Bioinfo: May 2006

Wednesday, May 31, 2006

freshmeat.net: Project details for amoeba

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)."

JAVAMATION: WidgetServer

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."

Tuesday, May 30, 2006

Upload MAX MySQL

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

Thursday, May 25, 2006

symfony PHP5 framework » Symfony at a glance

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

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

Wednesday, May 24, 2006

Serendipity Weblog System

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. :-)

Saturday, May 20, 2006

MicroArray Explorer Page

Friday, May 19, 2006

AurigaDoc

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

Xaraya :: about

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:
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

Thursday, May 18, 2006

J/maanova

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) ]

Wednesday, May 17, 2006

Oracle Migration Workbench

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

Tuesday, May 16, 2006

Norwegian bioinformatics platform

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.

Resources

Course compendium (html)

Course compendium (pdf)

Course schedule (pdf)

WSDL for ELMdb (Exercise 1 and 2)

XML Schema for ELM (Exercises 1 and 2)

Lecture Notes

Introduction (Wednesday)

XML, SOAP and WSDL (Thursday)

Web Service Development (Thursday)

Web Service Deployment (Friday)

Advanded topics, WSRF (Friday)

External Links

XML Tutorial

The SOAP W3C Recommendation

Web Services Interoperability (WS-I)

Python Web Services and SOAPpy

Which style of WSDL should I use?

Eclipse Web Tools Platform (WTP)

Apache Ant

Apache Tomcat

Glimmer (Gene Prediction Tool)

EMBRACE Network of Excellence

Web Services at NCBI

Taverna

WS-Resource Framework

Web Services Security

An (Opinionated) Guide to Microarray Data Analysis

An (Opinionated) Guide to Microarray Data Analysis:

This site is organized as follows

Experimental design

This section discusses how many replicates are needed, whether to pool samples, and designs for two color arrays.

Pre-processing of Spotted Arrays

This section discusses steps along the way from quantification of the image, through background correction, quality control, and normalization, to obtain reliable estimates of relative gene abundance in the samples.

Pre-processing of Affymetrix Chips

The Affymetrix multiple-probe system offers a unique set of statistical challenges before one even gets to interpreting biological meaning. This section discusses image quantification and background, MAS5.0, normalization, multi-chip algorithms for estimation, and model-based quality control..

Exploratory Analysis

A preliminary examination of data confirms that groups are homogeneous. Many studies aim to find unknown co-regulated genes. This section discusses how to achieve these goals using multi-dimensional scaling, and clustering.

Statistical Tests for Identifying Differentially Expressed Genes

This section discusses methods and problems in determining which genes are differentially expressed between groups of samples, covering t-tests, multiple-testing corrections, false discovery rate, empirical Bayes methods, and analysis of variance.

Monday, May 15, 2006

how to use a perl script

how to use a perl script: how to use a perl script - What is CGI and How To Use Your CGI-BIN CGI Tutorial and Perl Introduction for Beginners - A tutorial for Webmasters - Learn how to take advantage of the CGI and SSI capabilities your host or ISP provides, and how to use those free scripts available on the Web. Also includes an introduction to the Perl language. … using the Perl language. When a Perl programmer writes a script they may choose to make it … used by the script. Serious Perl script programmers will also include a readme …
country decorating sites - Rustic Wildlife Home Furnishings & Decor For Log Home, Lodge … - Decorating Info Sites Visit our friends by clicking on their link under their name. … Country home decorating from traditional to contemporary. …
basic inventory - Superfreaker Studios : PayPal | Cart Tutorial - BASIC INVENTORY MANAGEMENT USING PAYPAL’S IPN (INSTANT PAYMENT NOTIFICATION). I. GOAL II. OVERVIEW III. IPN PROCESS IV. THE IPN PAGE V. OUR PURCHASE PAGE …
search engine ranking new zealand - Search Engine Ranking - Improve your search engine ranking using the search engine optimization knowledge … Kamcom Web Design is a New Zealand business providing search engine …
web developer duties - Bioinformatics.Org: NHGRI/NIH: Web Developer (Perl) - SPECIFIC DUTIES OF POSITION: Provide web development, programming, and administrative support for scientists involved in genome-based efforts. …

Saturday, May 13, 2006

Claroline.net - Open Source eLearning

Claroline.net - Open Source eLearning: "Claroline is a free application based on PHP/MySQL allowing teachers or education organizations to create and administrate courses through the web.

Developed from teachers to teachers, Claroline is built over sound pedagogical principles allowing a large variety of pedagogical setup including widening of traditional classroom and online collaborative learning.

Claroline is translated in 32 languages and used by hundreds of institutions around the world. The software is released under Open Source licence (GPL). Downloading and using Claroline is completely free of charge."

