Bioinfo

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 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 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 (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"

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

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: "CoXpress: differential co-expression in gene expression data"

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!: "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 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: "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:

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"
Availability: Clearcut source code is available for downloadat: http://bioinformatics.hungry.com/clearcut

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 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: "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 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:

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

New Features in CodonCode Aligner version 1.6:

Roundtrip editing

New Features in CodonCode Aligner version 1.5:

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

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"
PHP, MySQL

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 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/

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: "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.

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
Three changes:
1)

<Connector port="8080" maxHttpHeaderSize="8192"
to:

<Connector port="9091" maxHttpHeaderSize="8192"
2)
<Server port="8005" shutdown="SHUTDOWN">
to:
<Server port="8105" shutdown="SHUTDOWN">
3)

<Connector port="8009"
enableLookups="false" redirectPort="8443" protocol="AJP/1.3" />
to:

<Connector port="8109"
enableLookups="false" redirectPort="8443" protocol="AJP/1.3" />

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

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. "

httpFileManager.com - Home - Remote administration of files over HTTP: "httpFileManager is a file management script written in PHP allowing the remote administration of files over HTTP.

httpFileManager will turn your standard browser into a 'Windows Explorer' and allow managing files on your web server on the fly. It's a complete replacement of traditional FTP, allowing you to manage files on your web server just with a web browser instead of a FTP client. It also will provide extended features which are impossible with FTP such as creating and editing HTML files right on the server and zipping and unzipping files on the fly.

The purpose of httpFileManager is allowing file management and Web site maintenance right on the server. It may be used to manage a single site or multiple sites. The root of the files to be managed must of course be Web accessible.

httpFileManager is a simple, yet powerful tool allowing the administration of files through HTTP."

PhpLabware: "Phplabware is a web-driven database management system. Phplabware runs on a server and is accessed through a web browser. Databases can be designed within a web-interface. Data-entry takes place in forms, which can be altered using phplabware's plugin mechanism. Search results can be output in reports, which are generated based on simple HTML templates. Phplabware supports file and image uploads and allows for full-text searches in uploaded materials. A UNIX-like user and group access control mechanism allows for fine-grained read and write control at both the level of a complete database as well as individual records. The (php-based) plugin mechanism allows for easy and fast adaptation of phplabware to any specific needs.

Phplabware was developed at a number of Molecular Biology labs, and therefore ships with predefined databases targeted to the needs of Life Sciences labs. Currently, modules are available for antibodies, protocols, pdfs, pdbs, and files.

One of the design goals is that users only have to enter as little data as possible. The local pdf reprint module, for instance, (the virtual library) only requires the pdf file, and the unique identifier from Pubmed.

Apart from the provided modules, phplabware's functionality can be extended and tailored to your specific needs. A web-interface lets the system administrator easily design new tables, which are completely integrated with phplabware
Phplabware consists of a number of php scripts. It uses adodb as a database wrapper, and is developed using postgres and mysql as an SQL server (and will probably work with others too). Installation is simple, and version upgrades are completely taken care of by the php scripts. It has been tested on both Linux (Suse, RedHat, Mandrake) and Mac OS X, and should work in Windows too."

Smarty: Smarty is a template engine for PHP. More specifically, it facilitates a manageable way to separate application logic and content from its presentation. This is best described in a situation where the application programmer and the template designer play different roles, or in most cases are not the same person.

Home | Getahead: "Welcome to Getahead

Getahead is a family run IT consultancy. We create websites, from small interactive sites to complex high volume ones."

ZK - Simply Rich: "ZK is an open-source Ajax Web framework that enables rich UI for Web applications with no JavaScript and little programming. With event-driven feature-rich components, developing becomes as simple as programming desktops. With a markup language, designing becomes as simple as authoring HTML."

Asynchronous JavaScript Technology and XML (AJAX) With Java 2: "Asynchronous JavaScript Technology and XML (AJAX)
With Java 2 Platform, Enterprise Edition"

NEBC Software Documentation Pages: "NEBC Software Documentation Pages"

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments -- Masoudi-Nejad et al. 34 (Supplement 2): W459 -- Nucleic Acids Research: "EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments"

Array2BIO :: Comparative functional analysis of microarray data:
Array2BIO is an integrative platform for the analysis of microarray data.

Main features of Array2BIO include:
- multi-step statistical analysis (details) of array intensities
- balance analysis of low- and high-expressors to reliably select up- and down-regulated outliers
- Gene Ontology and KEGG functional classification of genes and pathways
- clustering of expression data
- integrated Creme 2.0 prediction of regulatory mechanisms underlying observed coexpression patterns (human genome)
- ECR Browser evolutionary conservation analysis of genes
- different statistical methods to handle the "multiple testing" correction
- prediction of biomarkers
- external storage of input/output files and processing results
... more details

SnipSnap :: start: "SnipSnap is a free and easy to install weblog and wiki tool written in Java."

Dynamic Drive: .htaccess password generator: "Use this tool to generate all the necessary codes needed to password protect a directory or selects files within it on your site via .htaccess. It encrypts the desired passwords, then outputs the corresponding codes to put inside your .htaccess and .htpasswd files."

