http://www.bioinfo-user.org.uk/dokuwiki/ 2008-08-25T16:06:51+01:00 http://www.bioinfo-user.org.uk/dokuwiki/ http://www.bioinfo-user.org.uk/dokuwiki/lib/images/favicon.ico text/html 2008-08-24T15:48:02+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=hpm:links:bioinformatics&rev=1219589282&do=diff Bioinformatics sites, software and databases Accelrys GCG The sequence analysis tool set BIMAS Home Page BioInformatics and Molecular Analysis Section, NIH BioConductor Open source software project for the analysis and comprehension of genomic data. Bioinformatics @ The University of Manchester Details of bioinformatics courses and resources at the University of Manchester Bioinformatics.Org: The Open-Access Institute Open Source bioinformatics BioJava Java library for use in bioin… text/html 2008-08-23T19:07:36+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=hpm:about:jic_1998-2001&rev=1219514856&do=diff 16th March 1998 to 7th January 2001 John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK * Curation, development and publication of the BrassicaDB genome database * Development of a CORBA Interface to ACEDB (CITA) * Development of a graphical Java interface to ACEDB databases, using CITA. * Maintence of the JIC Biological Information Server * Data managment for the BBSRC Brassica SSR Programme * Development for BBSRC's Brassica Genome Project text/html 2008-08-23T19:06:45+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=hpm:about:ebi_2005&rev=1219514805&do=diff 1st July 2005 to present European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK * SRS administration * Maintenance and development for <http://srs.ebi.ac.uk/> * Migration planning for SRS 7.1.3.x to SRS 8.x text/html 2008-08-17T16:22:40+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=hpm:notes:eeepc_1000_and_ubuntu&rev=1218986560&do=diff Install Ubuntu Download the latest Ubuntu LiveCD for x86, currently Ubuntu 8.04.1 LTS (hardy heron), and burn the image to a CD. If the EeePC is your only Internet connected computer, then also download the Array.org kernel and save it to a USB drive or SD card (see Download the Kernel Manually). This is needed later to get the ethernet and wireless working. text/html 2008-08-17T09:23:19+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=notes&rev=1218961399&do=diff * UNIX System Information: methods for collecting information about a UNIX system * Apache httpd, Tomcat & mod_jk2: setting up Apache httd, Tomcat and mod_jk2 * MythTV on a EPIA SP13000: setting up a MythTV box * LCD/CRT Switching on an IBM Thinkpad R50e * Linux on an Apple iBook * PNY Flash Card Reader and Linux * BogoMips for Linux without Installing * GenericNQS: configuring the batch queue system * XDMCP: using Cygwin to access a remote X windows desktop * RAM Speeds: vari… text/html 2008-07-12T13:19:31+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=notes:thinkpad_r50e_video&rev=1215865171&do=diff While CRT/LCD switching works perfectly under Ubuntu 7.10, the upgrade to Ubuntu 8.04 breaks it. However it turns out the restoring LCD/CRT switching with the Fn+F7 key combo is actually quite simple. i810switch The i810switch and i810rotate programs are used to control the device output is sent to, so they need to be installed: text/html 2008-07-11T00:41:55+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=notes:unixsysteminformation&rev=1215733315&do=diff Operating System Information OS: Generic On all UNIX and UNIX-like systems the uname command can be used to get some information about the operating system and platform. The simplest usage is to display all the information available. For example: text/html 2008-06-28T15:51:11+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=projects:ita&rev=1214664671&do=diff About ITA is a single, simple, Java API to access AceDB databases via a selection of connection methods. The connections types are handled via specialist modules which are wrapped in a single interface. Connection Methods Database connections can be of the following types: text/html 2008-06-28T15:28:42+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=projects:acephp:readme&rev=1214663322&do=diff AcePHP ====== About ----- AcePHP is a pure PHP (http://www.php.net/) interface to AceDB (http://www.acedb.org/) databases. As well as the PHP APIs a collection of test/sample code and a basic database browser are provided. Installation ------------ 1. Download the distribution. 2. Unpack the distribution gunzip -c acephp-20040815.tar.gz | tar xvf - To get up and running quickly, you may want to ensure the directory the distribution is unpacked into is already under your web server an… text/html 2008-06-13T20:23:35+01:00 hpm http://www.bioinfo-user.org.uk/dokuwiki/doku.php?id=hpm:links:bioinformatics:workflows&rev=1213385015&do=diff Workflow engines and repositories in use in bioinformatics. Bioinformatic Workflow Builder Interface (BioWBI) Prototype workflow tool from IBM alphaWorks Galaxia Open Source workflow engine written in PHP Kepler Project Open-source scientific workflow system Microsoft Windows Workflow Foundation Workflow engine for Microsoft .NET applications myExperiment Repository of bioinformatics workflows Pegasus Scientific workflow management Pegasys: workflow management for bioinformatics W…