Bioinformatics

The Bioinformatics Core provides services and expertise to assist investigators in all fields of biomedical data analysis, project planning, and grant preparation.

We provide three levels of services
  1. Consultancy [free of charge]
    On short notice users can discuss their research project with a bioinformatics expert in order to identify potential points of interaction. In many cases, suitable web-based solutions are available to solve a given project. We assist the users in finding the appropriate tool and support them when using it. This service may lead to a follow-up of one of the following two:

  2. Fee-for-service [funding to be provided]
    In some cases, specific bioinformatics tools or services need to be programmed. Smaller projects can be conducted by staff from the bioinformatics core; for larger projects new staff can be hired and supervised by the Bioinformatics Core in order to full-fill project specific tasks.

  3. Scientific cooperation [common publication, funding can be shared]
    We are interested to engage in collaborative projects when these fall within the scope of our research, that is, in particular the genetics and metabolomics of diabetes and its co-morbidities. However, we are always interested in new and interesting challenges.

Resources

 

The WCM-Q bioinformatics core has implemented standardized protocols for next generation sequencing data analysis, following GATK best practice for variant calling from whole genome DNA data, and Cufflinks- and TopHat-based protocols for identifying differentially expressed genes in mRNA data (>450 whole genomes processed so far). The raw data flow is streamlined with the WCM-Q genomics core, and cutting-edge data storage and computing facilities are provided by the WCM Advanced Computing group (1,000 CPU cores, 2.5TB of RAM, 1.2 PB total data storage). Identification of candidate functional variants from DNA sequencing is supported by Ingenuity Variant Analysis (IVA) and identification of differentially expressed genes from mRNA sequencing is provided using Ingenuity Pathway Analysis (IPA). In addition to the application of standardized protocols, the core provides personalized and project-specific support tailored to the user's needs. The core is currently staffed with 8 FTE. Depending on the project size, it is possible to host and supervise postdoctoral researchers that are funded on NPRP projects within the core for a limited amount of time. The core also has processed a wide range of genome data from Qatar that can now be used as a population-specific reference (Kumar P, Al-Shafai M, Al Muftah WA, Chalhoub N, Elsaid MF, Aleem AA, Suhre K. Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance. BMC Res Notes, 7:747, 2014.). This data can be made available via dedicated web tools to users, built on the model of the SNIPA Web-Server: http://snipa.org/. Note however that access to these datasets is not public and subject to IRB approval.


The WCM-Q Bioinformatics Core further provides support in all other fields of bioinformatics:

  • Structural bioinformatics (normal mode analysis, homology modeling, molecular dynamics)
  • Protein bioinformatics (multiple sequence alignment, phylogeny, homology search)
  • Genome bioinformatics (comparative genomics, genome evolution, sequencing)
  • Functional bioinformatics (gene function prediction, protein domains)
  • Genetics (SNPs, CNVs, genome-wide association studies)
  • Metabolomics (mass spectrometry and NMR based, targeted and non-targeted)
  • Systems Biology (network reconstruction, Gaussian graphical modeling)
  • Web server development
  • see Karsten Suhre Lab Homepage for publications of the Suhre Lab in these fields
  • Access to different supercomputing facilities
    (if local computing resources are not sufficient, we can help)

Links

  • Ingenuity Pathway Analysis [5 floating licenses]
    (we can conduct Ingenuity Pathway Analysis pop up on your data)
  • Ingenuity Vatiant Analysis [licenses available on a per-genome basis]
  • SNIPA.ORG - A tool for annotating and browsing genetic variants
  • GWAS.EU - The Metabolomics GWAS Server
  • ELNEMO.ORG - The Web-interface to the Elastic Network Model (ENM), a fast and simple way for computing the low frequency normal modes of a macromolecule
  • MASSTRIX.ORG - The Mass TRanslator into Pathways annotates metabolites in high precision mass spectrometry data
  • MetaP Server - The metaP server automates data analysis for the processing of metabolomics experiments
  • Bioinformatics Link Directory pop up
    (we can help you finding and applying the appropriate tools from this directory)

 

Contact

Karsten Suhre, PhD
Professor of Physiology and Biophysics
Director of Bioinformatics
Joel Malek
Phone: (974) 4492 8482



Last modified on Monday, 18-Jan-2016 14:33:17 AST