Launch4j - Cross-platform Java executable wrapper: "Cross-platform Java executable wrapper

Launch4j is a cross-platform tool for wrapping Java applications distributed as jars in lightweight Windows native executables. The executable can be configured to search for a certain JRE version or use a bundled one, and it's possible to set runtime options, like the initial/max heap size. The wrapper also provides better user experience through an application icon, a native pre-JRE splash screen, a custom process name, and a Java download page in case the appropriate JRE cannot be found."

MoinMoinWiki - MoinMoin: "The MoinMoin Wiki Engine"

MoinMoin is an advanced, easy to use and extensible WikiEngine with a large community of users. Said in a few words, it is about collaboration on easily editable web pages. MoinMoin is Free Software licensed under the GNU GPL.

If you want to learn more, first read about WikiWikiWeb, then about WhyWikiWorks and the WikiNature.
If you want to play with it, please use the WikiSandBox.
MoinMoinFeatures documents why you really want to use MoinMoin rather than another wiki engine.
MoinMoinScreenShots shows how it looks like. You can also browse this wiki or visit some other MoinMoinWikis.

Links|eJournals: "Journals"

Scope: Bioinformatics / Computational Biology

AMB - Algorithms for Molecular Biology: Soon to be launched by BioMedCentral.
Applied Bioinformatics: - Reviews of computational and methodological developments
- Original research articles on all areas of bioinformatics including microarray analysis, databases and datamining, phylogenetics, forensics, protein structure prediction and evolution, and genomics
[Search PubMed]
Bioinformatics (formerly CABIOS): Main focus on new developments in genome bioinformatics and computational biology.
ISI impact factor of 5.742 (2004), 6.701 (2003), 4.615 (2002), 3.421 (2001)
[Search PubMed]
Biological Knowledge: Forum for scientific communication regarding analysis of the content and the role of knowledge in biology and medicine. The fields covered by the journal include: ontologies, knowledge representation, and knowledge bases; reasoning, discovery, and machine learning; natural language processing and linguistics; history, philosophy, sociology, and anthropology; cognitive science, including cognitive and social psychology; and education.
Open access online journal, to be launched soon, see recent updates.
BMC Bioinformatics: Publishes original research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology.
Open access online journal.
ISI impact factor of 5.42 (2004), 4.896 (estimated, 2003)
[Search PubMed]
Briefings in Bioinformatics: An international forum for researchers and educators in the life sciences, Briefings in Bioinformatics publishes reviews for the users of databases and analytical tools in contemporary genetics and molecular biology.
[Publisher] - [ToC] - [Search PubMed]
Comparative and Functional Genomics: - studies of complex and model organisms
- bioinformatic and computational tools for the study of gene and genome organisation
- pharmacogenomics and genomics-based drug target identification methods
Computational Biology and Chemistry: Formerly known as Computers & Chemistry
Computer Methods and Programs in Biomedicine: Covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice.
Computers in Biology and Medicine: Application of the computer to the fields of biomedical engineering and medical informatics.
- Analysis of biomedical systems: solutions of equations
- Synthesis of biomedical systems: simulations
- Special medical data processing methods
- Special purpose computers and clinical data processing
- Medical diagnosis and record processing
Audience: Physicians, Surgeons, Physiologists, Bacteriologists
IJBRA - International Journal of Bioinformatics Research and Applications
IJDMB - International Journal of Data Mining and Bioinformatics: Launched recently
IJMI - International Journal of Medical Informatics: ISI impact factor of 1.326 (2004), 1.178 (2003)
Available on Science Direct
[Search PubMed]
Journal of Biomedical Informatics: Formerly known as "Computers and Biomedical Research"
ISI impact factor of 0.855 (2003)
JBCB - Journal of Bioinformatics and Computational Biology: Aims to publish high quality, original research articles, expository tutorial papers and review papers as well as short, critical comments on technical issues associated with the analysis of cellular information.
JIB - Journal of Integrative Bioinformatics: Focuses on
- molecular biological databases and applications
- integration of data sets relevant for biological systems
- integration of applications relevant for biological systems
- design of metabolic, regulatory and expression networks
- interdisciplinary studies of these networks
- evaluation of original experimental data with biocomputational tools
- online resources for experimental scientists
JCB - Journal of Computational Biology: Forum for the communication of technical issues associated with the analysis, management, and visualization of cellular information at the molecular level. Includes papers on genomics, mathematical modeling and simulation, distributed and parallel biological computing, designing biological databases, pattern matching and pattern detection, linking disparate databases and data, new tools for computational biology, relational and object-oriented database technology for bioinformatics, biological expert system design and use, reasoning by analogy, hypothesis formation and testing by machine, and management of biological databases
ISI Impact Factor of 4.600 (2003)
JTB - Journal of Theoretical Biology: The forum for theoretical papers that give insight into biological processes.
ISI Impact Factor of 1.550 (2003)
[Search PubMed]
LNCS Transactions on Computational Systems Biology
OJB - Online Journal of Bioinformatics
PloS Computational Biology: Open access, launched in June 2005.
[Search PubMed]

Scope: Machine Learning

JMLR - Journal of Machine Learning Research: Provides an international forum for the publication of scholarly articles in all areas of machine learning.
Incl. special issues on Kernel Methods, ICML 2001, Machine Learning for Text and Images, Variable and Feature Selection. Published in a quarterly paper volume and immediately on receipt electronically.
ISSN 1532-4435 (Paper), 1533-7928 (Electronic)
JMLG - Journal of Machine Learning Gossip: "Provides an archival source of important information that is often discussed informally at conferences but is rarely, if ever, written down."

