Scrollable HTML table

A CSS tip I learned today: you can get a scrollable HTML table by using overflow in the associated CSS stylesheet.

<table style=' width:500px;border-collapse:collapse; font-family: sans-serif;border: 1px solid blue;' >
<thead><tr><th>ACC</th><th>Position</th></tr></thead>
<tbody style="height:105; overflow-y:auto;overflow-x:hidden;">
<tr><td>NP_001004053</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&p
osition=chr22:14636331-14667937">chr22:14636331-14667937</a></td></tr>
<tr><td>NP_001005239</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&p
osition=chr22:14828823-14829804">chr22:14828823-14829804</a></td></tr>
<tr><td>Q9UJS3</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15451647-15453700">chr22:15451647-15453700</a></td></tr>
<tr><td>Q5GH77</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15644305-15682584">chr22:15644305-15682584</a></td></tr>
<tr><td>Q2WGN9</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15822826-15869112">chr22:15822826-15869112</a></td></tr>
...many rows...
</tbody>
</table>

the result:

shhh... doesn't display correctly within blogger

Introduction of new relationship types in GO

FYI: via the GO-friends mailing list.
We are pleased to announce that The Gene Ontology Consortium will
introduce three new relationship types

• regulates


• negatively_regulates


• positively_regulates

into the BiologicalProcess ontology.

Thomson scientific launches www.researcherid.com

http://www.researcherid.com

Thomson scientific launches researcher id.com to associate a researcher with their published works:

Unique Identifier Ensures An Accurate Record Of A Researcher’s Output And Attribution and Builds a World-class Author Community

Researcher ID is a global, multi-disciplinary scholarly research community. Each researcher listed is assigned a unique identifier, to aid in solving the common problem of author misidentification. Search the registry to find citations, collaborators, and more.

see also: http://scientific.thomson.com/press/2008/8429910/

Pierre

Nucl. Acids Res.: Database issue, January 2008

The annual database issue of NAR is freely available at:http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl?etoc

The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list.

Who can say: "I'm a specialist in the databases in biology" ?

Scientists for Better PCR

Via:Coffee and Science.

JAVA Native Interface (JNI): notebook

The JAVA Native Interface (JNI)allows Java code running in the Java virtual machine to call and (be called) some methods from libraries written in C/C++. I've learned this technology by trying to use the CURSES library (an API allowing the programmer to write text user interfaces in a terminal).

We starts by creating a java class: NCurses.java

1 /* A JNI test */
2 public class NCurses
3 {
4 public NCurses() {}
5 /** initializes the ncurses library */
6 public native static int install();
7 /** disposes the ncurses library */
8 public native static int uninstall();
9 /** set character on screen */
10 public native static void setCharAt(int x,int y,int ch);
11 /** update the screen */
12 public native static void refresh();
13 /** get the number of rows */
14 public native int getRowCount();
15 /** get the number of columns */
16 public native int getColumnCount();
17 /** inverse video */
18 public native int standout();
19 /** normal video */
20 public native int standend();
21
22 /** draw a string at the given position */
23 public void drawString(String s,int x, int y)
24 {
25 int maxx= getColumnCount();
26 for(int i=0;i< s.length() && i+x < maxx;++i)
27 {
28 if(i+3< s.length() && s.substring(i,i+3).equals("<b>"))
29 {
30 standout(); i+=2; continue;
31 }
32 else if(i+4< s.length() && s.substring(i,i+4).equals("</b>"))
33 {
34 standend(); i+=3; continue;
35 }
36 setCharAt(i+x,y,s.charAt(i));
37 }
38 }
39
40 public static void main(String[] args)
41 {
42 //load the C library
43 System.loadLibrary("NCurses");
44 //init curses
45 NCurses.install();
46
47 NCurses sample = new NCurses();
48
49 //draw a box
50 for(int i=1;i+1< sample.getRowCount();++i)
51 {
52 sample.setCharAt(1,i,'*');
53 sample.setCharAt(sample.getColumnCount()-2,i,'*');
54 }
55 for(int i=1;i+1< sample.getColumnCount();++i)
56 {
57 sample.setCharAt(i,1,'*');
58 sample.setCharAt(i,sample.getRowCount()-2,'*');
59 }
60 /* draw some strings */
61 int n=0;
62 for(int i=2;i+3< sample.getRowCount();i+=3)
63 {
64 sample.drawString("<b>Menu \t"+(++n)+"</b>: Hello Menu",5,i);
65 }
66 /* update the screen */
67 sample.refresh();
68 /* wait 10 sec */
69 try{ Thread.sleep(10000); } catch(Exception err) {}
70 //dispose ncurses
71 NCurses.uninstall();
72 }
73 }

