CF Life Science Computing

The facility provides 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 properties (e.g., data from CF Next Generation Sequencing or CF Proteomics). Towards this, the facility maintains a Unix-based infrastructure and several software services for institute-wide use. Moreover, it offers custom bioinformatics and statistical analysis of research data.

Computational Systems:

  • Operate network of Unix clients, servers and storage units; support computational users
  • Operate community software, e.g. SGE, RStudio, GitLab
  • Web hosting of scientific resources, e.g. AgeFactDB, Nothobranchius Genome Browser

Scientific Software Services:

  • Operate central service software, e.g. Electronic Laboratory Notebook (ELN), research data archive (fliDA), animal databases
  • Consultation for needs in scientific software, including custom developments
  • Support and training in Research Data Management (RDM)

Bioinformatics & Statistics:

  • Bioinformatics analyses on client's experimental data, in particular:
    • Differential expression analysis of transcriptomics, proteomics or metabolomics experiments
    • Chromatin-related experiment analysis, e.g. ChIP-seq, ATAC-seq, CUT&Tag
    • (Epi)genetic variant discovery and genotype analysis
    • Gene set / pathway enrichment analysis
    • Further directions upon client's requests
  • Consultation and training on bioinformatics and biostatistics
  • 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:

Additional information (intranet)

Download (doc) Bioinformatics Project Form

External users:
Please inquire.

Team*

NamePhoneEmailPosition
Karol Szafranski+49 3641 656804karol.szafranskileibniz-flideCore Facility Manager
Philipp Koch+49 3641 656053philipp.kochleibniz-flidePostdoc
Jeanne Wilbrandt+49 3641 656873jeanne.wilbrandtleibniz-flidePostdoc
Fabian Monheim+49 3641 656872fabian.monheimleibniz-flideResearch Engineer
Bernd Senf+49 3641 656455bernd.senfleibniz-flideResearch Engineer
Steve Hoffmann+49 3641 656810steve.hoffmannleibniz-flideScientific Supervisor

* incomplete due to Data protection

For publications of individual CF members:  publications search 

Contact

Karol Szafranski
CF Manager
+49 3641 65-6804
karol.szafranskileibniz-flide

Overview CF Life Science Computing