FreeStyle Menus - TwinHelix: "This is an XHTML compliant, CSS-formatted menu script, designed to work with the current generation of standards-based websites. The menu data is stored in the HTML document itself (unlike other JavaScript menus) as either nested lists or disparate DIV tags, and the script manages the showing and hiding of these elements with customisable timer delays."

FireBug - JoeHewitt.com: "FireBug lets you explore the far corners of the DOM by keyboard or mouse. All of the tools you need to poke, prod, and monitor your JavaScript, CSS, HTML and Ajax are brought together into one seamless experience, including a debugger, error console, command line, and a variety of fun inspectors."

iSQL-Viewer - Independent SQL Tool: "iSQL-Viewer is an open-source JDBC 2.x compliant database front end written in Java. It implements across multiple platforms features of the JDBC API. It does everything through a single interface.

iSQL-Viewer works with most database platforms, including PostgreSQL, MySQL, Oracle, and Informix. iSQL-Viewer provides a variety of tools and features to carry out common database tasks. It includes:

* Scripting support using JPython and the IBM BSF framework
* A guided query builder for creating simple and complex SQL queries
* Enhanced object viewing for images, HTML, and other binary format files
* A friendly SQL console for executing SQL statements
* Batch processing of SQL files
* Database introspection
* 'Bookmarks' to store SQL commands you commonly use
* Import and export to popular file formats such as Microsoft Excel, XML, HTML and ASCII delimited.
* Enhanced interface support across platforms"

alahup!, the agile web development CMS: alahup! is both a framework that lets web designers develop full featured, professional, standards compliant dynamic web sites, and an integrated content management system.
Developer features
100% control over the output, at the tag level
100% of the content (including images) stored in a single database
SQLite and MySQL/InnoDB support
PHP5 & Smarty templates powered

Protolize.org - Essential web tools in one place: "About Protolize

This is a place where web designers and developers collaborate to create an ultimate collection of web-tools. Only the most useful and current tools will be considered to be on the list.

If you have any tools that you use that you find useful or just found one let us know."

Snipplr - Code 2.0: "Snippets"
Snipplr is a public source code repository that gives you a place to store and organize all the little pieces of code that you use each day. Best of all, it lets you share your code snippets with other coders and designers.

JSP 2D Taglib: With the JSP 2D Taglib, your web applications now have full access to the Java 2D API for dynamically rendering beautiful graphics primitives directly in your web page without limitation. Yes, the web page itself becomes a canvas on which you can leverage the full power of the Java 2D API for graphics. Literally all browsers are supported... no Applets, JavaScript, Ajax, Flash, Plug-Ins, Cookies, Lazlo or any other hackery required on the client!

Eclipse Plugin Central :: Eclipse plugin resource center and marketplace for Eclipse and Plugin Ecosystem: "Eclipse Plugin Central (EPIC) offers the Eclipse community a convenient, information-rich portal that helps software developers find open source and commercial Eclipse plug-ins, tools, and products that enhance the entire Java software development life-cycle. "

SourceForge.net: Eclipse SQLExplorer plugin: "Eclipse IDE plugin for database query/schema viewer for nearly any kind of JDBC database. It supports plugins for specialized functionality for individual databases (Oracle and data tools ( like Hibernate, Oracle or Sybase )"

Download the SQLExplorer file net.sourceforge.sqlexplorer_2.2.3.zip.

Extract the SQLExplorer .zip file to the /eclipse directory. is the directory in which Eclipse is installed

Having installed the SQLExplorer plugin, we shall configure the SQLExplorer plugin in the Eclipse 3.01 IDE. First, set the SQLExplorer perspective in the Eclipse IDE. Click on the "Open a perspective" button in the Eclipse IDE to open a perspective. Figure 1 illustrates the "Open a perspective" button. (more)

Securimage CAPTCHA Generator: "Description: A highly customizable PHP class for generating CAPTCHA images to prevent programs from filling out your forms. This does everything from create and output the image, to validate the code entered by the user in the form. It can show an image and validate the user entered code in just 3 lines of PHP. This class provides a simple interface to using CAPTCHA images so you can easily make your own custom forms that implement this class. It supports variable length codes, custom TTF fonts, custom colors, optional lines over the text to help confuse programs, angled text, transparent text and more. Includes several code examples and various sample images in the zip file."