This class contains some native methods that are not implemented in this class but they will be loading (line 43 by calling System.loadLibrary)

We can compile this class:

javac NCurses.java

We can run JAVAH on this class. javah will generate the C header file that are needed to implement our native methods.

javah NCurses

This generates the following file: NCurses.h

1 /* DO NOT EDIT THIS FILE - it is machine generated */
2 #include <jni.h>
3 /* Header for class NCurses */
4
5 #ifndef _Included_NCurses
6 #define _Included_NCurses
7 #ifdef __cplusplus
8 extern "C" {
9 #endif
10 /*
11 * Class: NCurses
12 * Method: install
13 * Signature: ()I
14 */
15 JNIEXPORT jint JNICALL Java_NCurses_install
16 (JNIEnv *, jclass);
17
18 /*
19 * Class: NCurses
20 * Method: uninstall
21 * Signature: ()I
22 */
23 JNIEXPORT jint JNICALL Java_NCurses_uninstall
24 (JNIEnv *, jclass);
25
26 /*
27 * Class: NCurses
28 * Method: setCharAt
29 * Signature: (III)V
30 */
31 JNIEXPORT void JNICALL Java_NCurses_setCharAt
32 (JNIEnv *, jclass, jint, jint, jint);
33
34 /*
35 * Class: NCurses
36 * Method: refresh
37 * Signature: ()V
38 */
39 JNIEXPORT void JNICALL Java_NCurses_refresh
40 (JNIEnv *, jclass);
41
42 /*
43 * Class: NCurses
44 * Method: getRowCount
45 * Signature: ()I
46 */
47 JNIEXPORT jint JNICALL Java_NCurses_getRowCount
48 (JNIEnv *, jobject);
49
50 /*
51 * Class: NCurses
52 * Method: getColumnCount
53 * Signature: ()I
54 */
55 JNIEXPORT jint JNICALL Java_NCurses_getColumnCount
56 (JNIEnv *, jobject);
57
58 /*
59 * Class: NCurses
60 * Method: standout
61 * Signature: ()I
62 */
63 JNIEXPORT jint JNICALL Java_NCurses_standout
64 (JNIEnv *, jobject);
65
66 /*
67 * Class: NCurses
68 * Method: standend
69 * Signature: ()I
70 */
71 JNIEXPORT jint JNICALL Java_NCurses_standend
72 (JNIEnv *, jobject);
73
74 #ifdef __cplusplus
75 }
76 #endif
77 #endif

I've implemented the C methods in the following file: NCurses.c

1 #include "NCurses.h"
2 #include <string.h>
3 #include <curses.h>
4 #include <signal.h>
5
6 JNIEXPORT jint JNICALL Java_NCurses_install(JNIEnv *env, jclass clazz)
7 {
8 //(void) signal(SIGINT, finish); /* arrange interrupts to terminate */
9
10 (void) initscr(); /* initialize the curses library */
11 keypad(stdscr, TRUE); /* enable keyboard mapping */
12 (void) nonl(); /* tell curses not to do NL->CR/NL on output */
13 (void) cbreak(); /* take input chars one at a time, no wait for \n */
14 (void) noecho(); /* don't echo input */
15 clear();
16 move(0,0);
17 refresh();
18 return 0;
19 }
20
21 JNIEXPORT jint JNICALL Java_NCurses_uninstall(JNIEnv *env, jclass clazz)
22 {
23 endwin();
24 return 0;
25 }
26
27 JNIEXPORT jint JNICALL Java_NCurses_getRowCount(JNIEnv *env, jobject obj)
28 {
29 int h, w;
30 getmaxyx(stdscr, h, w);
31 return h;
32 }
33
34
35 JNIEXPORT jint JNICALL Java_NCurses_getColumnCount(JNIEnv *env, jobject obj)
36 {
37 int h, w;
38 getmaxyx(stdscr, h, w);
39 return w;
40 }
41
42 /*
43 * Class: NCurses
44 * Method: setCharAt
45 * Signature: (III)V
46 */
47 JNIEXPORT void JNICALL Java_NCurses_setCharAt
48 (JNIEnv *env, jclass object, jint x, jint y, jint chr)
49 {
50 mvaddch(y,x,chr);
51 }
52
53 /*
54 * Class: NCurses
55 * Method: refresh
56 * Signature: ()V
57 */
58 JNIEXPORT void JNICALL Java_NCurses_refresh
59 (JNIEnv *env, jclass object)
60 {
61 refresh();
62 }
63
64
65 /*
66 * Class: NCurses
67 * Method: standout
68 * Signature: ()I
69 */
70 JNIEXPORT jint JNICALL Java_NCurses_standout
71 (JNIEnv *env, jobject object)
72 {
73 standout();
74 }
75
76 /*
77 * Class: NCurses
78 * Method: standend
79 * Signature: ()I
80 */
81 JNIEXPORT jint JNICALL Java_NCurses_standend
82 (JNIEnv * env, jobject object)
83 {
84 standend();
85 }

