Info on Bioinformatics Platform at MDC/BIMSB, Berlin

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