JBuilder and Embedded Tomcat =

Embedded Tomcat
To enable use of the embedded Tomcat versions, a Web Module project must be created. This is accomplished
by following these steps:
1. Create a new Project in JBuilder X (select File ? New Project... from the pull-down menu and accept the default settings).
2. Select the File pull-down menu, followed by New.
3. Select the Web node on the left, the Web Module icon on the right, and click OK.
4. Select Create Empty Web Module and click Next.
5. Enter webapp (or any desired value without spaces) in the Name and Directory fields, and click Next.
6. Click Finish.

set the directory for "estweb Web Module properties/ module / Archive" (war file) to
"C:\map\jakarta-tomcat-5.5.9\webapps" directory.

After completing these steps, the project must be configured to use the appropriate Tomcat server.
This can be achieved by the following steps:
1. Right-click the project icon in the Project window and select Properties from the context menu.
2. Select the Server node from the list on the left.
3. Select the desired Tomcat server from the Single server for all services in project combo box.

To launch Tomcat, right-click on either a Servlet/JSP in the project and select Web Run or Web Debug.

Or

Copy and paste "estweb.war" into "C:\map\jakarta-tomcat-5.5.9\webapps" directory.

Embedded Tomcat
To enable use of the embedded Tomcat versions, a Web Module project must be created. This is accomplished
by following these steps:
1. Create a new Project in JBuilder X (select File ➪ New Project... from the pull-down menu
and accept the default settings).
2. Select the File pull-down menu, followed by New.
3. Select the Web node on the left, the Web Module icon on the right, and click OK.
4. Select Create Empty Web Module and click Next.
5. Enter webapp (or any desired value without spaces) in the Name and Directory fields, and
click Next.
6. Click Finish.
After completing these steps, the project must be configured to use the appropriate Tomcat server. This
can be achieved by the following steps:
1. Right-click the project icon in the Project window and select Properties from the context menu.
2. Select the Server node from the list on the left.
3. Select the desired Tomcat server from the Single server for all services in project
combo box.
To launch Tomcat, right-click on either a Servlet/JSP in the project and select Web Run or Web Debug.

Apache Tomcat Servlet and JavaServer Pages Development with JBuilder Foundation: "Apache Tomcat Servlet and JavaServer Pages Development with JBuilder Foundation

Debbie Carson and Ken Chan
Senior Technical Writer, and R&D Engineer, JBuilder
Inprise/Borland

The steps outlined in this document were tested on and will work with JBuilder 3.5 Foundation and Tomcat 3.1. You can also use this document to set up Tomcat to work with JBuilder 3.5 Professional and Enterprise editions."

Genopolis
AMDA - Automatic Microarray Data Analysis InstanceEndEditable
InstanceBeginEditable name="EditRegion4" On this page you can find the R Package for AMDA (Linux/MacOSX/Windows). Instructions for the Installation, as well as a description of how to use the package can be found in the AMDAwidgetManual.pdf Moreover you may download an archive of CEL-file examples, derived from a publically available dataset published by Aebischer et al., 2005, as well as the necessary phenodata file, containing the experimental design. The AMDAexampleReport.pdf shows the final results of the analysis as performed in the manual. AMDA is available free of charge under GPL-license

Quanta Plus Home: "Quanta Plus is a highly stable and feature rich web development environment. The vision with Quanta has always been to start with the best architectural foundations, design for efficient and natural use and enable maximal user extensibility. We recognize that we don't have the resources to do everything we would like to so our target is to make it easy for you to help make this the best community based desktop application anywhere. Pretty much everything in Quanta is designed so you can extend it. Even the way it handles XML DTDs is based on XML files you can edit. You can even import DTDs, write scripts to manage editor contents, visually create dialogs for your scripts and assign script actions to nearly any file operation in a project. You can even look at and communicate with a wide range of what happens inside Quanta using DCOP.
"

AjaxTags: Home: "The AJAX Tag Library is a set of JSP tags that simplify the use of Asynchronous JavaScript and XML (AJAX) technology in JavaServer Pages.

AJAX is primarily rooted in JavaScript. However, many server-side developers do not have an extensive knowledge of client-side programming in the browser. It's much easier in some cases for J2EE developers, especially, to simply add a JSP tag to the page to gain the function desired.

This tag library fills that need by not forcing J2EE developers to write the necessary JavaScript to implement an AJAX-capable web form. The tag library provides support for live form updates for the following use cases: autocomplete based on character input to an input field, select box population based on selections made from another field, callout or balloon popups for highlighting content, refreshing form fields, and toggling images and form field states on/off.

The implementation is a combination of Java classes and JavaScript source files. The Java code should be OS independent as there are no client side components. However, the Java is dependent on JDK 1.4+ and requires a Servlet container to run. The JavaScript should run in at least Firefox 1.0+ and Internet Explorer 5.0+.

To get started, check out the installation and usage guides."

