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Thomas Ostermann
Application specialist on electron microscopy
Responsibilities
- Electron microscopy application specialist & EM-facility management
- Bioinformatics
- Server IT-administration
Electron microscopes (Zeiss Libra 120 and DSM 950)
- Technical management and application
- Supervision of all users at the microscopes
- Monitoring of all components and adjustment
- Training and support of different user groups
Special applications at the Zeiss Libra 120
- With the electron energy loss spectroscopy (EELS) it is possible to detect elements in the preparation due to different losses of energy.
- Based on different losses of energy the element distribution (ESI, Electron Spectroscopic Imaging) can be represented.
- With HCI (High Contrast Imaging) thin sections can be photographed without staining.
Server IT-administration
- IT-administration of Windows and Linux server systems at the institute
- IT-administration of special IT-infrastructure and special IT-applications for research at the institute
- Disaster-recovery and backup-strategies
IT projects
Macrostomum EST database (MacEST)
A public Macrostomum sequence database available at http://flatworm.uibk.ac.at/macest/ was created. More than 23.000 Expressed Sequence Tags (EST) of Macrostomum lignano are available from different sequencing projects. These data were processed using different bioinformatic methods. The idea was to analyze all available EST's with the same pipe of bioinformatic tools and provide the analyzed data to the community. We used EST2uni to run programs needed for analysis (EST preprocessing, clustering, annotation). EST2uni is an open source tool for automated EST analysis and database creation, with a data mining web interface. All results provided by different programs are parsed and feeded into a relational MySQL database. EST2uni provides a web page connected to the database. This end-user interface allows to run queries for sequence names, blast results, Gene Ontology categories in all available Macrostomum libraries. Furthermore EST2uni provides statistics on gene sequence numbers, quality, length, singletons and contigs. In addition BLAST searches against the MacEST database can be performed. Finally all search results, sequence data and chromatograms can be downloaded by any user.
ZID GRID
The central IT-Services operates a cluster (ZID GRID). By friendly support of Reinhard Bischof (IT-Services) and Katharina Nimeth (Institute of Astro- and Particle physics) it is possible to use these resources for large-scale sequence analyses (also used for Macrostomum EST database).
IT administrator at the Institute of Zoology
As the IT-administrator I am responsible for allocating all IP addresses and user accounts at the Institute and I am the contact person to the IT-Services.