Shopify

Shopify lets you build shops with as much style and flair as you see fit. When you signup for Shopify, you can choose from one of our growing number of custom-made designs or get really creative and create your own designs.

Tigermouse

Tigermouse is a framework for development of highly interactive web applications in MVC architecture. It utilizes AJAX technology extensively and pays attention to be lightweight for low latency and high responsiveness.

Applications based on Tigermouse are written with three steps in mind:

• show some HTML to user,
• listen to what user does,
• react and do what user expected to.

JpGraph - PHP Graph Creating Library

JpGraph - PHP Graph Creating Library: "JpGraph is a Object-Oriented Graph creating library for PHP >= 4.3.1 The library is completely written in PHP and ready to be used in any PHP scripts (both CGI/APXS/CLI versions of PHP are supported).

The library can be used to create numerous types of graphs either on-line or written to a file. JpGraph makes it easy to draw both 'quick and dirty' graphs with a minimum of code as well as complex graphs which requires a very fine grained control. The library assigns context sensitive default values for most of the parameters which minimizes the learning curve. The features are there when you need them - not as an obstacle to overcome! "

Google Sitemap Generator for Windows :: GSiteCrawler

Google Sitemap Generator for Windows :: GSiteCrawler: "Google (and Yahoo!) Sitemap Generator for Windows

Google Sitemaps allows the webmaster to help Google index their pages optimally. The GSiteCrawler will help you generate the best Google Sitemap file for your website. The GSiteCrawler uses different ways to find all the pages in your website and can generate all sorts of files, statistics and more. The sitemaps file format has lately been also adapted by Yahoo! - even MSN/Live.com is pledging it's support."

How to Run a Batch File Before Logging on to Your Computer

How to Run a Batch File Before Logging on to Your Computer: "How to Run a Batch File Before Logging on to Your Computer"

ajax: Project jMaki

ajax: Project jMaki: "jMaki is an Ajax framework that provides a lightweight model for reusable Ajax-enabled widgets of your own design or for those extending existing toolkits such as the Dojo toolkit. jMaki facilitates the passing parameters to your widgets and provides the means to better connect your widgets to your server-side resourcess using XML or JSON. Currently the jMaki server-side runtime is provided as a JSP tag library or a JSF component. "

Bioinformatics software - GAAS: Gene Array Analyser Software

Bioinformatics software - GAAS: Gene Array Analyser Software

GAAS is an integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments. It is structured in management, analysis and visualization sections that allow dealing with several gene expression dataset formats, custom differential expression data analyses, suitable visualization, and storage of results.

The management section is based on a relational database system, allowing handling and analyzing gene expression data generated by different high-throughput array technologies, independently from storage formats. Besides, it ensures management and exportability of result data through custom templates defining formats of output databases where storing analysis results.

In the analysis section several sequential processing steps are performed: background and spot quality evaluation; background correction and data normalization; evaluation of differential gene expression in a single experiment (i.e. test vs. control condition); determination of gene regulation (i.e. significant differential gene expression) across multiple replica experiments.

In the visualization section, a graphical user interface enables to interactively navigate within numerical results of gene differential expressions and their graphical plots.

GAAS is designed for a multi-user environment, enabling each user to store its own parameter values used to perform the analyses, and define data visualization schema and format of the output data.

BioMed Central | Full text | CoXpress: differential co-expression in gene expression data

BioMed Central | Full text | CoXpress: differential co-expression in gene expression data: "CoXpress: differential co-expression in gene expression data"

JUICE - EST Data Management System

JUICE - EST Data Management System: "JUICE: a Data Management System that facilitates the Analysis of Large Volumes of Information in an EST Project Workflow

Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task."

Official XOOPS Website - Powered by You!

Official XOOPS Website - Powered by You!: "XOOPS is an extensible, OO (Object Oriented), easy to use dynamic web content management system written in PHP. XOOPS is the ideal tool for developing small to large dynamic community websites, intra company portals, corporate portals, weblogs and much more. Read the All about XOOPS page for more details.

If you are looking for XOOPS support in your own language, check out the list of International XOOPS Support websites!"

PHPLiveX -> An Open Source PHP/Ajax Library

PHPLiveX -> An Open Source PHP/Ajax Library

PHPLiveX is a php class library which can be used to call PHP functions from Javascript in Web pages using AJAX. In addition, the class has a flexible preloading property. PHPLiveX is unique with its easy usage.

developerWorks: Ajax how-to articles, tutorials, and community support for developers

developerWorks: Ajax how-to articles, tutorials, and community support for developers: "Ajax resource center"

Check out two exciting resource centers on developerWorks for developers of Web based applications -- the new Ajax (Asynchronous JavaScript and XML) resource center and the PHP resource center.