SAMS Homepage: "'Sequence Analysis and Management System' (SAMS)"

Every genome project generates thousands of ESTs or shotgun reads. Users have high interest in a first look at the DNA sequence content of the individual reads, before they are assembled (in case of shotgun reads) or clustered (in case of ESTs). Several steps are necessary to provide the researcher with high quality sequences, as well as an overview of their content. For all these purposes we have implemented some additional extensions to GenDB within the SAMS system.

SAMS is a simple, easy to install and maintain open source system that provides the mechanisms to run a variety of tools on each read/EST, presenting the results in a web form. The pipeline includes the processing of the raw sequence data (e.g. base calling, quality and vector clipping), the processing of ESTs using different tools (e.g. BLAST), and also the clustering and assembly of the sequences. Finally, the system provides a web based visualization of the results.

Further information about SAMS can be found on the SAMS homepage.

GenDB: "GenDB is a genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. The GenDB annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome."

Oracle XML Publisher: "Oracle XML Publisher is a Java-based product within the Oracle Fusion Middleware family. Utilizing a set of familiar desktop tools such as Adobe Acrobat and Microsoft Word, users can create and maintain their own report formats based on development delivered xml data extracts. XML Publisher will then convert these documents to the XSL-FO format. Users can also obtain third-party provided PDF forms e.g. government tax forms and merge xml data generated from the E-Business Suite to fill the forms with the required data."

Improve PHP Performance by Caching Database Results | Database Change Notification: "Learn how to use Database Change Notification to keep cached data up to date."

Memória Persistente - Gaudí:

Data Structures Visual Editor

"Build around JDBC and XML, this tool allows you to maintain visual repesentations of a database's layout, edit table's data, generate code to bind objects to tables, and export and import data in XML format to easely move data from one database to another."

EasyEclipse packages together the Eclipse IDE and key open source plug-ins: "EasyEclipse packages together the Eclipse IDE and key open source plug-ins"
EasyEclipse packages together the Eclipse IDE and key open source plug-ins. It is intended to make Eclipse easier to download, install, and use.

Top 10 Web Developer Libraries - Cameron Olthuis: "Top 10 Web Developer Libraries"

1) Moo.fx - A superlightweight, ultratiny, megasmall javascript effects library, written with prototype.js. It’s easy to use, fast, cross-browser, standards compliant, provides controls to modify Height, Width, and Opacity with builtin checks that won’t let a user break the effect with multiple crazy clicks. It’s also optimized to make you write the lesser code possible.

2) Rico - An open source JavaScript library for creating rich internet applications. Provides full Ajax support, drag and drop management, and a cinematic effects library.

3) Swat - Developed by silverorange, Swat is an open source web application toolkit built with PHP.

4) ColorCombos - Who would’ve thought a color library would end up mixed in with a bunch of JavaScript and PHP libraries? Well they do have a pretty sweet little color library for finding color combinations, all you do is select the color and they show you some nice combos that work with that color.

5) script.aculo.us - Provides you with easy-to-use, compatible and, ultimately, totally cool JavaScript libraries to make your web sites and web applications fly, Web 2.0 style. I’m sure I’m not alone when I say this library is my favorite.

6) Mochikit - A kick-ass lightweight JavaScript library that will help you get shit done fast.

7) Dynamic Drive CSS Library - Here you’ll find original, practical CSS codes and examples such as CSS menus to give your site a visual boast.

8) PEAR - A framework and distribution system for reusable PHP components. PEAR provides the above mentioned PHP components in the form of so called “Packages”.

9) DHTML Goodies - A good sized library of DHTML and AJAX scripts.

10) dojo - Open source JavaScript toolkit that makes professional web development better, easier, and faster.

11) Cross Browser | Toys - Huge JavaScript library.

12) Yahoo UI Library - The Yahoo! User Interface (YUI) Library is a set of utilities and controls, written in JavaScript, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. The YUI Library also includes several core CSS resources.

Rico: An open source JavaScript library for creating rich internet applications. Provides full Ajax support, drag and drop management, and a cinematic effects library.

SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera: "SPODOBASE"

The SPODOBASE database provides integrated access to expressed sequence tags (EST) from the lepidopteran insect Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for scientific community. SPODOBASE is available from URL: http://bioweb.ensam.inra.fr/spodobase

For technical information about these pages see:
ACEDB Home Page
AcePerl Lincoln Stein Home Page

Creating PDF Files in PHP: "Creating PDF Files in PHP"

Use PHP to Create Dynamic pdf Files: "The php_pdf.dll extension is enough to produce pdf files on the fly. "

PortableApps.com | Your Digital Life, Anywhere™:

Apps Hosted Here

Nvu - The Complete Web Authoring System for Linux, Macintosh and Windows: "Nvu (pronounced N-view)
Finally! A complete Web Authoring System for Linux desktop users as well as Microsoft Windows and Macintosh users to rival programs like FrontPage and Dreamweaver. Nvu (which stands for 'new view') makes managing a web site a snap. Now anyone can create web pages and manage a website with no technical expertise or knowledge of HTML."

FPDF

FPDF is a PHP class which allows to generate PDF files with pure PHP, that is to say without using the PDFlib library. F from FPDF stands for Free: you may use it for any kind of usage and modify it to suit your needs.

