Most recent publications

  • The Mycobacterium tuberculosis Regulatory Network and the Hypoxic Response. Nature
    Galagan, J., Minch, K., Peterson, M., Lyubetskaya, A., Azizi, E., Sweet, L., Gomes, A., Rustad, T., Dolganov, G., Glotova, I., Abeel, T., Mawhinney, C., Kennedy, A., Allard, R., Brabant, W., Krueger, A., Jaini, S., Honda, B., Yu, W., Hickey, M., Zucker, J., Garay, C., Weiner, B., Sisk, P., Stolte, C., Camacho, D., Dreyfuss, J., Liu, Y., Dorhoi, A., Mollenkopf, H., Drogaris, P., Lamontagne, J., Zhou, Y., Piquenot, J., Tae Park, S., Raman, S., Kaufmann, S., Mohney, R., Chelsky, D., Moody, B., Sherman, D., Schoolnik, G., Van de Peer, Y., Iazzetti, P., Winkler, J.
  • Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012. BMC Bioinformatics
    Goncearenco, A., Grynberg, P., Botvinnik, O., Macintyre, G., Abeel, T.
  • Don't Wear Your New Shoes (Yet): Taking the right steps to become a successful Principal Investigator. PLOS Computational Biology
    de Ridder, J., Abeel, T., Michaut, M., Satagopam, V., Gehlenborg, N.

GenomeView

GenomeView logo

GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.

Other software

Java-ML logo Java-ML is a collection of machine learning algorithms with a common interface for each type of algorithms. The library is aimed at software engineers and programmers, so no GUI, but clear interfaces. It provides reference implementations for algorithms described in the scientific literature, it has well documented source code and provides plenty of code samples and tutorials.

Other projects

Open Source projects:
Abeel Java Toolkit (AJT), PHP-agenda, EPSGraphics

Scientific software:
EP3, ProSom, pppBenchmark

Recent posts

Downloading or mirroring a website with wget

Thu, 2011-11-10 18:22 — thomas

The easiest way to download/mirror a complete website is using WGET and use the mirror option. If you want to see your website with the correct layout and all images, make sure you also supply the --page-requisites flag.

The full command:

wget -p -m -k -K -E http://your.website.com/

See wget --help for an explanation of all command-line options, but these should give you a good start.

AJT 2.8 released

Thu, 2011-11-10 17:17 — thomas

Even though it's been a while, AJT 2.8 was released with some more improvements.

LineIterator has become even more versatile. Added some more GUI widgets. Extended the tricks of FrequencyMap to make it more intelligent.

Download AJT
API

Linux breaking lines to fixed length

Tue, 2011-05-17 21:18 — thomas

Break line in fixed width with the linux fold command.

I keep forgetting this command, so here goes.

The Linux 'fold' command, can be used to wrap each input line to fit in specified width.

If width is not specified using -w option, by default, 'fold' breaks lines wider than 80 columns. The output is split into as many lines as necessary.

AJT 2.6 released

Mon, 2011-01-24 23:49 — thomas

AJT 2.6 adds a peek method to the LineIterator class that allows you to look at the next line, but not yet consume it.

Download
API documentation

AJT 2.5 released

Wed, 2010-10-27 17:36 — thomas

AJT 2.5 adds new functionality to the TimeInterval class, implements a NullStream to simulate /dev/null, adds a LRUCache implementation, fixed a comment identifier bug in LineIterator, adds a new toolkit to work with Sets and fixes a bug in ExtensionManager with respect to upper case extensions.

Download
API documentation

Howto change a default Eclipse project to an Eclipse Java project

Thu, 2009-12-03 17:30 — thomas

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>

Replacing text in a directory tree

Fri, 2009-11-20 18:49 — thomas

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’ {} \;

AJT 2.2 released

Mon, 2009-11-02 23:17 — thomas

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

AJT 2.1 released

Fri, 2009-09-11 23:58 — thomas

AJT 2.1 adds transparent handling of GZIP files to the LineIterator class.

Download
API documentation

Java memory usage

Mon, 2009-08-10 17:49 — thomas

We all know that Java is a memory hog. This page aims to give you an idea how much it actually hogs without using a profiler.
Primitive types
A reference to an object is in this listing also considered to be a primitive type.

  • boolean: 1 byte
  • byte: 1 byte
  • char: 2 bytes
  • short: 2 bytes
  • int: 4 bytes
  • long: 8 bytes
  • float: 4 bytes
  • double: 8 bytes
  • reference: 4 bytes

Objects
Each Java object uses the following:

  • 8 byte Object overhead