Head of Facility

Dr. Thomas Manke
Dr. Thomas Manke
Phone:+49 761 5108 738
Email:manke@...

Opportunities

Would you like to learn more? Please feel free to contact manke@ie-freiburg.mpg.de.

Headline

High-performance Data Center Zoom Image
High-performance Data Center
Interactive Training and Tutorials Zoom Image

Interactive Training and Tutorials

Bioinformatics Facility

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Service

Services:

  • Galaxy Server for analysis of NGS data, data access and sharing
  • R-Studio: Webinterface to R software environment for statistical computing and graphics
  • Genomatix Genome Analyzer: commercial package for deep-sequencing analysis)
  • NGS primary analysis: quality control and mapping of NGS data
  • Data hosting: we operate a state-of-the-art high performance storage unit (HP 3PAR) that hosts all internal data (e.g. BAM files) in a central place and can be accessed through our linux servers and Galaxy
  • High performance computing: we also operate a range of different servers that run webservices like Galaxy and R-Studio, provide centralised home directories and logins, serve as data capture for the sequencing machines or are simply compute servers to run analysis on. Two of these compute servers (solserv1, deep8) are also available to any institute member. They run on linux (CentOS) and knowledge of the command line is required to operate them. All widely used bioinformatics tools are already installed (e.g. samtools, bedtools, bowtie, macs, deepTools).  Contact Sarah Diehl to get a login and details on the access.

Software:

  • deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data (also available in our Galaxy Server)
  • MicroSNiPer: a web-tool for prediction of SNP/mutation effects on microRNA targets
  • ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation

Training:

  • Galaxy course: In cooperation with the University Freiburg we offer a one week Galaxy course twice a year, which covers the basics of Galaxy, ChIP-seq, RNA-seq and methylation analysis. Upcomming courses are announced via the institute email. A quick introduction to Galaxy is also available as a step-by-step guide from within Galaxy.
  • R course: materials from our past R courses and the R Club are still available from the epicenter website
  • Linux course: materials from our Linux course are also still available on the website

 
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