Get access to the latest technical information on Ajax and PHP technologies, including tools, software downloads, articles, tutorials, events, and documentation. Take advantage of the technical forums and other community tools for information exchange with fellow developers, programmers, and IT architects.

The Ajax resource center helps developers create more interactive Web applications with Ajax technologies. It gathers together technical resources for PHP, ATOM, RSS, Ruby, and Web development frameworks like Spring, Shale, Struts, Rails, and Tapestry.

The PHP project resource center, part of the developerWorks Open source zone, goes in-depth with tutorials and articles on new PHP technologies, including object oriented programming, IDE comparison, debugging techniques, and how-tos on using the latest version of PHP.

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis -- Hong et al. 22 (22): 2825 -- Bioinformatics

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis -- Hong et al. 22 (22): 2825 -- Bioinformatics:

Availability: RankProd is available at Bioconductor http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd

Clearcut: a fast implementation of relaxed neighbor joining -- Sheneman et al. 22 (22): 2823 -- Bioinformatics

Clearcut: a fast implementation of relaxed neighbor joining -- Sheneman et al. 22 (22): 2823 -- Bioinformatics: "Clearcut: a fast implementation of relaxed neighbor joining"
Availability: Clearcut source code is available for download at: http://bioinformatics.hungry.com/clearcut

Pligg CMS

Pligg CMS: "In a world with so many Content Management Systems fighting for control it can seem nearly impossible to pick out a perfect CMS to suit your needs. "
Pligg is unique compared to most other content management systems because of it's flexibility. A web designer can do pretty much anything with Pligg because the software was designed to be used in as many ways as possible. Not only can a person with very little knowledge of PHP and MySQL install it, but they can modify and administer it with relatively little difficulty. For those who have a greater understanding of web languages, Pligg can act as the first step in a highly customized personal content management system.

TCExam (assessment, e-exam, CBT)

TCExam (assessment, e-exam, CBT): "TCExam is an assessment software system that enables educators and trainers to author, schedule, deliver, and report on surveys, quizzes, tests and exams. The software is used all over the world by universities, schools, companies and independent teachers. TCExam is open source and completely free to use.
"

[A] m p a c h e : For the love of music since May 5th 2001

[A] m p a c h e : For the love of music since May 5th 2001: "Ampache is a PHP-based tool for managing, updating and playing your MP3/OGG/RM/FLAC/WMA/M4A files via a web interface. It allows you to save playlists, create user accounts, and share your music catalogs with other Ampache servers."

Retrieving XML With Curl and SimpleXML - PHP Tutorials

Retrieving XML With Curl and SimpleXML - PHP Tutorials: "Retrieving XML With Curl and SimpleXML"
PHP 5 introduces SimpleXML and its a perfect name as parsing XML data is truly simple. In this tutorial we'll be using curl to retrieve the XML data from a remote web server. We're going to create a class to connect to the remote web server and pass POST data to the server and based on the POST data the remote server will return valid XML. The class will parse the XML response and return an array containing the data. For the sake of simplicity in this tutorial we're not going into detail on the workings of the remote server generating the XML responses.

CodonCode Aligner Tutorials: EST analysis

CodonCode Aligner Tutorials: EST analysis
CodonCode Aligner Tutorials:

From this page, you will be able to view tutorials for CodonCode Aligner. Currently available tutorial are:

• Tips for using CodonCode Aligner
• Quality-based consensus sequences

New Features in CodonCode Aligner version 1.6:

• Roundtrip editing

New Features in CodonCode Aligner version 1.5:

• Assembling in groups (by name)
• Comparing contigs
• Starting BLAST searches

This Quick Tour will show the most important features of CodonCode Aligner:

The tour is divided into three parts:

• Part 1: Basic Features. This part shows you Aligner's main functions, and can be done in Demo mode, without requesting a trial license. It demonstrates how to call bases with Phred, trim ends, vector screen, assemble, and edit.
• Part 2: Importing, Exporting, and Saving. This part first shows how to request a fully functional, time-limited trial license that you need for this second part of the tour. It then shows how to add sequences and assemblies to Aligner projects, how to save Aligner projects, and how to export sequences and entire projects.
• Part 3: Analyzing Heterozygous Mutations. This part describes how to find and analyze heterozygous mutations in CodonCode Aligner - heterozygous point mutations as well as heterozygous insertions and deletions ("indels").

