1 Pjotr Prins

Pjotr is a scientist/biologist/open source programmer, currently employed by the Laboratory of Nematology, Wageningen University and a visiting research fellow of the Groningen Bioinformatics Centre of University of Groningen.

You can find Pjotr's official Blog here, and social networking site here . Pjotr's recent write-ups are:

• Big data GFF3 parser
• Nextgen Sequencer BAM/SAM support in BioLib (Perl, Python and Ruby)
• Scala by example, for Bioinformatics
• Why everyone in Bioinformatics should learn Scala

1.1 Articles

• BioRuby: Bioinformatics software for the Ruby programming language by Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama, Bioinformatics, August 29, 2010, doi:10.1093/bioinformatics/btq475
• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows by Toshiaki Katayama et al., Journal of Biomedical Semantics 2010, 1:8 doi:10.1186/2041-1480-1-8
• A Secreted SPRY Domain-Containing Protein (SPRYSEC) from the Plant-Parasitic Nematode Globodera rostochiensis Interacts with a CC-NB-LRR Protein from a Susceptible Tomato, by Sajid Rehman, Wiebe Postma, Tom Tytgat, Pjotr Prins, Ling Qin, Hein Overmars, Jack Vossen, Laurentiu-N. Spiridon, Andrei-J. Petrescu, Aska Goverse, Jaap Bakker, and Geert Smant, Molecular Plant-Microbe Interactions, March 2009, Volume 22, Number 3, Pages 330-340, DOI: 10.1094/MPMI-22-3-0330
• Nix fixes dependency hell on all Linux distributions, by Pjotr Prins, Jeeva Suresh, and Eelco Dolstra, linux.com, December 22, 2008
• Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans, by Yang Li, Olga Alda Alvarez, Evert W Gutteling, Marcel Tijsterman, Jingyuan Fu, Joost A. G. Riksen, Esther Hazendonk, Pjotr Prins, Ronald H. A. Plasterk, Ritsert C. Jansen, Rainer Breitling, Jan E Kammenga, PLoS Genetics, 2006, doi:10.1371/journal.pgen.0020222.eor (36 citations)
• Ruby: Productive Programming Language, by Pjotr Prins, Linux Journal 2002
• GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP, by Ling Qin, Pjotr Prins, John T. Jones, Herman Popeijus, Geert Smant, Jaap Bakker and Johannes Helder, Nucleic Acids Research, 2001, Vol. 29, No. 7 1616-1622 (22 citations)
• More information on publications ...

1.2 Book Contributions

• Linking cDNA-AFLP-Based Gene Expression Patterns and ESTs Ling Qin, Pjotr Prins, and Johannes Helder, Chapter Differential Display Methods and Protocols of series Methods Mol Biol 317, 123-138, Edited by Peng Liang, ([2nd edition] October 2005) ISBN: 1-59259-968-0