My Knowledge Place :: My Knowledge Place

My Knowledge Place :: My Knowledge Place: "My Knowledge Place consolidate web resources, related with e-learning process (distance learning). Here you can find short reviews and links to most of the existing world wide e-learning systems. Our website has information about working e-learning systems, and about most of the projects around the world, connected with the development of e-learning environment. Also you can submit your link here - just follow these 3 steps, displayed on the right."

My Knowledge Place

Claroline.net - Open Source eLearning

My Knowledge Place :: My Knowledge Place

Friday, May 12, 2006

FOP

FOP: "FOP (Formatting Objects Processor) is the world's first print formatter driven by XSL formatting objects (XSL-FO) and the world's first output independent formatter. It is a Java application that reads a formatting object (FO) tree and renders the resulting pages to a specified output. Output formats currently supported include PDF, PCL, PS, SVG, XML (area tree representation), Print, AWT, MIF and TXT. The primary output target is PDF."

XML for Molecular Biology as compiled by Paul Gordon

XML for Molecular Biology as compiled by Paul Gordon: "XML "
DTDs | Data | Tools | Community | References

cat: Bioinformatics

EMBL in XML

EMBL in XML: "XEMBL has been a service to display data from the EMBL Nucleotide Sequence Database in XML formats, BSML and AGAVE.

Now that nucleotide sequence data in the EMBL database are available from the EBI in two supported XML formats (EMBLxml, INSDseq), we are migrating former XEMBL users to the new services. This XML functionality is incorporated into the existing cgi-based DBfetch service, and SOAP webservice WSDbfetch"

cat: Bioinformatics

DATABASE BROWSING

DATABASE BROWSING: "What is dbfetch?

Dbfetch is an acronym for 'database fetch'. Dbfetch provides an easy way to retrieve entries from various databases at the EBI in a consistent manner. It can be used from any browser as well as well as within a web-aware scripting tool that uses wget, lynx or similar."
How to use dbfetch?

From the browser

Follow these instructions...
1. Selecting a database:
  -If you are using the first form to paste your search items: choose a database name from this form...more
  -If you are using the second form to upload your search items: the database name will be included at the beginning of each line line of the upload file followed by a colon...more
2. Entering your search terms:
  These MUST BE in the appropriate database format, up to 200 search items can be queried in one run.
  -If you are using the first form: seperate search items with a comma or space...more
  -If you are using the second form: seperate search items with a new line...more
3. Choosing an output format:
  Here you can choose the simpler fasta format, or the databases' default format for the chosen database...more
4. Style:
  You can get your results as text, ot html...more
5. Retrieve!
  You are now ready to fetch your results, by pressing the Retrieve button.
cat: Bioinformatics

Career in Bioinformatics

Career in Bioinformatics: "A career in bioinformatics will offer you excellent long-term career prospects. In addition to the IT industry, the pharmaceutical industry, the newly emerging bioinformatics industry and the biotechnology industry are all in need of the talent bioinformatics experts can bring to product development and improvement."

The following links provide you with further information should you consider bioinformatics as your future career.

Thursday, May 11, 2006

DataDirect XQuery – XQuery and XQJ for Oracle, SQL Server

DataDirect XQuery – XQuery and XQJ for Oracle, SQL Server, DB2 and more: Products: Home:

DataDirect XQuery™ is an implementation of XQuery and the XQuery for Java API that can query XML and relational data. It supports most relational databases, runs on any Java platform, and is easily embeddable into almost any Java program. Although no application server is required, it works with any J2EE Application Server. And two separate XQuery GUI development environments are available to make it easier to write and test your queries.

DataDirect XQuery is ideal for applications that do XML Publishing, XML Report Writing, Data Integration, XML processing for SOAP and Web Services, or Dynamic Web sites. Using DataDirect XQuery significantly simplifies application development by reducing the amount of code developers write and maintain to use XML and relational data together.

Welcome to Source Code for Biology and Medicine

Welcome to Source Code for Biology and Medicine: "Source Code for Biology and Medicine is an open access, peer-reviewed, online journal soon to be launched by BioMed Central.

DNA and Protein Microarrays

DNA and Protein Microarrays: "Microarray Station"

Wednesday, May 10, 2006

ktharray.se

ktharray.se
Analysis of DNA microarray data using the KTH-package and the R environment for statistical computing

Monday, May 08, 2006

Good PHP Tutorials - Using JavaScript and PHP For Web Syndication

Good PHP Tutorials - Using JavaScript and PHP For Web Syndication
JavaScript is a useful tool for syndicating content to other websites. For example, this page displays ads by Google using JavaScript. When you viewed this page, your browser fetched a script from Google then ran the script and displayed ads on the page.

