01 December 2011

Suggest some new terms for the EDAM Ontology for Bioinformatics

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EDAM is an ontology of general bioinformatics concepts, including topics and data types, formats, identifiers and operations . Is your spe...
20 November 2011

Processing json data with apache velocity.

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I've written a tool named " apache velocity " which parse json data and processes it with " Apache velocity " (a te...
16 November 2011

"VCF annotation" with the NHLBI GO Exome Sequencing Project (JAX-WS)

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The NHLBI Exome Sequencing Project (ESP) has released a web service to query their data. "The goal of the NHLBI GO Exome Sequencing P...
3 comments:
01 November 2011

The paper about BioStar has been published in "PLoS Computational Biology"

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The article describing BioStar has been published in PLoS Computational Biology : BioStar: An Online Question & Answer Resource fo...
21 October 2011

A reference genome with or without the 'chr' prefix

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The name of the chromosomes in the fasta files for the human genome are prefixed with ' chr ' : $ grep ">" hg19.fa ...
3 comments:
07 October 2011

Knime4Bio: a set of custom nodes for the interpretation of NGS data with KNIME

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Our paper has just been published in Bioinformatics  :-) http://bioinformatics.oxfordjournals.org/content/early/2011/10/07/bioinformatics....
05 October 2011

Grouping mutations/Gene=f(sample)

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GroupByGene is a small C++ tool grouping the data: CHROM POS REF GENE SAMPLE by gene=f(sample). This tool is available on google co...

Verticalize: printing the input stream vertically.

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A useful tool: verticalize is a small C++ tool printing the input stream vertically. The source is available on github : https://github.com...
26 September 2011

PostScript as a Programming Language for Bioinformatics: mynotebook

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" PostScript (PS) is an interpreted, stack-based programming language . It is best known for its use as a page description language in...
3 comments:
23 September 2011

Joining genomic annotations files with the tabix API.

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Tabix is a software that is part of the samtools package. After indexing a file, tabix is able to quickly retrieve data lines overlapping...