1.3 Talks

• MQM: Multiple QTL Model mapping with R/qtl, Pjotr Prins, Danny Arends, Ritsert Jansen and Karl Broman, 1st SYSGENET meeting (Braunschweig, April 8, 2010)
• R/xqtl: High throughput modeling, mapping and exploration of Big Data , Danny Arends, Pjotr Prins, Ritsert Jansen and Karl Broman, 1st SYSGENET meeting (Braunschweig, April 8, 2010)
• High throughput complex trait analysis with xQTL, Invited lecture at Centre for Bioinformatics, University of Kerala, with Dr Achuthsankar S Nair (Trivandrum, March 4th, 2010)
• High throughput complex trait analysis with xQTL, Invited lecture at Department of Crystallography and Biophysics, University of Madras, with Dr. P. Karthe (Chennai, Feb. 18th, 2010)
• Open Source Software (OSS) development in Biology, Invited lecture at the Institute of Bioinformatics and Applied Biotechnology (IBAB), with Prof. Yathindra (Bangalore, Feb. 16th, 2010)
• Open Source Software (OSS) development in Biology, Invited lecture at the Indian Institute of Science (IISc), with Dr. Nagasuma Chandra (Bangalore, Feb. 15th, 2010)
• Qnorm: A library of parallel methods for gene-expression Q-normalization, BOSC 2009 (Stockholm, Sweden, June 27-28 2009)
• BioLib Development Report, BOSC 2009 (Stockholm, Sweden, June 27-28 2009)
• Introducing BioLib - C and C++ libraries for BioPerl, BioJAVA, BioPython, BioRuby, BOSC 2008 lightning talk (in absentia) BOSC 2008 (Toronto Canada, July 19th, 2008)
• Microarray experiments - dealing with noise, symposium organised by Prof. Oswaldo Trelles, Computer Architecture Department University of Malaga (Malaga, May 15, 2008)
• Bio* Projects - some observations BioHackathon 2008, Towards integrated web service in life science with Open Bio* libraries organised by Database Center for Life Science DBCLS (Tokyo, 15 February 2008)
• Linux: Wheels within wheels - on virtualisation, Using Linux - MAC/OSX mini-symposium at WUR (June 2007)
• Searching the genome for pathogen protein-protein interactions, exploring evidence of positive selection, BIOEXPLOIT meeting (March 2007)
• 7th annual Bioinformatics Open Source Conference (BOSC 2006 in conjunction with ISMB, Fortaleza Brasil): Ruby in Bioinformatics (cancelled because of airline problems)
• Groningen Bioinfomatics Center Seminar: MAQi using Cancer Classification, GBiC (12 June 2006)
• NLUUG Conference Languages and Tools: Introducing Ruby on Rails for systemadministration, NLUUG autumn conference (November 2005)
• Genetical genomics approaches for C. elegans - with Olga Alvarez - specifically Assessing quality of microarrays in relation to genetical genomics experiments, 4th Annual Meeting of the Complex Trait Consortium (July 2005)
• Introducing Cfruby / Cfengine for management of large scale (and heterogenous) computing environments WURLUG (December 2004)
• GlLug talk on ROCK Linux: Power to the user (London September 2001, see http://gllug.linux.co.uk/meetSept2001.html)
• OxLug talk on the Deployment of ROCK Linux and CFengine in large environments (Oxford Februari 2001, see http://www.oxlug.org/events.html)
• Co-chaired SANE 2000 conference BoF session on ROCK Linux, see http://www.nluug.nl/events/sane2000/daily/24/bof.html (May 2000)
• NLUUG Conference Multi-platform Open Source Projects (see http://www.nluug.nl/events/vj99/algemeen/index.html) (June 1999)

1.4 Posters

• Systems Genetics: from man to microbe, from genotype to phenotype, 1-2 October 2009, Groningen: User friendly cluster computing for QTL analysis, Danny Arends, K. Joeri van der Velde, Pjotr Prins, Ritsert C. Jansen, Morris A. Swertz

1.5 Conference Proceedings

• Adaptive Hypermedia Conference 2004 Programming adaptivity of course material by use of an action module by Egbert Heuvelman, Pjotr Prins and Sander Steenbergen (August 2004)

1.6 Tutorials

• Bioruby tutorial
• MQM for R/qtl tutorial

1.7 Other

• BioPerl Mentor for the 2010 Google Summer of Code (for Nescent and the Open Bioinformatics Foundation) on (BioPerl) Alignment Subsystem Refactoring
• Google Summer of Code mentor 2009 for Biolib and Ruby::PhyloXML (as part of of the Nescent SoC program ).

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1.8 Projects

• Biolib: libraries for the Bio* languages
• BioRuby testing - running with BioRuby development on github; the BioRuby project aims to implement an integrated environment for Bioinformatics with the Ruby language
• Ruby SoC Mentor for the Google summer of code project 2008 (Nescent Phyloinformatics)
• rtags (Ruby tags)
• SciRuby the Ruby for Science book
• Cfruby is a set of modules that make it easier to write scripts for general, cross-platform system maintainence
• WURLUG Wageningen University Linux User Group

Not so active projects

• GenEst a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP
• logtodo is a command line time logger
• The first ROCK Linux Guide

and much more...

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1.9 Other

• Del.icio.us bookmarks
• Boinc machines contributing to Malaria Control
• Open cycle map and Open streetmap projects

If you want to reach Pjotr send an E-mail to pjotr.public01 @ thebird.nl

for signing/encryption use the GNUPG (GPG) key at http://thebird.nl/main/pjotr/pjotr.pub

Biobliography