before compiling the C source, I set the variable LD_LIBRARY_PATH. For my machine it was:

export LD_LIBRARY_PATH=${PWD}:/usr/local/lib:/usr/lib

We can now compile NCurses.c and create the C library. You may need to add the path the java C headers which are contained in ${JAVA_HOME}/include/ and ${JAVA_HOME}/include/{your-machine}

gcc -fpic -c NCurses.c -o NCurses.o
gcc -shared -o libNCurses.so NCurses.o -lcurses

Let's run our java program:

java NCurses

The result looks like this:

 *********************************************
 *      Menu  1    : Hello Menu              *
 *                                           *
 *                                           *
 *      Menu  2    : Hello Menu              *
 *                                           *
 *                                           *
 *      Menu  3    : Hello Menu              *
 *                                           *
 *                                           *
 *      Menu  4    : Hello Menu              *
 *                                           *
 *                                           *
 *      Menu  5    : Hello Menu              *
 *                                           *
 *                                           *
 *      Menu  6    : Hello Menu              *
 *                                           *
 *                                           *
 *                                           *
 *********************************************

That's it.
Pierre

My fNotebook: Apache Tomcat / Bioinformatics

Hi all,
here is how I installed created and installed today a web application based on JSP (Java Server Page) and running on tomcat.

A prior knowledge on how deploying a web application with tomcat is required so this post is more a notebook than a tutorial.

First download tomcat 6.0, extract it:

wget -q "http://apache.cict.fr/tomcat/tomcat-6/v6.0.14/bin/apache-tomcat-6.0.14.tar.gz"
tar xfz apache-tomcat-6.0.14.tar.gz

Fetch the mysql java connector, extract it, and move in into the tomcat 'lib' folder

wget -q "ftp://ftp.inria.fr/pub/MySQL/Downloads/Connector-J/mysql-connector-java-5.1.5.tar.gz"
tar xfz mysql-connector-java-5.1.5.tar.gz
mv mysql-connector-java-5.1.5/mysql-connector-java-5.1.5-bin.jar apache-tomcat-6.0.14/lib/

I need the java standard template library JSTL library. I fetch and extract it.

wget "http://people.apache.org/builds/jakarta-taglibs/nightly/projects/standard/jakarta-taglibs-standard-20060823.tar.gz"
tar xfz jakarta-taglibs-standard-20060823.tar.gz

I create a database of snp.

mysql -u root -p -D test -e 'create table snp(chrom varchar(10) ,chromStart int not null,chromEnd int not null,name varchar(20) unique not null)'

I fill this database with a few snp from dbsnp@ucsc

mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select chrom,chromStart,chromEnd,name from snp126 where chrom="chrM" ' |\
gawk -F ' ' '{printf("insert into test.snp(chrom,chromStart,chromEnd,name) values (\"%s\",%s,%s,\"%s\");\n",$1,$2,$3,$4);}' |\
mysql -u login -p

I add a mysql connection pool in apache. In apache-tomcat-6.0.14/conf/context.xml , I add the following code just before the last tag </Context>

<Resource name="jdbc/MYSQL" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="10000"
username="login" password="yourpassword" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://localhost:3306/test?autoReconnect=true"/>

we also need to setup a few properties before running tomcat:

export JAVA_HOME /usr/your-path/java1.6
export CATALINA_HOME=${PWD}/apache-tomcat-6.0.14
export CATALINA_BASE=${PWD}/apache-tomcat-6.0.14

we can now run tomcat.

./apache-tomcat-6.0.14/bin/startup.sh
Using CATALINA_BASE: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14
Using CATALINA_HOME: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14
Using CATALINA_TMPDIR: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14/temp
Using JRE_HOME: /usr/your-path/java1.6/jre

we then create a few new directories

mkdir -p ./src/jsp
mkdir -p ./src/org/lindenb/jsp

We create a first JSP Custom TAG in src/org/lindenb/jsp/Anchor2DbSNP.java. This custom JSP tag will be used to create a automatic anchor to dbSNP.

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;

/**
* This is a simple printing a link to dbSNP.
*/
public class Anchor2DbSNP extends BodyTagSupport
{
static private final Pattern RS_PATTERN=Pattern.compile("rs[0-9]+");

public int doEndTag() throws JspException
{
try
{
BodyContent bodyContent= getBodyContent();
if(bodyContent==null) return EVAL_PAGE;
String input=bodyContent.getString().trim().toLowerCase();
if(RS_PATTERN.matcher(input).matches())
{
getPreviousOut().print(
"<a href='http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs="+
input.substring(2)+
"'>"+
input+
"</a>"
);
}
else
{
getPreviousOut().print(input);
}
} catch(java.io.IOException err)
{
throw new JspException(err);
}
return EVAL_PAGE;
}
}

Another two custom tags will be used to display a simple genomic map in SVG.

Here is src/org/lindenb/jsp/ChromosomeTag.java

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;
import java.util.*;

public class ChromosomeTag extends BodyTagSupport
{
private static class Position
{
int position=0;
String name=null;
public Position(int position,String name)
{
this.position=position;
this.name=name;
}
}

private Vector<Position> items= null;
private int svgWidth=500;
private int itemHeight=20;


public int doStartTag() throws JspException
{
items= new Vector<Position>();
return EVAL_BODY_INCLUDE;
}

public void addPosition(int position,String name)
{
if(position<0 || name==null) return;
this.items.addElement(new Position(position,name));
}

public int doEndTag() throws JspException
{
//if(this.items.isEmpty()) return EVAL_PAGE;
int max=0;
int min=Integer.MAX_VALUE;
for(Position p:this.items)
{
max=Math.max(p.position,max);
min=Math.min(p.position,min);
}
try
{
JspWriter out= pageContext.getOut();
out.write("<svg xmlns:xlink='http://www.w3.org/1999/xlink' xmlns='http://www.w3.org/2000/svg' width='"+svgWidth+"' height='"+ (this.items.size()*itemHeight)+"' style='font-size:"+(itemHeight-10)+"pt;stroke-width:1;'>");
out.write("<rect x='0' y='0' width='"+svgWidth+"' height='"+ (this.items.size()*itemHeight)+"' style='fill:white; stroke:gray;'/>");
int y=0;
for(Position p:this.items)
{
int x= (int)(((p.position-min)/(float)(max-min))*(svgWidth-200))+100;
out.write("<line x1='"+x+"' y1='"+y+"' x2='"+x+"' y2='"+(y+itemHeight)+"' style='stroke:blue;'/>");

out.write("<line x1='0' y1='"+y+"' x2='"+svgWidth+"' y2='"+(y)+"' style='stroke:gray;'/>");

out.write("<text x='"+(x+4)+"' y='"+(y+5+itemHeight/2)+"' >"+p.name+"</text>");
y+=itemHeight;
}

out.write("</svg>");

}
catch(java.io.IOException err)
{
throw new JspException(err);
}
items=null;
return EVAL_PAGE;
}

public void release()
{
items=null;
}
}

and

src/org/lindenb/jsp/ChromItemTag.java

package org.lindenb.jsp;
import javax.servlet.jsp.*;
import javax.servlet.jsp.tagext.*;
import java.util.regex.*;


public class ChromItemTag extends BodyTagSupport
{
private int position=-1;
private String name="";

public void setPosition(int position) { this.position= position;}


public int doEndTag() throws JspException
{
BodyContent bodyContent= getBodyContent();
if(bodyContent!=null) this.name =bodyContent.getString().trim();
if(this.name==null || name.length()==0) this.name=String.valueOf(this.position);
Tag parent= findAncestorWithClass(this,ChromosomeTag.class);
if(parent==null) return EVAL_PAGE;
ChromosomeTag ct= ChromosomeTag.class.cast(parent);
ct.addPosition(this.position+20,this.name);
return EVAL_PAGE;
}

public void release()
{
name=null;
position=-1;
}
}

the file src/bio.tld is the file used to declare the three custom tags.