FPDF has other advantages: high level functions. Here is a list of its main features:

Choice of measure unit, page format and margins
Page header and footer management
Automatic page break
Automatic line break and text justification
Image support (JPEG and PNG)
Colors
Links
TrueType, Type1 and encoding support
Page compression

Serpia: Python tutorials: "Python tutorials"

A very basic Python tutorial, just to wet your toe: python

How to use wxPython and wxGlade to build a GUI: wxGlade

Using the very popular MySQL database using MySQLdb: MySQL

About SPE, a free Python IDE: SPE

Building a GUI for wxPython using XML: XRCed/XML

Creating graphs in Python with PyGTK, Glade and Matplotlib: PyGTK/Glade/Matplotlib

Building a simple search engine in Python, as used on this website: Search engine

CherryPy, a fantastic Python web framework: CherryPy

Some code snippets that I am collecting: Snippets

cat: OpenSource

Free RSS to HTML PHP Script: "Free RSS to HTML PHP Script"

BayBoots: a model-free Bayesian tool to identify class markers from gene expression data.

SpotWhatR: "SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normalization, determination of differentially expressed genes, summarization by Gene Ontology terms, and clustering analysis. SpotWhatR allows researchers who are not familiar with computational programming to choose the most suitable analysis for their microarray dataset. Along with well-known procedures used in microarray data analysis, we have introduced a stand-alone implementation of the HTself method, especially designed to find differentially expressed genes in low-replication contexts. This approach is more compatible with our local reality than the usual statistical methods. We provide several examples derived from the Blastocladiella emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR

SBEAMS - Microarray Description: "SBEAMS - Microarray provides MIAME-compliant Affymetrix GeneChip microarray database functionality under the SBEAMS framework. Researchers can enter their experimental design and sample information into the database prior to or after an experiment. Labeling, hybridization, scanning, and measurement steps are performed by the researcher or by core facility staff, and information about each step and data products of the assays from GCOS are automatically ingested into the database. SBEAMS - Microarray provides a simple query tool allows quick access to data for known genes of interest, plus a full web-based interface based on the BioConductor web interface package webbioc to provide normalization and analysis functionality. Output from the analysis pipeline is loaded into the database from which researchers may perform analysis queries or export to other analysis packages."

WebLogo - About:

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Click here to create your own sequence logos.

Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments -- Vacic et al. 22 (12): 1536 -- Bioinformatics: "Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge."
Availability: http://www.twosamplelogo.org

GenRGenS: software for generating random genomic sequences and structures -- Ponty et al. 22 (12): 1534 -- Bioinformatics: "GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time."
Availability: Source and executable files of GenRGenS (in Java)and the complete user's manual are freely available at http://www.lri.fr/bio/GenRGenS

Lock only a few cells on a worksheet: "Lock only a few cells on a Excel worksheet"

Select the entire worksheet by clicking the Select All button (the gray rectangle directly above the row number for row 1 and to the left of column letter A).
Click Cells on the Format menu, click the Protection tab, and then clear the Locked check box.
This unlocks all the cells on the worksheet

Note If the Cells command is not available, parts of the worksheet may already be locked. On the Tools menu, point to Protection, and then click Unprotect Sheet.
Select just the cells you want to lock and repeat step 2, but this time select the Locked check box.
On the Tools menu, point to Protection, click Protect Sheet, and then click OK.
Note In the Protect Sheet dialog box, you have the option to specify a password and select the elements that you want users to be able to change. See Protect worksheet or workbook elements for more information.

Webcpp :: home(): "Webcpp converts programmer's source code into syntax highlighted HTML."
Web C Plus Plus is a command line utility that takes your source code, and converts it into an HTML file using a fully customizable syntax highlighting engine and colour schemes. This is useful if you want to post your code online and make it easier to read, or to make online programming tutorials.

MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics: "The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5-6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behaviour of the cell can be observed using large-scale metabolomic studies. The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions. Description: MeMo is a formal model for representing metabolomic data and the associated metadata. Two predominant platforms (SQL and XML) are used to encode the model. MeMo has been implemented as a relational database using a hybrid approach combining the advantages of the two technologies. It represents a practical solution for handling the sheer volume and complexity of the metabolomic data effectively and efficiently. The MeMo model and the associated software are available at http://dbkgroup.org/memo/."

Adobe Labs - Spry framework for Ajax: "The Spry framework for Ajax is a JavaScript library for web designers that provides functionality that allows designers to build pages that provide a richer experience for their users. It is designed to bring Ajax to the web design community who can benefit from Ajax, but are not well served by other frameworks.

The first release of the Spry framework is a preview of the data capabilities that enable designers to incorporate XML data into their HTML documents using HTML, CSS, and a minimal amount of JavaScript, without the need for refreshing the entire page. The Spry framework is HTML-centric, and easy to implement for users with basic knowledge of HTML, CSS and JavaScript. The framework was designed such that the markup is simple and the JavaScript is minimal. The Spry framework can be used by anyone who is authoring for the web in their tool of choice."

