MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'YOKOFAKUN' source. Wed, 19 Nov 2008 22:56:08 +0100 http://plindenbaum.blogspot.com/2008/11/sparql-for-solubilityrdf-my-notebook.html In a recent thread on FriendFeed , I've transformed Jean-Claude's Bradley's data about the solubility of some compounds into RDF. The original data set looks like this: The RDF version looks like this: (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1951953 Tue, 11 Nov 2008 05:00:00 +0100 1951953 http://plindenbaum.blogspot.com/2008/11/ibm-many-eyes-wikified.html I've just received my invitation to test the wikified version of ManyEyes. http://manyeyes.alphaworks.ibm.com/wikified/ (see my old post about ManyEyes [here]). This wikified version is really cool. Your data are edited in a wiki. For example I've downloaded a count of the snps on the human genome from the UCSC:mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select chrom,( (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1939157 Wed, 05 Nov 2008 05:00:00 +0100 1939157 http://plindenbaum.blogspot.com/2008/10/ebiintact-web-service-api-my-notebook.html This post covers my experience with the IntAct API at EBI. IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. This web service is invoked for searching binary interactions, it is described (but not documented...) as a WSDL file (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1924518 Thu, 30 Oct 2008 04:00:00 +0100 1924518 http://plindenbaum.blogspot.com/2008/10/emblstrings-find-interactors-at-2.html Thank (again) to the Life Scientists on FriendFeed I've discoreved the API of STRING8 ( STRING 8—a global view on proteins and their functional interactions in 630 organisms NAR 2008): STRING is a database and web resource dedicated to protein–protein interactions, including both physical and functional interactions.. I've used this API to find the partners of a protein at two degrees of (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1921009 Wed, 29 Oct 2008 04:00:00 +0100 1921009 http://plindenbaum.blogspot.com/2008/10/survey-of-proteins-on-wikipedia.html Via FriendFeed I've started a collaboration with Andrew Su on the state of the articles about the proteins in wikipedia. I've used the media wiki (http://en.wikipedia.org/w/api.php) to extract the revisions, the sizes of all the articles containing the Template:PBB_Summary. A result of this survey is available here. We first tried to use IBM/Many eyes to display the results, but the applet ran (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1921008 Wed, 29 Oct 2008 04:00:00 +0100 1921008 http://plindenbaum.blogspot.com/2008/10/javadoc-is-not-enough-java2dia.html I just wrote a tiny tool used to draw a graph for a java hierarchy. The input of the program is a set of jar files and the name of the classes to be displayed. The source code is available here: http://code.google.com/p/lindenb/source/browse/trunk/proj/tinytools/src/org/lindenb/tinytools/Java2Dot.java. The information about each class is obtained using the java.lang.reflect API and the classes (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1901575 Tue, 21 Oct 2008 04:00:00 +0100 1901575 http://plindenbaum.blogspot.com/2008/10/creating-dia-diagrams-from-mysql-via.html During a conversation on FriendFeed about using inkscape and Dia, Chris Lasher asked me if I tried to use inkscape to create diagrams in SVG format. This gave me the idea to have a new/fresh look at Dia and see if I could use it for my self-interest (I should soon manage a mysql database with plenty of tables but I'm missing such schema). Dia (http://www.gnome.org/projects/dia/ ) can be used to (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1876100 Mon, 13 Oct 2008 04:00:00 +0100 1876100 http://plindenbaum.blogspot.com/2008/10/what-is-in-list-of-snp-again-but-gui.html In a previous post I described how I generated some wrappers in java to map the tables of the mysql database at the UCSC, and I wrote a tool to get the data about a set of snp (cytoband, genes, hapmap...). Today I was asked if I could transform this application into a GUI (the fear of the infamous command line.. again...) That was straightforward to embed my code into an interactive software. I (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1868561 Thu, 09 Oct 2008 04:00:00 +0100 1868561 http://plindenbaum.blogspot.com/2008/10/building-presentation-with-inkscape.html