31 August 2012

The 500th post: Generating a pipeline of analysis (Makefile) for NGS with xslt.

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This is my 500th post ! Happy birthday my blog ! (I know, I know, I have been unfaithful since the beginning of the year) . In my previ...
1 comment:
30 August 2012

Next Generation Sequencing, GNU-Make and .INTERMEDIATE

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I gave a crash course about NGS to a few colleagues today. For my demonstration I wrote a simple Makefile . Basically, it downloads a subset...
1 comment:
27 August 2012

Reasoning with the Variation Ontology using Apache Jena #OWL #RDF

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The Variation Ontology (VariO), "is an ontology for standardized, systematic description of effects, consequences and mechanisms of va...
14 August 2012

Apache Pig: first contact with some 'bio' data.

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via wikipedia: " Apache Pig is a high-level platform for creating MapReduce programs used with Hadoop . The language for this platfo...
5 comments:
13 July 2012

Parsing the Newick format in C using flex and bison.

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The following post is my answer for this question on biostar "Newick 2 Json converter" . The Newick tree format is a simple form...
4 comments:
10 July 2012

GNU C++ hash_set vs STL std::set: my notebook

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A set is a C++ container that stores unique elements. The C++ Standard Template library  (STL) defines a C++ template set<T> that is...
1 comment:
09 July 2012

Using the flickr XML/API as a source of RSS feeds.

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You may know that I seek from time to time royalty free pictures   on flickr.com for my other personal blog . The flickr API can be used ...
06 July 2012

The LZW compression algorithm as a measure of the short-reads complexity

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The LZW algorithm, is a dictionary-based universal lossless data compression algorithm. The algorithm is easy to implement, here is a pseud...
08 May 2012

Downloading the XML data from the Exome Variant Server

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From EVS : "The goal of the NHLBI GO Exome Sequencing Project (ESP) is to discover novel genes and mechanisms contributing to heart, lu...
4 comments:
24 April 2012

Mapping the genes involved in a category of disease: the GeneWikiPlus + SPARQL way.

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In my previous post , I've used the RDF/XML files of the Disease Ontology to map all the genes involved in a cardiac disease. Andrew...