Showing posts with label library. Show all posts
Showing posts with label library. Show all posts
18 July 2013

Running a picard tool in the #KNIME workflow engine

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http://www.knime.org/ is "a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initi...
24 May 2013

A Tribble/FeatureCodec handling JSON-based annotations files.

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I wrote a java FeatureCodec for JSON with a the tribble library. Citing the GATK tream: "The Tribble project was started as an effor...
11 February 2013

Counting the reads in a BAM file using SGE and the Open-MPI library: my notebook.

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In the current post, I'll describe my first Open MPI program. Open MPI is "a Message Passing Interface (MPI) library, a standard...
1 comment:
25 January 2013

Samtools tview as a library to display the BAM

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I've forked samtools and modified the code of tview to use it as a library to display the alignments. The original code is an inreracti...
3 comments:
28 June 2011

The java library for BigBed and BigWig: my notebook

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Jim Robinson and his team, from the Broad Institute/IGV, have recently released a java library parsing the BigBed and the BigWig formats . ...
3 comments:
03 February 2011

Using the #Gephi toolkit to draw a graph from PSI-MI data, my notebook

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GEPHI , interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs . ...
02 September 2010

Playing with the ming API , a C library for SWF/Flash.My notebook.

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Ming is a C library generating some simple Flash/SWF movies. In this post I will describe how I used the Ming API by try to converting to S...
2 comments:
03 October 2008

Java Wrappers for the tables of the UCSC/GoldenPath

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Years ago, Jim Kent (UCSC) (the author of the BLAT algorithm) published in the Linux Journal "autoSql and autoXml: Code Generators fr...
2 comments:
10 January 2008

JAVA Native Interface (JNI): notebook

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The JAVA Native Interface (JNI)allows Java code running in the Java virtual machine to call and (be called) some methods from libraries wri...
4 comments:
18 October 2007

Information R/evolution

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A beautiful video about the science of information...
04 May 2007

(Trying to use) The NCBI ASN.1 library

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Motivation: I was looking for a way to store and to read my linkage data using a binary format, (then I could get a faster and a smaller s...
3 comments: