YOKOFAKUN

SciFOAF 2.0

2008-07-21T00:08:00.000+02:00

If you're following me on twitter or on friendfeed you may know that I've re-written a new version of SciFOAF. Here is the documentation: What is SciFOAF SciFOAF is the second version of a tool I created to build a FOAF/RDF file from your publications in ncbi/pubmed. The FOAF project defines a semantic format based on RDF/XML to define persons or groups, their relationships, as well as their

Bioinformatics Zen : Bioinformatics Career Survey

2008-07-01T18:32:00.000+02:00

Via Bioinformatics Zen: Loading... If you’d like to embed this form in your own webpage or blog, using the following HTML.Loading...

Parsing JSON with javacc my Notebook.

2008-07-01T14:04:00.000+02:00

Although I didn't wrote a new great programming language, I had a little experience with C lexers/parsers especialy with lex/yacc|flex/bison , a LALR parser. Now I'm programming in Java, I've been looking for the parsers available for this language: the most popular tools seems to be the top-down parsers javacc and antlr. In this post I show how I wrote a simple javacc parser reading a JSON

bye ! bye ! my private web server !

2008-07-01T10:18:00.001+02:00

I'm about to leave my current job. Thus, soon or later, the web server where I stored my stuff will diseappear. Most of those items have been introduced on this blog. Pubmed2connotea: A Greasemonkey user script which alters the content web page when browsing your bibliography on NCBI pubmed by inserting a new hyperlink "Add to Connotea/citeulike/delicious". I've transfered the script on http://

Pubmed, impact factors, sorting and FriendFeed

2008-06-10T22:06:00.001+02:00

I recently said on twitter that I wished I could sort the articles on pubmed using the impact factors of the journals. What followed was a demonstration of the power of friendfeed and was also observed under some other circumstances by Deepak Singh, Pedro Beltrao and some others... Within a day several persons joined the conversation on friendfeed and among them, Lars Juhl Jensen and Deepak

I'm looking for a job !

2008-06-10T13:07:00.000+02:00

Hi all, I've just given my letter of resignation to my current employer , thus I'll be free from my professional obligations on September 1st and from now on I'm looking for a new fascinating job combining biology and informatics near Paris, France. This blog is a proof of my passion and my motivation for this area of interest. Recruiters can contact me via e-mail ( plindenbaum at yahoo fr ) and

NCBI Blast+ XSLT => XHTML + SVG

2008-05-27T16:10:00.001+02:00

This post was inspired by the article Processing and duplicons on human chromosomes sent by Paulo Nuin yesterday and the short discussion that followed on FriendFeed. Paulo described in this article how the processing tool was used to display an output of ncbi-blast. Here I show how a XSLT stylesheet can be used to transform a Blast into a XHTML+SVG page. The stylesheet described here is

Science!

2008-05-26T09:08:00.000+02:00

SCIENCE !

Leonard Colebrook: Creating a Biography in Wikipedia

2008-05-25T17:31:00.000+02:00

Today I created a new article in wikipedia about Leonard Colebrook who was an " English medical researcher who introduced the use of Prontosil, the first sulfonamide drug, as a cure for puerperal, or childbed, fever, a condition resulting from infection after childbirth or abortion (Encyclopaedia Britannica)" (Let's be clear, I didn't know who was that guy till today). Here is how I wrote this

Twitter m'a tuer

2008-05-16T09:45:00.000+02:00

Just like Paweł Szczęsny ( on http://freelancingscience.com), I'm using less and less this blog favor of twitter, especially for the short posts . For example, yesterday I sent this information on twitter: "NCBI announces a pyhton and a perl wrapper for the NCBI C++ toolkit". I'm also starting using friendfeed. Image found here Pierre

Bio-Twitters, Unite !

2008-04-14T21:59:00.001+02:00

If your a scientist, a bioinformatician, etc... join the scientific community of the biotwitters on http://twitter.com. Follow @biotecher to find all the biotwitters in one place (Thanks Attila !) and follow me on @yokofakun. If you don't know twitter, here is a short video about it: Pierre

BerkeleyDB and Hapmap: My notebook.

2008-04-04T20:57:00.000+02:00

I'm currently trying to find the best way to store some genotypes. For example I need to store 278.766.958 illumina genotypes (marker,individual, allele1, allele2) and mysql, even with indexes, is getting slow when I'm looking for the Mendelian incompatibilities. Deepak suggested via twitter to use HDF5 but as far as I understand the documentation, HDF5 is "just" a smarter implementation of the

Study Collaborators Included in PubMed

2008-04-03T21:02:00.000+02:00

Via NLM Technical Bulletin: As of November 2007, there were over 57,000 occurrences of group (corporate) authors in MEDLINE/PubMed with over 17,000 citations with no co-occurring personal authors. Not everyone involved in a group is actually writing or authoring the paper, however. NLM agrees (...) that "Authorship credit should be based onsubstantial contributions to conception and design, or

xul4wikipedia

2008-03-17T06:24:00.001+01:00

I've added a few more individuals in my History Of Science and I've also tried to generate an iCal version of this dataset to display the birth/death dates of all those persons (http://lindenb.integragen.org/xulhistory/history.ical) however there is a bug in this file as the events are not correctly displayed in google-calendar. Does anyone knows why ? There is now a new beautiful version of

pubmed xml references to wikipedia ref

2008-03-16T21:13:00.000+01:00

I wrote a simple xsl stylesheet which transform the XML output from pubmed to a wikipedia . The xsl fle is available here: http://lindenb.googlecode.com/svn/trunk/src/xsl/pubmed2wiki.xsl I used it with an article about Sir John Robert Vane who discovered the action of aspirin on prostaglandin biosynthesis.

Custom Search Engine For Bioinformatics

2008-03-10T20:21:00.000+01:00

Mostly because I need this every time, I wrote a few "Custom Search" engines for dbSNP, Hapmap and the ICSC Genome Browser. Those engines are available at http://lindenb.integragen.org/opensearch/opensearch.html. Pierre

Freebase Wikipedia Extraction (WEX)

2008-02-19T11:06:00.000+01:00

Via the Freebase blog. The Freebase Wikipedia Extraction (WEX) http://download.freebase.com/wex/ is a processed dump of the English language Wikipedia. The wiki markup for each article is transformed into machine-readable XML, and common relational features such as templates, infoboxes, categories, article sections, and redirects are extracted in tabular form. Freebase WEX is provided as a set

Freebase and the History of Sciences

2008-02-14T21:15:00.001+01:00

(feed readers, this post is better displayed on the web site) I've been looking for a way to get a structured description of the biographies of the scientists threw the History. One of my investigation led to wikistory, a webstart application based on the data extracted from Wikipedia by the project DBPedia. However, the data collected from DBPedia are mostly based on the infoboxes and most of

Creating a XUL extension for Mozilla/Firefox: my notebook.

2008-02-02T21:34:00.000+01:00

(RSS readers, this file is better displayed on my blog) Here is my notebook on how to create an extension for firefox. The following example was tested with firefox 2.0.0.11. This extension is used to insert a few default templates (such as Template:Infobox_scientist ) when editing a biography on Wikipedia. Infoboxes are used , for example by DBPedia, to create a structured version of wikipedia.

Scrollable HTML table

2008-01-24T21:06:00.000+01:00

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

ACC	Position
NP_001004053	Scientists for Better PCR 2008-01-11T15:09:00.000+01:00 Via:Coffee and Science. JAVA Native Interface (JNI): notebook 2008-01-10T16:01:00.000+01:00 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

ACC

Position

NP_001004053

Scientists for Better PCR

2008-01-11T15:09:00.000+01:00

Via:Coffee and Science.

JAVA Native Interface (JNI): notebook

2008-01-10T16:01:00.000+01:00

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