<?xml version="1.0" encoding="ISO-8859-1" ?>
<taglib xmlns="http://java.sun.com/xml/ns/j2ee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-jsptaglibrary_2_0.xsd"
version="2.0">

<description>Bioinfo JSP TAG library</description>
<display-name>Bioinfo</display-name>
<tlib-version>1.1</tlib-version>
<short-name>bio</short-name>
<uri>http://jsp.lindenb.org</uri>

<tag>
<name>rs</name>
<tag-class>org.lindenb.jsp.Anchor2DbSNP</tag-class>
<body-content>JSP</body-content>
<info>display a link to dbSNP</info>
</tag>

<tag>
<name>chrom</name>
<tag-class>org.lindenb.jsp.ChromosomeTag</tag-class>
<body-content>JSP</body-content>
<info>svg map</info>
</tag>

<tag>
<name>item</name>
<tag-class>org.lindenb.jsp.ChromItemTag</tag-class>
<body-content>JSP</body-content>
<info>svg item</info>
<attribute>
<name>position</name>
<required>true</required>
<rtexprvalue>true</rtexprvalue>
</attribute>
</tag>


</taglib>

the file cat src/jsp/page.jsp is our JSP. It displays a SVG map and a table of a few SNP. It uses the JSTL and our custom tags.

<jsp:root
xmlns:jsp="http://java.sun.com/JSP/Page"
xmlns:c="http://java.sun.com/jsp/jstl/core"
xmlns:sql="http://java.sun.com/jsp/jstl/sql"
xmlns:bio="http://jsp.lindenb.org"

version="2.0">
<jsp:directive.page contentType="text/xml; charset=iso-8859-1"/>
<jsp:output doctype-root-element="html"
doctype-public="-//W3C//DTD XHTML 1.0 Strict//EN"
doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"
omit-xml-declaration="true"
/>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>JSP Tutorial For Bioinformatics</title>
<!-- <meta http-equiv="Content-Type" content="application/xhtml+xml; charset=iso-8859-1" /> -->
</head>
<body>
<sql:query var="snps" dataSource="jdbc/MYSQL">select * from snp limit 10</sql:query>
<bio:chrom>
<c:forEach var="row" items="${snps.rows}">

<bio:item position="${row.chromStart}"><c:out value="${row.name}"/></bio:item>
</c:forEach>
</bio:chrom>

<sql:query var="snps" dataSource="jdbc/MYSQL">select * from snp limit 10</sql:query>
<table>
<tr><th>Position</th><th>Name</th></tr>
<c:forEach var="row" items="${snps.rows}">
<tr>
<td><c:out value="${row.chrom}"/>:<c:out value="${row.chromStart}"/>-<c:out value="${row.chromEnd}"/></td>
<td><bio:rs><c:out value="${row.name}"/></bio:rs></td>
</tr>
</c:forEach>
</table>
</body>
</html>
</jsp:root>

Tomcat needs src/web.xml as a descriptor to learn how to deploy this web application.

<?xml version="1.0" encoding="ISO-8859-1"?>
<web-app
xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
version="2.5">
<display-name>Application Name</display-name>
<description>Application Description</description>


<taglib>
<taglib-uri>http://jsp.lindenb.org</taglib-uri>
<taglib-location>/WEB-INF/bio.tld</taglib-location>
</taglib>

<!-- see http://www.developer.com/java/ejb/article.php/1447551 -->
<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt</taglib-uri>
<taglib-location>/WEB-INF/fmt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/fmt-rt</taglib-uri>
<taglib-location>/WEB-INF/fmt-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/core</taglib-uri>
<taglib-location>/WEB-INF/c.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/core-rt</taglib-uri>
<taglib-location>/WEB-INF/c-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/sql</taglib-uri>
<taglib-location>/WEB-INF/sql.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/sql-rt</taglib-uri>
<taglib-location>/WEB-INF/sql-rt.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/x</taglib-uri>
<taglib-location>/WEB-INF/x.tld</taglib-location>
</taglib>

<taglib>
<taglib-uri>http://java.sun.com/jstl/x-rt</taglib-uri>
<taglib-location>/WEB-INF/x-rt.tld</taglib-location>
</taglib>


</web-app>

and we finally need src/build.xml to build all this stuff with ant.