This quick tour is available online at http://www.codoncode.com/aligner/quicktour/. If you downloaded and installed CodonCode Aligner, a copy of this tour has been installed in your installation directory as an Adobe PDF file named "QuickTour.pdf".

Steps:
Base Calling
Clip Ends
Trim Vector
Assemble with options... / Unassemble existing contigs (assemble from the scratch)
(Algorithm tab: Use PHRAP and Use built-in algorithm)

S.A.G.E. - Statistical Analysis for Genetic Epidemiology | S.A.G.E. - Statistical Analysis for Genetic Epidemiology

S.A.G.E. - Statistical Analysis for Genetic Epidemiology | S.A.G.E. - Statistical Analysis for Genetic Epidemiology: "S.A.G.E. - Statistical Analysis for Genetic Epidemiology S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is an annually licensed software package (free to nonprofit organizations) containing programs for use in the genetic analysis of family, pedigree and individual data.

RankProd

RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis of microarray data

Ocimumbio.com - Bioinformatics - Genowiz™

Ocimumbio.com - Bioinformatics - Genowiz™: "Genowiz™ is a powerful gene expression analysis program that has been designed to store, process and visualize gene expression data efficiently. It includes a suite of advanced analysis methods and allows researchers to select analysis methods appropriate for their dataset. Genowiz™ allows researchers to organize experimental information (MIAME), import data files quickly and easily, work with multiple experiments at the same time, import gene annotation files, pre-process and normalize data, perform cluster analysis, classify and view gene information, perform functional classification and track down intricate correlations in data by performing pathway analysis. All analysis done is tracked, saved into a database and can be retrieved at any point of time."

How to Encrypt Passwords in the Database

How to Encrypt Passwords in the Database: "How to Encrypt Passwords in the Database"
PHP, MySQL

Passing Javascript variables to PHP

Passing Javascript variables to PHP: "Passing Javascript variables to PHP

JavaScript is mainly used as a client side scripting language, while PHP is a server side technology. Unlike Java or ASP.Net, PHP doesn't have tools to make it work client side. That is why you need to combine JavaScript and PHP scripts to develop powerful web-applications."

Simple Machines - Home of SMF: Free PHP and MySQL forum software

Simple Machines - Home of SMF: Free PHP and MySQL forum software: "Simple Machines Forum - SMF in short - is a free, professional grade software package that allows you to set up your own online community within minutes. Its powerful custom made template engine puts you in full control of the lay-out of your message board and with our unique SSI - or Server Side Includes - function you can let your forum and your website interact with each other. SMF is written in the popular language PHP and uses a MySQL database. It is designed to provide you with all the features you need from a bulletin board while having an absolute minimal impact on the resources of the server. SMF is the next generation of forum software, and best of all it is and will always remain completely free!"
http://themes.simplemachines.org/

Comparative gene marker selection suite.

Entrez PubMed: "An important step in analyzing expression profiles from microarray data is to identify genes that can discriminate between distinct classes of samples. Many statistical approaches for assigning significance values to genes have been developed. The Comparative Marker Selection suite consists of three modules that allow users to apply and compare different methods of computing significance for each marker gene, a viewer to assess the results, and a tool to create derivative datasets and marker lists based on user-defined significance criteria. AVAILABILITY: The Comparative Marker Selection application suite is freely available as a GenePattern module. The GenePattern analysis environment is freely available at http://www.broad.mit.edu/genepattern."

Software - Broad

Software - Broad: "Expression Analysis"

Expression Analysis

GenePattern
GenePattern is a software package for the analysis of molecular profiles, e.g., genome-wide microarray expression signatures. It includes a collection of analytic and visualization tools, interfaces for the easy construction of analytic pipelines and integration of new modules without additional programming. Gene Pattern is available for MacOS, Windows, and Linux platforms.

Gene Set Enrichment Analysis (GSEA)
GSEA is a computational method that determines if a given set of genes shows statistically significant differences between two biological states. It is useful for interpreting the results of gene expression studies.

GeneCruiser
GeneCruiser is an annotation tool that allows users to map genes from genomic databases to Affymetrix probes, find information about Affymetrix probes in genomic databases and find where Affymetrix probes are located in the human genome.

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)