OK, I hate PowerPoint ... ... and I hate OpenOffice/Impress Next week, I'll present a talk about how to handle a bibliography with the tools available on the web (RSS, social bookmarking, zotero, etc...). Today I tried to build the slides using inkscape (the SVG editor) and apache batik (a Java-based toolkit for applications that want to use images in the SVG format). Each slide was drawn (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1865517 Wed, 08 Oct 2008 04:00:00 +0100 1865517 http://plindenbaum.blogspot.com/2008/10/java-wrappers-for-tables-of.html Years ago, Jim Kent(UCSC) (the author of the BLAT algorithm) published in the Linux Journal "autoSql and autoXml: Code Generators from the Genome Project" the tools generate database definitions for SQL, write C header files with your data definitions and function prototypes, write C code to get data to and from C structures and generate C code for an XML parser. For example the following 'as' (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1852642 Fri, 03 Oct 2008 04:00:00 +0100 1852642 http://plindenbaum.blogspot.com/2008/09/center-for-study-of-human-polymorphisms_19.html In my previous post I showed how I used apache velocity to generate some 'C' code for the Operon project based on BerkeleyDB. I also generated the Makefiles and some Lex and Yacc files to create a simple language to query each database. Today I've compiled and linked my first applications. Each application will use my simple language to query each database without having to write a new piece of (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1809807 Fri, 19 Sep 2008 04:00:00 +0100 1809807 http://plindenbaum.blogspot.com/2008/09/generating-c-code-with-apache-velicity.html I'm currently working on Operon ( http://regulon.cng.fr/) a database developped by Mario Foglio at The National Center of Genotyping. The whole database/storage is developped around the Berkeley C API and I've been asked to write a clean 'C' API to access the data. Most data are stored with C structures and I wanted to quickly write the methods to: * create a new instance of each structure * free (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1806330 Wed, 17 Sep 2008 04:00:00 +0100 1806330 http://plindenbaum.blogspot.com/2008/09/what-is-in-list-of-snp.html Here is a common question: "Here is a list of snp genotyped with a high p-value. Is there anything interesting in this snp list ? is there a common link between those snp ?". Today, to answer this question, I've played with NCBI ELink. ELink checks for the existence of an external or link from a list of one or more primary IDs; retrieves IDs and relevancy scores for links to (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1802747 Tue, 16 Sep 2008 04:00:00 +0100 1802747 http://plindenbaum.blogspot.com/2008/09/center-for-study-of-human-polymorphisms.html I've started my first week at the center Center for the Study of Human Polymorphisms and today we had our first meeting with Mario Foglio and some other to define what will be my job in the following monthes. As I said, I will collaborate with the National Center of Genotyping on Operon, a feasible bioinformatics platform to centralize scientific software and biomedical data with internal results (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1768943 Fri, 05 Sep 2008 04:00:00 +0100 1768943 http://plindenbaum.blogspot.com/2008/09/ubiquity-arf-arf-smooch-achoo-wee-woo.html Ok, after a few others (Pawel, Thomas Lemberger, Egon, )I've succumbed to Mozilla Ubiquity, an experimental Firefox extension that (they say) gives you a powerful way to interact with the Web. The following useless script comics inserts a speech balloon using the font samples from http://www.dafont.com/ CmdUtils.CreateCommand({ name: "comics", author: { name: "Pierre Lindenbaum", email: " (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1754747 Tue, 02 Sep 2008 04:00:00 +0100 1754747 http://plindenbaum.blogspot.com/2008/09/im-not-looking-for-job-anymore-welcome.html Today was my first day as a bioinformatician at the Center for the Study of Human Polymorphisms (CEPH http://www.cephb.fr/en/cephdb) and I want to thank my former colleagues Christine K and Philippe Gesnouin (philguess on twitter/FF ) who helped me to find this position. It's a short term contract (one year). The CEPH is