BASE setup

1. edit my.cnf:
add:
default-storage-engine=INNODB

#skip-innodb
# Uncomment the following if you are using InnoDB tables
innodb_data_home_dir = C:/map/mysql/
innodb_data_file_path = ibdata1:10M:autoextend
innodb_log_group_home_dir = C:/map/mysql/
innodb_log_arch_dir = C:/map/mysql/
# You can set .._buffer_pool_size up to 50 - 80 %
# of RAM but beware of setting memory usage too high
set-variable = innodb_buffer_pool_size=16M
set-variable = innodb_additional_mem_pool_size=2M
# Set .._log_file_size to 25 % of buffer pool size
set-variable = innodb_log_file_size=5M
set-variable = innodb_log_buffer_size=8M
innodb_flush_log_at_trx_commit=1
set-variable = innodb_lock_wait_timeout=50

2. JAVA_HOME and JRE_HOME

Multiple Tomcat HOWTO

Multiple Tomcat HOWTO
Three changes:
1)
<!-- Define a non-SSL HTTP/1.1 Connector on port 8080 -->
<Connector port="8080" maxHttpHeaderSize="8192"
to:
<!-- Define a non-SSL HTTP/1.1 Connector on port 8080 -->
<Connector port="9091" maxHttpHeaderSize="8192"
2)
<Server port="8005" shutdown="SHUTDOWN">
to:
<Server port="8105" shutdown="SHUTDOWN">
3)
<!-- Define an AJP 1.3 Connector on port 8009 -->
<Connector port="8009"
enableLookups="false" redirectPort="8443" protocol="AJP/1.3" />
to:
<!-- Define an AJP 1.3 Connector on port 8009 -->
<Connector port="8109"
enableLookups="false" redirectPort="8443" protocol="AJP/1.3" />

NVOSSSetupLinux - Main - Space Telescope Science Institute

NVOSSSetupLinux - Main - Space Telescope Science Institute: "Configuring your Linux laptop"

>setenv JAVA_HOME /usr/local/java/j2sdk1.4.2_08 (for csh users)
or
>JAVA_HOME=/Library/Java/Home; export JAVA_HOME (for bash users)

PartiGene

PartiGene: "Expressed sequence tags (ESTs)"
Expressed sequence tags (ESTs) offer a low cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organising this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite which uses freely available public domain software to:
(1) process raw trace chromatograms into sequence objects suitable for submission to dbEST;
(2) place these sequences within a genomic context;
(3) perform customisable annotation of the data; and
(4) present the data as HTML tables and an SQL database resource.

PartiGene has been used to create a number of non-model organism database resources including NEMBASE ( http://www.nematodes.org). The packages are readily portable, freely available and can be run on simple Linux based workstations.

AVAILABLE SOFTWARE:

trace2dbest: software to process sequence trace files ready for submission to NCBI dbEST. Versions for simple processing of sequence trace files, and for processing GSS sequences, are also available.

PartiGene: software for processing sequences (usually ESTs) into clusters representing putative genes, and for annotating and databasing them.

prot4EST: software for accurate prediction of translations from clustered EST datasets

annot8r: software for functional annotation of gene datasets contained in a PartiGene database

wwwPartiGene: software for preparing a PartiGene database for presentation and querying via the www

CLOBB: software for clustering sequences into putative gene objects (incorporated in PartiGene)

SimiTri: software for visualisation of the similarity relationships (BLAST, expression, etc) of one dataset against three others

Entrez PubMed

Entrez PubMed: "MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology (Bylesjo, et al., 2005). Further abilities of the application are outlined and illustrated. AVAILABILITY: MASQOT-GUI is Java-based and licensed under the GNU Lesser General Public License (LGPL). Source code, documentation and binary files for the Windows and Linux platforms are available for download at http://masqot-gui.sourceforge.net/"

Bioinformatics JOB

Bioinformatics Job
There are some good web sites out there that you might want to check:

• International Society for Computational Biology, job listings
• biotech find
• bioplanet
• BioSpace Career Center Search for bioinformatics or computational
• jobsearchtech
• Color Base Pair
• bio.com career center
• Hire bio
• Future Bio Jobs
• Bioinform
• Canadian bioinformatics jobs
• Bioinformatics jobs in Boston area
• Georgia Tech "career outlook in bioinformatics"
• Science magazine's listing of bioinformatics job ads (mainly faculty positions)

Swingweb

Swingweb: "Swingweb is a web-application framework that enables AWT/Swing application to operate inside a web container and presented as a web application to the web browser, purely in HTML/CSS/javascript. The swing application will render and behave in the web-container the same as it would as a desktop application. There is little knowledge required for the developer to start developing swingweb application as long as they are familiar with swing UI development. "