07 November 2007

JOBS 20071106

Programmer to install and maintain genome database software:

Bioinformatician/Biostatistician position at the Centre for Molecular Oncology, Institute of Cancer
Immediate opening for a highly motivated Bioinformatician/Biostatistician with strong numerical skills and a track record of the analysis of high throughput technologies.

05 November 2007

Job@Novartis 20071105

Position Title Research Investigator II/Bioinformatics
Work Location Switzerland - Basel
Company/Legal Entity Switzerland Novartis Pharma AG, Basel
Functional Area Research
Job Type Full Time

02 November 2007

job@swissprot 2007-11-02

The Swiss-Prot group at the Swiss Institute of Bioinformatics (SIB) in Geneva (Switzerland) is looking for a Java developer.

See http://www.isb-sib.ch/infos/careers_070625.htm for more details.

OpenSocial, a google API for social networks, is alive

OpenSocial, the new Google API is alive at : http://code.google.com/apis/opensocial/.

OpenSocial provides a common set of APIs for social applications across multiple websites. With standard JavaScript and HTML, developers can create apps that access a social network's friends and update feeds.

Common APIs mean you have less to learn to build for multiple websites. OpenSocial is currently being developed by Google in conjunction with members of the web community. The ultimate goal is for any social website to be able to implement the APIs and host 3rd party social applications. There are many websites implementing OpenSocial, including Engage.com, Friendster, hi5, Hyves, imeem, LinkedIn, MySpace, Ning, Oracle, orkut, Plaxo, Salesforce.com, Six Apart, Tianji, Viadeo, and XING.
In order for developers to get started immediately, Orkut has opened a limited sandbox that you can use to start building apps using the OpenSocial APIs.

01 November 2007


The C preprocessor contains some predefined macros that can be used to identify the date when your pogram was compiled:

printf("%s Compiled on %s at %s.\n",argv[0],__DATE__,__TIME__);

Java has no preprocessor, and is missing this kind of information: I wrote a custom ant task generating a java file called Compilation.java and containing all the needed informations.

<taskdef name="compileInfoTask"
<compileInfoTask name="Pubmed2Wikipedia" package="org.lindenb.util" dir="build/compile"/>


package org.lindenb.util;
import java.util.GregorianCalendar;
public class Compilation
private Compilation() {}
public static String getName() { return "Pubmed2Wikipedia";}
public static String getPath() { return "~/lindenb";}
public static String getUser() { return "pierre";}
public static GregorianCalendar getCalendar() { return new GregorianCalendar(2007,10,1,22,30,11);}
public static String getDate() {return "2007-11-01 at 22:30:11"; }
public static String getLabel() { return (getName()==null?"":getName()+" : ")+"Compiled by "+getUser()+" on "+getDate()+" in "+getPath();}
public static void main(String args[]) { System.out.println(getLabel());}

The source code is available here:



Ant custom tasks

Ant, the java Make can be extended by creating your own custom task. I had fun today by creating a new Ant Task called SplashTask. It generates an new logo on the fly to be used as a java splashScreen.


(...) <taskdef name="makeSplash"
<target name="splash" depends="compile-ant-tasks">
<makeSplash title="Hello World !" file="task.jpeg"/>


pierre@linux:~/lindenb> ant x
Buildfile: build.xml


[makeSplash] Saved SplashScreen "Hello World !" to task.jpeg[349 x 85]


The source code is available at http://lindenb.googlecode.com/svn/trunk/src/java/org/lindenb/ant/SplashTask.java



I've created a java tool called pubmed2wikipedia: I wrote it to quickly create a new entry for wikipedia.
First, the user select a set of articles about a given subject from pubmed, the software then download, prepare and format the data for a new wikipedia page. For example it creates the 'references' part and suggest the Categories: from the Mesh terms. I've also included a dictionary which recognize some regex patterns to help create a wikipedia internal link.
I first tried to use my own tool to create an entry about NSP3, a viral protein I studied during my PhD but with hundred of articles I felt I was not any more an expert about this protein :-) so I created a small article about another protein: RoXaN.

I hosted this tool on http://code.google.com. It is available at: http://lindenb.googlecode.com/files/pubmed2wikipedia.jar