Google AJAXSLT: "AJAXSLT is an implementation of XSL-T in JavaScript, intended for use in fat web pages, which are nowadays referred to as AJAX applications. Because XSL-T uses XPath, it is also an implementation of XPath that can be used independently of XSL-T."

PHP: Regular Expression Functions (Perl-Compatible) - Manual: "The syntax for patterns used in these functions closely resembles Perl. The expression should be enclosed in the delimiters, a forward slash (/), for example. Any character can be used for delimiter as long as it's not alphanumeric or backslash (\). If the delimiter character has to be used in the expression itself, it needs to be escaped by backslash. Since PHP 4.0.4, you can also use Perl-style (), {}, [], and <> matching delimiters. See Pattern Syntax for detailed explanation."

freshmeat.net: Project details for amoeba: "amoeba is an XML-based framework for Web environment development backed by XML databases (Berkeley DB XML or eXist native XML database). It's deployable as a war archive in servlet containers (like Tomcat and/or Jetty). Almost no Java knowledge or Java programming is required while developing with amoeba, except for extending base framework functionality. Programming in amoeba means writing XML documents. The environment has seven domain-specific languages: pipeline (general XML processing using language features and by calling tasks), sitemap (for connecting the Web environment to all other languages), form (HTTP forms processing), modification (XML document modifications), resource (file resource processing), berkeley-db-xml, and test (unit testing and XML Diff)."

WidgetServer : A Java/XML server-side GUI-framework: "WidgetServer is a Java/XML server-side GUI-framework which enables an application to run as either a monolithic Swing app, a client/server Swing app, or as a Web app without any change and without loss of functionality. A rich widget set is supported that includes tree views, tabbed panes, split panels, and much more. A unified widget-based, object-oriented programming interface for Web and Swing GUIs is offered to the developer to control and assemble the GUI. Web applications are fully AJAX enabled. For Swing client/server applications, the framework handles client/server communication, including compression and security layers. A GUI builder is included."

You may get a 'Packet too large' error from the server.
In this case you will have to increase the value of the *server* variable
max_allowed_packet above the default value of 1M to 32M. This can be done
by adding the following line to the [mysqld] section of your my.cnf file and
restarting the MySQL server daemon.

[mysqld]
max_allowed_packet = 32M

symfony PHP5 framework » Symfony at a glance:

Overview

Symfony is an object-oriented PHP5 framework based on the MVC model. Symfony allows for the separation of business rules, server logic and presentation views of a web application. It also contains numerous tools and classes aimed at shortening the development time of a complex web application.

What is a framework?

A framework adds new mechanisms on top of a programming language, and these mechanisms automate many of the development patterns used for a given purpose. A framework also adds structure to the code, and pushes the developer to write better, more readable and maintainable code. A framework also makes programming easier, since it packages complex operations into simple statements.

A framework is usually developed with the same language that it extends. A PHP5 framework is a set of files written in PHP5.

A framework will add layering to an application. In general, they divide applications in three layers:

The presentation logic handles the interactions between the user and the software
The data source logic carries the access to a database or other data providers
The domain logic, or business logic, is the remaining piece. It involves calculation made on inputs, manipulation of data from the presentation, and dispatching of data source logic according to the commands received from the presentation.

Web application frameworks intend to facilitate the development of... web applications (websites, Intranets, etc.). Building a basic dynamic website can be easily achieved with existing programming languages, and PHP is known for its simplicity and broadly adopted for that purpose. With PHP alone, you can already query a database, manage session cookies, access files in the server, etc. But when it comes to building a more complex website, where business logic increases the volume of code to maintain, the need of a web application framework arises.

What is symfony?

Symfony is a complete framework designed to help and speedup the development of web applications.

It is based on the following concepts:

compatible with as many environments as possible
easy to install and configure
simple to learn
enterprise ready
convention rather than configuration, supporting fallback calls
simple in most cases, but still flexible enough to adapt to complex cases
most common web features included
compliant with most of the web "best practices" and web "design patterns"
very readable code with easy maintenance
open source

XWiki.com . Company . Solutions

http://www.xwiki.org/xwiki/bin/view/Download/WebHome

XWiki.org OpenSource project to develop a Java eXtended Wiki engine.

XWiki is a WikiWiki clone written in Java which supports many popular features of other Wikis like:

Wiki syntax (uses Radeox engine)
Content management (view/edit/preview/save)
Version Control
Attachments
Rights Management
Full-text Search
Document Templates to ease creation of common documents.
Relational Database storage using Hibernate.
Design Engine for Meta-Data and Forms.
In-place (inline) editing of form information in pages.
Powerful programming API in documents (Velocity or Groovy)
Search API for more detailed searching in the Meta-Data.
Plugin System in Java.
Scalability and Performance using J2EE.
Complete Design Skin System (templates content as well as CSS) have a look to nice websites powered by XWiki
RSS output and display of external RSS feeds
Multi-Lingual capabilities
XML/RPC Remote API
Portlet Integration
Integrated Statistics
PDF Export
WYSIWYG HTML Editing

Serendipity Weblog System: "Serendipity - a PHP Weblog/Blog software"

Serendipity is a weblog/blog system, implemented with PHP. It is standards compliant, feature rich and open source (BSD License).

