Abeel online

Abeel, T, Van Parys T, Weiner B, Saeys Y, Galagan J, Van de Peer Y.  2010.  GenomeView: next-generation sequencing visualization. VIB seminar 2010, Blankenberge, Belgium; EMBO Workshop on Visualizing Biological Data 2010, Heidelberg, Germany; 2nd Statseq workshop, Gent, Belgium.

To change a default Eclipse project to an Eclipse Java project you can follow the steps below.

1. First close the project in Eclipse (right-click project folder > close project)
2. Open the .project file in a text-editor outside Eclipse
3. Add the Java builder and nature to the .project file
4. Save and close file
5. Open project in Eclipse and it now is a Java project

Example:
Original .project file

<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
	<name>A project</name>

Sometimes you want to replace one piece of text with another in all files in a whole directory tree.

*nix and sed to the rescue.


find ./ -type f -exec sed -i ’s/queryString/replaceString/g’ {} \;


Weiner, B, Peterson M, McGuire A, Lun D, Zucker J, Abeel T, White J, Sherrid A, Sherman D, Galagan JE.  2009.  Network modeling of Mycobacterium tuberculosis via integration of ChIP-Seq and Transcriptomics. TB sysbio meeting, Seattle.

Gellesch, M, Stolte C, Jen D, Heilman E, Abeel T, Engels R, Borenstein D, Sykes S, Sisk P, Koehrsen M et al..  2009.  Searching and Visualizing Polymorphisms in M. tuberculosis using Next Generation Sequencing. Broad Retreat 2009.

Abeel, T, Saeys Y, Helleputte T, Van de Peer Y, Dupont P.  2010.  Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics. 26(3):392-398.

AJT 2.2 fixes a bug in the handling of TitledComponent, the component inside the border now properly expands in both directions.

Download
API documentation

Abeel, T, Van Parys T, Galagan JE.  2009.  Visualization of next-generation sequencing data. . Broad Retreat.

McGuire, AM, Weiner B, Riley R, Peterson M, Zucker J, Abeel T, Wapinski I, White J, Koehrsen M, Pearson MD et al..  2009.  Comparative Analysis of Mycobacterium tuberculosis. Broad Retreat.

Abeel, T, Saeys Y, Van de Peer Y.  2009.  Towards a gold standard for promoter prediction evaluation.. ISMB 2009.