service requests on transcriptome sequencing, regarding experimental design for complex sample group combinations, project-specific settings and tailored analyses, such as composite genomes, non-model organisms etc.
- initial data analysis for projects sequenced at the Core Facilities
- updated information on recently developed analysis software, mainly open source (incl. R/Bioconductor), as well as user-friendly desktop and web-based analysis tools
- testing of recently published analysis tools for data which are relevant in the context of the experimental portfolio of the Core Facility RNA Genomics, and eventually integration of novel tools into the initial analysis workflows
- analysis of the images produced in-house by the MACsima, CyTOF Hyperion, MALDI-MSI, Xenium, Olympus IXplore SpinSR, and other imaging instruments from our facilities
- background evaluation, and detection of imaging artifacts.
- image segmentation algorithm available for MACSima and CyTOF Hyperion. Tailored algorithms can be made on request upon agreement.
- individual consultation with customers of the Core Facilities, before or after performing a sequencing experiment
- liaising with technological companies for personalized experiments and analysis
- tutorials for colleagues at MedUni Vienna
- speaker at technological seminars and workshops
- information on computing resources for bioinformatics at MedUni Vienna jointly with ITSC
- bioinformatic networking at MedUni Vienna and beyond, including match-making of researchers with other bioinformaticians for collaborative data analysis
Mag.a Dr.in Sophia Derdak
Bioinformatics / Transcriptomics