Our Services

Data Integration

We host locally various external data-sources such as the The Cancer Genome Atlas (TCGA), International Genome Consortium (ICGC), UCSC Genome Browser, among others. Local hosting reduces the processing time by reducing a the network latency.

Moreover, in advanced relational database management systems we store in-house generated data. The anonymized data can be accessed and modified remotely using the highest security standards.

Please contact us if want to have access to our data sources.

Bioinformatics

We develop, maintain and make accessible open-source and proprietary bioinformatics tools.

Due the nature of state of the art research, custom tools and pipelines are being developed and maintained on a regular basis. All the (developed) tools and pipelines can be accessed through our high-performance CCBC server.

Please contact us if your research is related to cancer and you want to have access to our server.

Computational Biology

Our expertise is to analyze, visualize and integrate big data sets from Genomics, Transcriptomics and Proteomics projects. Furthermore, we develop computational algorithms to gain insight into cancer progression and for improving cancer treatment.

  1. RNA-seq (Fig 1. & Fig 2.)
  2. Whole-Genome/Exome analysis
  3. 4C-seq (Fig 3.)
  4. Targeted Chromatin Capture (T2C) (Fig 4.)
  5. Proteomics analysis
  6. ChIP-seq
  7. Supervised and Unsupervised Cluster analysis (Fig 1. & Fig 2.)
  8. Pathway analysis

Please contact us if you have questions or want to collaborate with the CCBC.


PCA

Figure 1. Principal Component Analysis of TCGA RNA-seq data.

Heatmap

Figure 2. RNA-seq Hierarchical Cluster analysis of differentially expressed genes.

4C-seq contact profile of Naive (red) vs. Committed Cells (cyan).

Figure 3. 4C-seq contact profile: Naive(red) vs. Committed Cells(cyan).

Targeted Chromatin Capture (T2C) contact profile

Figure 4. Target Chromatin Capture (T2C) contact profile.


Data Access

We make use of Pydio to share our data and we also allow sFTP and SSHFS mounting of server folders to more easily work with large data-sets.

Please contact us for access to make use of these services or view our wiki.

CLCBio Workbench

We host two stand-alone CLCBio Genomics Workbenchs on high-performance computers. CLCBio software can be used for advanced analysis of large Next Genration Sequences datasets .

Please contact us if your are interested in getting access to these computers.

Web design

The CCBC develops websites using public and proprietary templates or developing new templates using CSS 3.0/Bootstrap and HTML5.

Websites can be integrated with SQL databases and advanced javascripts and JSON objects.

We maintain Erasmus MC Intranet websites with the Content Management System (CSM) Alterian.