This document summarizes the Bioinformatics Platform at the Max Delbruck Center for Molecular Medicine in Berlin-Buch. The platform provides data analysis and computational resources to support genomic and epigenomic research. Services include maintaining databases and scientific software, providing scientific IT support, training courses, and collaborating with researchers on data analysis projects. Walk-in consultations are also offered monthly to help with bioinformatics problems.

1. BIMSB Bioinforma-cs Pla2orm
Overview
Altuna Akalin
@AltunaAkalin
BIOINFORMATICS PLATFORM

2. Bioinforma-cs Pla2orm at MDC/
BIMSB
- Gene regula-on
- Comp. (Epi)genomics: disease and development
Data-intensive computa-onal methods
to infer biological knowledge
Research
Collabora-on
Training
Scien-fic IT
Support
BIOINFORMATICS
PLATFORM
-Maintain databases
- Maintain scien-fic soNware
hOp://bioinforma-cs.mdc-berlin.de

3. Scien-fic IT support

4. MDC Hubs and UCSC Genome browser
hOp://genome.mdc-berlin.de
hOps://bimsbsta-c.mdc-berlin.net/

5. Scien-fic SoNware Support
hOp://guix.mdc-berlin.de
Tired of trying to
install soNware?
Can’t demul-plex?
Try GNU Guix

6. Galaxy @ BIMSB
• “Galaxy is an open web-based pla2orm for data-intensive
biomedical research” (only available within campus)
hOp://galaxy.mdc-berlin.net

7. Databases and Virtual Machines
• BIMSB databases and virtual machines that
host the web apps and databases are
maintained by BIMSB sys. admins.

8. Training
• Pla2orm provides training for development of
bioinforma-cs skills
• ~10 courses/tutorials un-l now
– R, computa-onal genomics, galaxy and unix
related courses
• Yearly computa-onal genomics course open
to external applicants

9. Public trainings/workshops
More info hOp://bioinforma-cs.mdc-berlin.de/training.html

10. Learning material produced by the
pla2orm
• Computa-onal genomics material
– Includes introductory material for computa-onal
genomics and hands-on data analysis
– hOp://compgenomr.github.io/book
• Unix + SGE material
– Includes basic Unix and SGE commands needed to
get started on a Unix+SGE environment
– hOp://bioinforma-cs.mdc-berlin.de/
intro2UnixSGE

11. BIMSB Bioinforma-cs walk-in clinics
Collabora-on No ac-on Referral Consulta-on
Advise you how to
proceed with your
data analysis
Walk-in clinic outcome
Refer you to a group
more experienced in
that par-cular
problem
Some-mes there is
nothing to be done
~ monthly event dedicated to providing consulta-on for bioinforma-cs problems

12. Collabora-on

13. Main collabora-on structures
• Small scale
– Running workflows we established outpudng predefined
reports (currently: RNA-seq, BS-seq, ChIP-seq, SNP/CNV calling)
– Sta-s-cal modeling with already processed data
– Depends on:
• available man-hours
• Large scale
– Needs integra-on and analysis of large number of samples
– Needs development of new workflows
– Depends on:
• Overlap with pla2orm research objec-ves
• Available man-hours
• In all cases, authorship status must be discussed in
advance.

14. More info at…
hOp://bioinforma-cs.mdc-berlin.de