Serendipity is constantly under active development, with a team of talented developers trying to make the best PHP powered blog on the net.

Serendipity has so far also proven 100% PHP5 compatible.

This wiki will help you guide through using, installing and enhancing Serendipity. You can also enlist your own Serendipity-Powered Blog in our Who is using section. This is a public wiki, and you can easily contribute to our Documentation and site - please note well that this is NOT a security flaw but just the way Wikis work. :-)

AurigaDoc: "AurigaDoc"
What Is AurigaDoc?

AurigaDoc is a java-xml-xsl based documentation tool for writing xml documents and converting them to other open formats like HTML(single and multi page), DHTML, PDF, PostScript, Formatting Object(FO), RTF, Java Help and HTML Help(.chm). AurigaDoc is a not an xml editor.

The idea is to keep a single document source(as xml) and convert it to various formats using XSLT.

In addition to the command line interface the conversion functionality of AurigaDoc can be called from java classes. Since the conversion of the source xml document to various output formats is done using XSL it is possible to customize the output by specifying a custom xsl as a parameter to the AurigaDoc converter.

Why AurigaDoc?

The formatting of the content (like bold, italic, list, tables, etc) can be specified by using a subset of well formed html tags. This reduces the learning curve and makes its easy for people already knowing html to write documents in AurigaDoc format.

Technology Used

AurigaDoc is built using open source software like

Xerces - A java based XML(Extensible Markup Language) parser from Apache.
Xalan - A java based XSLT(Extensible Stylesheet Transformation) engine from Apache.
FOP - A java based Formatting Object Implementation from Apache.
JFOR - A java based library for converting xsl-fo to rtf.
Java Help 2.0 - For generating output in Java Help 2.0 format.
Java Mail API - For generating MIME multipart/related message.
Steady State Software's CSS2 Parser: For parsing css stylesheets and applying them to pdf/postscript output.

Download

Click to download AurigaDoc.

Documentation

XML Source File in AurigaDoc Format
Single HTML Document
Multiple HTML Documents
MHT (Mime multipart/related) format. Can be opened in IE
DHTML Document
PDF Document
PostScript Document
Formatting Object Document
RTF Document
Java Help Format................................................. [Screenshot] [Java Web Start]
HTML Help File......................................................[Screenshot]
Oracle Help For Java (OHJ) (New)..................[Screenshot]
AurigaDoc Java API Documentation

PHP and XML: Parsing RSS 1.0 [PHP & MySQL Tutorials]:
"PHP and XML: Parsing RSS 1.0"
By Kevin Yank

Xaraya :: about: "Xaraya - cost effective, rapid and flexible website development

Xaraya is an extensible, Open Source web application framework written in PHP and licensed under the GNU General Public License. Xaraya delivers the requisite infrastructure and tools to create custom web applications that include fully dynamic multi-platform Content Management Solutions (CMS)."

Genomorama:
Genomorama is a software program for interactively displaying multiple genomes.
"Here is a brief comparison with other freely available 'Stand-alone' Genome viewers"

cat: Bioinformatics

index - The Jackson Laboratory: "J/maanova is a software for statistical analysis of MicroArray experiments. Written in Java and using R/maanova as the engine, J/maanova provides a powerful and interactive working environment for users to perform a variety of tasks."

J/maanova

Current Version 1.0b (July 15th, 2005)

[ Download | Installation | Status | Screen shots | Manual (pdf) ]

Oracle Migration Workbench: "Oracle Migration Workbench"

The Oracle Migration Workbench is a tool that simplifies the process of migrating third-party database systems to the Oracle platform (Oracle9i and Oracle10g). The Oracle Migration Workbench migrates the entire database schema, including triggers and stored procedures, in an integrated, environment.

Download MySQL 5.0 Beta

This is a special release of the new MySQL5 plugin, packaged with the core Migration Workbench for your convenience. Migrate all your MySQL5 objects including the new:

Stored Procedures
Views
Triggers
Cursors

Download the MySQL 5.0 Release here

Here is a great tutorial: http://technology.amis.nl/blog/index.php?p=436

And here: http://www.oracle.com/technology/documentation/migration.html

Norwegian bioinformatics platform: "Web Services in Bioinformatics"

The Computational Biology Unit, coordinator of the Norwegian FUGE Bioinformatics platform, is pleased to announce an introductory course in Web Services within bioinformatics. The format of the course will be a combination of lectures and practicals, with a main focus on practicals.

The use of Web Services in bioinformatics is growing, and many bioinformatic resources are currently available as Web Services. The course will provide an introduction to the Web Service technology. There will be demonstrations on the use of popular bioinformatic Web Services and attendants will learn how to set up their own Web Services. A basic knowledge of XML and programming is required. Although the methodology is language-independent, Java will be used as the main programming language for the course.