localized in Paris near the St-Louis Hospital and the "Place de la (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1750213 Mon, 01 Sep 2008 04:00:00 +0100 1750213 http://plindenbaum.blogspot.com/2008/08/mesh-fequencies-pubmed-articles.html In a recent post on his blog, David Rothman was asked for a 3rd Party PubMed/MEDLINE Tool: What I’d like to do is to be able to enter the PMIDs of several citations and have the tool search MEDLINE via PubMed for the assigned MeSH terms, and return a single list of the terms used by any of the entered citations with a measurement of frequency. For example, if I input PMIDs 16234728, 15674923, and (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1746353 Sat, 30 Aug 2008 04:00:00 +0100 1746353 http://plindenbaum.blogspot.com/2008/08/my-old-thesis-presentation.html I found the my thesis presentation (in french, 2000) in the old iBook I left in my cellar. RoXaN, une nouvelle protéine cellulaire interagissant avec la protéine non-structurale NSP3 du RotavirusView SlideShare presentation or Upload your own. (tags: roxan protein) It is really outdated now :-) .... I wonder how I would write this presentation now... this makes me think about this presentation (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1746352 Sat, 30 Aug 2008 04:00:00 +0100 1746352 http://plindenbaum.blogspot.com/2008/07/feeling-like-newbie-parsing-ncbi.html I've been recently interested in the new popular language Ruby and its web framework Rails for two reasons: First,this picture: Second, Matt Wood's blog about bioinformatics and ruby. So here is my very first experience with ruby. The book I used was Very good for learning but a little bit outdated. And I shoudl have started with a book about ruby only. I've downloaded rails as described here (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1652374 Fri, 25 Jul 2008 04:00:00 +0100 1652374 http://plindenbaum.blogspot.com/2008/07/scifoaf-20.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1640295 Mon, 21 Jul 2008 04:00:00 +0100 1640295 http://plindenbaum.blogspot.com/2008/07/bye-bye-my-personnal-server.html 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:// (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1560902 Tue, 01 Jul 2008 04:00:00 +0100 1560902 http://plindenbaum.blogspot.com/2008/07/parsing-json-with-javacc-my-notebook.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1560901 Tue, 01 Jul 2008 04:00:00 +0100 1560901 http://plindenbaum.blogspot.com/2008/07/bioinformatics-zen-bioinformatics.html Via Bioinformatics Zen: Loading... If you’d like to embed this form in your own webpage or blog, using the following HTML.Loading... (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1560900 Tue, 01 Jul 2008 04:00:00 +0100 1560900 http://plindenbaum.blogspot.com/2008/06/im-looking-for-job.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1508475 Tue, 10 Jun 2008 04:00:00 +0100 1508475 http://plindenbaum.blogspot.com/2008/06/pubmed-impact-factors-sorting-and.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1508474 Tue, 10 Jun 2008 04:00:00 +0100 1508474 http://plindenbaum.blogspot.com/2008/05/ncbi-blast-xslt-xhtml-svg.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1472521 Tue, 27 May 2008 04:00:00 +0100 1472521 http://plindenbaum.blogspot.com/2008/05/science.html SCIENCE ! (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1467881 Mon, 26 May 2008 04:00:00 +0100 1467881 http://plindenbaum.blogspot.com/2008/05/leonard-colebrook-creating-biography-in.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1467882 Sun, 25 May 2008 04:00:00 +0100 1467882 http://plindenbaum.blogspot.com/2008/05/twitter-ma-tuer.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1446129 Fri, 16 May 2008 04:00:00 +0100 1446129 http://plindenbaum.blogspot.com/2008/04/bio-twitters-unite.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1370781 Mon, 14 Apr 2008 04:00:00 +0100 1370781 http://plindenbaum.blogspot.com/2008/04/berkeleydb-and-hapmap-my-notebook.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1352088 Fri, 04 Apr 2008 04:00:00 +0100 1352088 http://plindenbaum.blogspot.com/2008/04/study-collaborators-included-in-pubmed.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1349607 Thu, 03 Apr 2008 04:00:00 +0100 1349607 http://plindenbaum.blogspot.com/2008/03/xul4wikipedia.