09 September 2011

Customizing "C printf" to print a FASTA sequence.

›
The GNU C library lets you define your own custom conversion specifiers for printf template strings . In the current post, I will show how ...
06 September 2011

Parsing a BAM file with javascript, yes we can. (Node.js and V8)

›
Node.js is an event-driven I/O server-side JavaScript environment based on V8 , Google's open source JavaScript engine. In the current...
1 comment:

Merging two XML files using the libxml streaming API.

›
I just wrote a program appending one or more XML files to another XML file using the libxml streaming API . This program named mergexml is ...
13 August 2011

A FUSE-based filesystem reproducing the NCBI Taxonomy hierarchy.

›
In this post I will show how I've used FUSE to create a new loadable filesystem for Linux, reproducing the tree of the NCBI Taxonomy ....
2 comments:
10 August 2011

Wikipedia OpenSearch and semantic bash completion

›
I wrote a tool that use the opensearch API for mediawiki to display the results of a query in wikipedia: $ opensearch Charles Darw Charles_...
09 August 2011

Quick tip: bash completion for Bioinformatics

›
The default behavior for the <tab> completion can be extended by creating a new file: ${HOME}/.bash_completion in your home. For ...
2 comments:
01 August 2011

Using the Freebase and the Bioportal Widgets to create a semantic object.

›
The following HTML code uses: a Widget from the NCBO Bioportal for the Protein-protein interaction Ontology And two Widgets from Freebase ,...
1 comment:

Memory-Mapping the Human Genome with 'mmap': my notebook

›
In this post, I've explored how to use a memory-mapped file to handle the 3Go of the Human Genome sequence as if it was entirely loaded...
2 comments:
31 July 2011

Storing some SNPs using the leveldb library. My notebook.

›
In this post I'll describe how I've used the leveldb API , a C++ key-value database, to store some SNPs (key=rs,value=sequence). ...
1 comment:
27 July 2011

Controlling IGV through a Port: my notebook.

›
A protocol for interacting with the The Integrative Genomics Viewer (IGV) is described here: http://www.broadinstitute.org/igv/PortCommands ...
3 comments: