CF Life Science Computing

The facility provides bioinformatics support to FLI scientists when the analysis of experimental data requires complex algorithms, advanced statistics or high performance computational power for processing, due to its large scale (e.g., data from CF DNA Sequencing or CF Proteomics). For operation, the facility maintains a Unix infrastructure and several software services for institute-wide use.

Main Service Portfolio:

  • Maintain Unix clients and servers
  • Software services: Electronic Laboratory Notebook, animal databases, R server, GitLab, Ingenuity Pathway Analysis (IPA), AgeFactDB, NfinGB etc.
  • Differential expression analyses of RNA-seq, proteomics or metabolomics experiments
  • Chromatin-related experiment analysis:ChIP-seq, ATAC-seq
  • (Epi)genetic variant discovery and genotype analysis
  • Gene set / pathway enrichment analysis
  • DNA and protein sequence analyses and database mining
  • Consultation and training on bioinformatics and biostatistics
  • Consultation for scientific software and its development
High-performance computing and storage systems are at hand for large-scale data processing.
FLI: High-performance computing and storage systems

Bioinformatics Analysis Requests

A bioinformatics project is initialized via discussion between users and the facility staff on the envisioned data structure and analysis goals. This initial step should ideally be an integral part of the design of the experimental work to follow. Bioinformatics solutions are realized by application of established methods and pipelines, as well as by the implementation or development of new software tools and approaches.

  • Roll-out of the Electronic Lab Notebook
  • Primary data management for long-term storage
  • Expression analyses of human, mouse, fish, fly and planarian RNA or protein samples
  • Development of software tools for expression and mutation analysis
  • PacBio-based microbial genome assembly and annotation
  • Improvements of the N. furzeri genome sequence with PacBio data
  • Organization of special interest group meetings for statistics and R scripting (R Club)

Internal users:
  Download (doc)  Bioinformatics Project Form

External users:
Please inquire.

Team*

Name Telefon E-Mail Tätigkeit
Karol Szafranski +49 3641 656804 karol.szafranski@leibniz-fli.de Core Facility Manager
Philipp Koch +49 3641 656053 philipp.koch@leibniz-fli.de Postdoc
Fabian Monheim +49 3641 656872 fabian.monheim@leibniz-fli.de Forschungsingenieur
Bernd Senf +49 3641 656455 bernd.senf@leibniz-fli.de Forschungsingenieur
Steve Hoffmann +49 3641 656810 steve.hoffmann@leibniz-fli.de Wissenschaftlicher Betreuer

* unvollständig aufgrund DSGVO

For publications of individual CF members:  publications search 

Contact

Dr. Karol Szafranski

Karol Szafranski
CF Manager
+49 3641 65-6804
karol.szafranski@leibniz-fli.de

Steve Hoffmann
Scientific Supervisor
steve.hoffmann@leibniz-fli.de

Group Website

Overview CF Life Science Computing

Overview CF Bioinformatics