This article examines the pros and cons of JavaScript syndication, explains how to implement it, and demonstrates a technique using PHP to make it even easier.

Sunday, May 07, 2006

JSP Tutorials, EJB Tutorials, JDBC Tutorials, Java Servlets Tutorials, WAP Tutorials, Spring Framework Tutorials, J2EE Tutorials, BioInformatics Tutor

JSP Tutorials, EJB Tutorials, JDBC Tutorials, Java Servlets Tutorials, WAP Tutorials, Spring Framework Tutorials, J2EE Tutorials, BioInformatics Tutorials, Java Server Faces Tutorials, Jboss Tutorials, Hibernate Tutorials, XML and MySQL Tutorials: "
This site contains many quality Java, JSP Tutorials, Hibernate Tutorials, Struts Tutorials, JSF Tutorials, RMI, MySQL Tutorials, Spring Tutorials, source codes and links to other java resources.

Saturday, May 06, 2006

Show and Hide

p
Some Text
span style="" language="javascript" onclick="if (document.all('about').style.display=='none') document.all('about').style.display='Inline';
else
document.all('about').style.display='none';"
Show Rest
/span
br
span
id="about"
style="display: none;"
Rest of the Text
/span

cat: WebDev

Friday, May 05, 2006

Xenoage Java Exe Starter

Xenoage Java Exe Starter: "Xenoage Java Exe Starter 2.0

(c) 2005 by Andreas Wenger, Xenoage Software

In Java you can generate executable Jar-files. But most windows users are only familiar with Exe files. Moreover it is not possible to assign icons to a Java Archive. This program solves these problems by generating an Exe with an arbitrary icon, that starts the Jar when it is launched. You can also choose which JRE versions are allowed and you can pack the Jar into the Exe file so that you need only to deliver one single file."

JSmooth

JSmooth: "JSmooth is a Java Executable Wrapper that makes a standard Windows executable binary (.exe) from a jar file. It makes java deployment much smoother and user-friendly, as it is able to find a Java VM by itself. When no VM is available, it provides feed-back to the users, and can launch the default web browser to an URL that explains how to download a Java VM."

GEPAS

GEPAS : Tools:
GEPAS is the next station in microarray analysis, it is composed of the following interconnected tools :

Normalization
DNMAD, Expresso
Preprocessing
preprocessor, knowledge filering, IDconverter
Clustering
SOTA, hierachical clustering, k-means, SOM, SOM-Tree, CAAT
Supervised classification
SVM predictions, Tnasas
Differential expression
T-Rex (t-test, Bayes, data adaptive, CLEAR, ANOVA, Pearson's test, Spearman's test, regression, survival)
Functional annotation
FatiGO, FatiGO+, Tissues Mining Tool, MARMITE, FatiScan, GSEA
CGH arrays
InSilicoArrayCGH
Viewers
PlotCorr, SotaTree, Tree, CAAT

cat: Bioinformatics, Microarray

UCT Microarray Portal - Experimental Design

UCT Microarray Portal - Experimental Design: "Planning your design can be aided by breaking down the problem into two parts:

1. Conceptual design - What question(s) am I asking of my experiment?
2. Statistical considerations - Does my design allow for statistically significant data analysis?
3. Practical considerations – What are my limiting factors?"

Creating and Using IntelliSense Code Snippets

Creating and Using IntelliSense Code Snippets: "IntelliSense Code Snippets provide a way for you to insert ready-made snippets of code into your projects."

Code Snippets (C#): Contains topics that describe IntelliSense Code Snippets for C# projects.
cat: WebDev

Wednesday, May 03, 2006

How to capture shortcut keys in Visual Studio .NET

How to capture shortcut keys in Visual Studio .NET:
"On This Page"
This article describes how to capture keyboard events in the Form object by using Microsoft Visual Studio .NET. The sample function demonstrates how to confirm that a user has entered a keyboard shortcut.

Oracle Developer Day Online

Oracle Developer Day Online: "Oracle Developer Day Online

Oracle Developer Day is a free workshop that gives you hands-on experience with emerging technologies and allows you to interact directly with the Oracle experts building the next generation of tools and infrastructure that support them. Workshops take place in cities worldwide on a regular basis.

For a preview of Oracle Developer Day content, or if you couldn't attend a workshop in person, view the broadband presentations and labs below."

BioPHP. PHP for bioinformatics

BioPHP. PHP for bioinformatics:

BioPHP PHP for Bioinformatics

Monday, May 01, 2006

How To Use the ODBC .NET Managed Provider in Visual C# .NET and Connection Strings

How To Use the ODBC .NET Managed Provider in Visual C# .NET and Connection Strings: "How To Use the ODBC .NET Managed Provider in Visual C# .NET and Connection Strings
View products that this article applies to."