<?xml version="1.0" encoding="ISO-8859-1"?>
<project name="Test" default="install" basedir=".">
<property name="tomcat.home" value="../apache-tomcat-6.0.14"/>
<property name="jstl.home" value="../jakarta-taglibs/standard"/>
<property name="webapps" value="${tomcat.home}/webapps"/>

<target name="compile">
<javac destdir="." srcdir="." debug="on">
<include name="org/lindenb/jsp/*.java"/>
<classpath>
<pathelement location="${jstl.home}/lib/jstl.jar"/>
<pathelement location="${jstl.home}/lib/standard.jar"/>
<pathelement location="${tomcat.home}/lib/servlet-api.jar"/>
<pathelement location="${tomcat.home}/lib/jsp-api.jar"/>
</classpath>
</javac>

<jar destfile="bio.jar"
basedir="."
includes="org/**"

/>

</target>

<target name="install" depends="compile">
<!-- yes, I know there is also war task... -->
<zip destfile="${webapps}/test.war">
<zipfileset dir="jsp" includes="*.jsp"/>
<zipfileset dir="." includes="web.xml" prefix="WEB-INF"/>
<zipfileset dir="${jstl.home}/tld" includes="*.tld" prefix="WEB-INF"/>
<zipfileset dir="." includes="*.tld" prefix="WEB-INF"/>
<zipfileset dir="${jstl.home}/lib" includes="*.jar" prefix="WEB-INF/lib"/>
<zipfileset dir="." includes="bio.jar" prefix="WEB-INF/lib"/>
</zip>
</target>

</project>

let's build this application. It creates a web archive (war) in the webapps folder of tomcat.

ant
Buildfile: build.xml

compile:
[jar] Building jar: /home/pierre/tmp/TOMCAT/src/bio.jar

install:
[zip] Building zip: /home/pierre/tmp/TOMCAT/apache-tomcat-6.0.14/webapps/test.war

BUILD SUCCESSFUL
Total time: 1 second

When you open "http://localhost:8080/test/page.jsp" you should get the following screen:

Pierre

ShiftHappens

A great presentation about the future of eductation (somehow disheartening...)





see also: http://shifthappens.wikispaces.com/

Embedded "ManyEyes" interactive visualization

Today ManyEyes launched the ability to embed an interactive visualization into your own blog, personal webpage or any other page you think makes sense: see http://blog.many-eyes.com/2007/12/12/embeddable-visualizations-have-arrived/.



Pierre

IBD Status applet

I've just released an applet called IBDStatus. This applet (java 6 is required) is freely available at:

http://lindenb.integragen.org/breakpoint/

This applet takes as input the breakpoint analysis data (Nature. Dib et al.(1996); 380:152-154) from the 'Fondation Jean-Dausset' (CEPH) and display the Identical By Descent (IBD) regions between a pair of related individuals. Two people share an allele identical by descent if the two copies of the allele were inherited from a common ancestor. A pair of siblings can share 0, 1, or 2 alleles:

• 0: not the same alleles


• 1: only one allele in common


• 2: both same alleles

Picture from Abel & Dessein

As an example, this IBD status can be used to design the controls of a CGH assay.

• Top left pane: a linkage table with genotype=f(individual,marker)


• Middle left pane: the list of individual: using the Ctrl-key select
  two related
  individuals an press the Add sib button. Your new pair is added in
  the bottom left table.


• Bottom left pane: the list of sib-pairs: for each pair, the IBD status
  is displayed in the right table



• Right table:
  
  
  
  • Marker index
  
  
  • chromosome
  
  
  • STS D-Number
  
  
  • Start-position (build 36)
  
  
  • End-position (build 36)
  
  
  • IBD status of each sib-pair(if any)
  
  
  • Count IBD with unknown status
  
  
  • Count IBD. 0
  
  
  
  • Count IBD. 1
  
  
  • Count IBD. 2
  
  
  
  

I wrote this software a few monthes ago but it was not much used, so I
was given the permission to release this version to the community.
Enjoy.

Pierre