What can we do for you?

Don’t ask what we can do for you. Ask what you can do for us.

Provided support

The Bioinformatics Laboratory provides support to (pre)clinical research groups at the Amsterdam UMC in a selected number of areas:

Due to limited capacity we cannot support projects that would consume our capacity for longer periods of time.

Collaboration

If you have hired a bioinformatician for your project but don’t want to supervise him/her then we can host this person in our group. Contact us for further information. 

Participation in projects

If you forsee a large need for bioinformatics (or computational modelling) in your project then you might consider to include us or another bioinformatics group in your project and to allocate budget to hire a bioinformatician for the analysis.  

Further information

For other support questions contact Antoine van Kampen.

What if you need other support?

Due to very limited support capacity in our group we cannot always help you. In addition, we may sometimes even lack the expertise -:)

We do not provide support for:

  • SAGE, DNA Microarrays, RNAseq
  • Whole Genome sequencing (WGS)  and Whole Exome Sequencing (WES)
  • Epigenetics (e.g., methylation arrays, CHiP seq)
  • Microbiome
  • Proteomics

For the analysis for RNAseq data we refer to the R2 Genomics Analysis van Visualization Platform developed by Dr. Jan Koster (Oncogenomics, Amsterdam UMC), or to the Core Facility Genomics headed by Daoud Sie.

For help with microbiome analyses you might ask prof. dr. Age Smilde for possibilities.

For FAIR (Findable, Accessible, Interoperable, Reusable) data management, and additional requirements (e.g. for WMO, GCP and GDPR) we refer to Research Data Management.

For help with R/Rstudio, PhD students might consider our Computing in R course.

Infrastructure and data storage

The Bioinformatics Laboratory has access to (high performance computing) ICT infrastructure, and uses dedicated (Unix) machines for its support. In most cases this infrastructure suffice for the support projects. If not, special arrangements may have to be made.

We also emphasize that we take good care of your data:

  • We do not distribute your data to third parties
  • Analyses are done on ICT infrastructure of the Amsterdam UMC, or using SURFsara facilities.
  • Analyses may also be performed on (private) laptops that are taken outside the AMC. However, harddisks will always be encrypted to prevent data access by non-authorized persons.
  • If you provide us unintentionally with personal/patient data, then we will remove this data and inform you immediately.

However, we don’t have the facilities to store or backup your data nor for all the (intermediate) results we produce for you. Once we finished an analyses we will, in principle, delete all data. Thus, make sure you have a (multiple) copies of your data.