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1306544 Mon, 17 Mar 2008 04:00:00 +0100 1306544 http://plindenbaum.blogspot.com/2008/03/pubmed-xml-references-to-wikipedia-ref.html 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. (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1306545 Sun, 16 Mar 2008 04:00:00 +0100 1306545 http://plindenbaum.blogspot.com/2008/03/custom-search-engine-for-bioinformatics.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1291046 Mon, 10 Mar 2008 04:00:00 +0100 1291046 http://plindenbaum.blogspot.com/2008/02/freebase-wikipedia-extraction-wex.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1241935 Tue, 19 Feb 2008 05:00:00 +0100 1241935 http://plindenbaum.blogspot.com/2008/02/freebase-and-history-of-sciences.html (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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1231876 Thu, 14 Feb 2008 05:00:00 +0100 1231876 http://plindenbaum.blogspot.com/2008/02/creating-xul-extension-for.html (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. First, create a new profile for firefox, say TEST by invoking firefox with option '-P' (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1196725 Sat, 02 Feb 2008 05:00:00 +0100 1196725 http://plindenbaum.blogspot.com/2008/01/scrollable-html-table.html A CSS tip I learned today: you can get a scrollable HTML table by using overflow in the associated CSS stylesheet. ACCPosition NP_001004053 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1174927 Thu, 24 Jan 2008 05:00:00 +0100 1174927 http://plindenbaum.blogspot.com/2008/01/introduction-of-new-relationship-types.html 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. (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1173230 Wed, 23 Jan 2008 05:00:00 +0100 1173230 http://plindenbaum.blogspot.com/2008/01/thomson-scientific-launches.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1158232 Thu, 17 Jan 2008 05:00:00 +0100 1158232 http://plindenbaum.blogspot.com/2008/01/nucl-acids-res-database-issue-january.html 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" ? (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1148189 Mon, 14 Jan 2008 05:00:00 +0100 1148189 http://plindenbaum.blogspot.com/2008/01/scientists-for-better-pcr.html Via:Coffee and Science. (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1146404 Fri, 11 Jan 2008 05:00:00 +0100 1146404 http://plindenbaum.blogspot.com/2008/01/java-native-interface-jni-notebook.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1142445 Thu, 10 Jan 2008 05:00:00 +0100 1142445 http://plindenbaum.blogspot.com/2007/12/my-fnotebook-apache-tomcat.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1108688 Thu, 20 Dec 2007 05:00:00 +0100 1108688 http://plindenbaum.blogspot.com/2007/12/shifthappens.html A great presentation about the future of eductation (somehow disheartening...) see also: http://shifthappens.wikispaces.com/ (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1100138 Mon, 17 Dec 2007 05:00:00 +0100 1100138 http://plindenbaum.blogspot.com/2007/12/embedded-manyeyes-interactive.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1091368 Thu, 13 Dec 2007 05:00:00 +0100 1091368 http://plindenbaum.blogspot.com/2007/12/ibd-status-applet.html 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 (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1090481 Wed, 12 Dec 2007 05:00:00 +0100 1090481 http://plindenbaum.blogspot.com/2007/12/google-chart-api-launched.html Today Google the Google Chart API a simple URL based tool for creating charts and graphs for websites. For example the following url: http://chart.apis.google.com/chart? chco=ff0000,00ff00,0000ff /* colors */ &cht=p3 /* Chart Type= Pie */ &chd=t:1,2,3,4 /* Values */ &chs=400x200 /* Dimension */ &chl=Nature|PNAS|Science|EMBO|Virology /* LABELS */ will display this image: Pierre (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1074980 Thu, 06 Dec 2007 05:00:00 +0100 1074980 http://plindenbaum.blogspot.com/2007/12/pivot.html FYI: I put 'pivot' in the project hosted at http://code.google.com/ where I put some of my (open) source codes. Pivot is a java command-line tool, it digests a tabular source and prints a summary of the data. See the wiki page for more information http://code.google.com/p/lindenb/wiki/Pivot. Pierre (Source: YOKOFAKUN) YOKOFAKUN blogs http://www.medworm.com/rss/comments.php?id=1064230 Sun, 02 Dec 2007 05:00:00 +0100 1064230