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.