GCB 2015

Two poster abstracts of the Bioinformatics group have been accepted at the GCB 2015: Riemenschneider et al.: SHIVA – A web application for drug resistance testing. Neumann et al.: Comparison of variable importance measures from random forest algorithms on strongly unbalanced data. Looking forward to Dortmund!

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Meeting in Melbourne

Our group recently started a research collaboration with the Burnet Institute in Melbourne, Australia. This collaboration is supported by the Bavarian Research Alliance (BayIntAn_HSWT_2015_87). Please find some impressions from our stay in Melbourne.

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Software UI mockup

Few days ago I’ve started developing a web application for analyses of metatranscriptome data. One really fantastic thing that helped me to quickly get a general idea of the user interface layout and design was the online tool moqups. It’s ideal to create GUI drafts especially for web based apps and it’s definitely better than…

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After work outdoor workout

I’m looking forward doing some sports outside with my colleagues enjoying the sun 🙂 Every Tuesday colleagues and students from WZ Straubing meet to have a gorgeous and effective workout session with our own fitness instructor Dima. We meet at 5.45pm at Turmair sports area going for a warm-up jogging round alongside the Danube river…

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SSPACE – Can’t locate getopts.pl

Today I tried to run the SSPACE Standard perl script for doing scaffolding of pre-assembled contigs, but I got this error message: Can’t locate getopts.pl in @INC (@INC contains: /Tools/SSPACE-STANDARD-3.0_linux-x86_64/dotlib/ /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at SSPACE_Standard_v3.0.pl line 124. getopts.pl is a Perl 4 core library but no longer included in…

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How to run velvet with OPENMP

Just few steps to make velvet working for de novo genome assembly using multiple CPU cores: 1) Download the latest version of velvet from http://www.ebi.ac.uk/~zerbino/velvet/ 2) $ tar -xzvf velvet_1.2.10.tgz 3) $ cd velvet_1.2.10 4) Edit the Makefile to compile with a higher Kmer length and enable longsequences for contigs longer than 32kb: $ vim…

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ISMB / ECCB 2015

Two poster abstracts of the Bioinformatics group have been accepted at the ISMB/ECCB 2015: Riemenschneider et al.: Multi-label classification for HIV-1 drug resistance prediction Neumann et al.: Non-invasive multivariate prediction model for myocardial infarction Looking forward to Dublin!  

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