Human and Clinical Genetics - LUMC

(Centrum voor Humane en Klinische Genetica)

Bioinformatics Support Group

The BioInformatics Support Group consists of:

• Ivo Fokkema: web administrator, LOVD and HCG database developer
• Michiel van Galen: Illumina (Solexa) 1G analyzer data analysis support and software development
• Matt Hestand: CORE_TF support for transcription factor binding site identification
• Quinta Helmer: primer design and data analysis software development for the FlexArrayer
• Gerard Schaafsma: LOVD tool developer (supported by Gen2Phen)
• Michel Villerius: local hardware/software support, Rosetta Resolver system administrator (software/hardware/backup support)
• Peter Taschner: coordinator, bioinformatics user support, Mutalyzer development

and maintains the following: 

Databases and systems

• CORE_TF transcription factor binding site identification
• NBIC Rosetta Resolver DNA chips and micro-array data storage and analysis provided via the NBIC (Rosetta Resolver access restricted to registered users from participating institutes)
• LOVD (Leiden Open source sequence Variation Database): Software for the easy setup of a web-based locus-specific database (LSDB). LOVD is used to maintain the Leiden Muscular Dystrophy pages and the TCA Cycle Gene mutation database. We also offer curators to maintain other LSDBs on our LOVD server. Current development of LOVD LSDB-in-a-box software is supported by Gen2Phen (EC (FP7/2007-2013) nº 200754)
• HKG database for storage and retrieval of lab resources (internal users only) See Instructions
• MUTALYZER v.1: MUTAtion  anaLYZER package to check the nomenclature of sequence variations, and (under development) determine their effects. More information

Webpages

• Bioinformatics Tools and Support Links to flowcharts and other bioinformatics tools and support

  BioInformatics Infrastructure information

• LUMC ICT - in Dutch
• Website access problem solving
• PC programs available (installed on request)
• Software available at the LGTC
• Rosetta Resolver Server for DNA chip and micro-array data storage and analysis (Rosetta Resolver access restricted to registered users from participating institutes)

The BioInformatics Support Group prefers to use open source operating systems, web server and programming resources

• Apache 1 and 2 - web server software
• Linux - operating system
• mySQL - database
• PERL 5.8.x - scripting language
• PHP 4.3.1 - server-side html-embedded scripting language
• Python - object oriented programming language
• Biopython - Python bioinformatics tools

BioInformatics Student Projects

Students may participate in the development and application of tools for one of the following topics:
• Prediction of the effect of sequence variations in disease genes - MUTALYZER: MUTAtion  anaLYZER package to determine the effect of sequence variations
• Large scale primer design (in collaboration with Jeroen Laros, Hendrik Jan Hoogenboom, Walter Kosters at the LIACS)
• Integrated analysis of genome data (data mining)
• Sequence data analysis from parallel sequencers (Solexa)

          For more information please contact Peter Taschner

If you have any comments or suggestions be sure to let us know !  mailto:p.taschner@lumc.nl

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