EasyEclipse

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 - 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

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

BioMed Central | Abstract | 1471-2105-7-322 | SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera

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: "Creating PDF Files in PHP"

Use PHP to Create Dynamic pdf Files

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™

PortableApps.com | Your Digital Life, Anywhere™:

Apps Hosted Here

• Portable AbiWord
• Portable ClamWin AV
• Portable FileZilla
• Portable Firefox
• Portable Gaim
• Portable GIMP
• Portable Miranda IM
• Portable NVU
• Portable OpenOffice.org
• Portable Sunbird
• Portable Thunderbird
• Portable VLC media player
• More apps...

Nvu - The Complete Web Authoring System for Linux, Macintosh and Windows

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

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

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: "Free RSS to HTML PHP Script"

BayBoots

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

SpotWhatR

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

1. 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).
2. 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.

3. Select just the cells you want to lock and repeat step 2, but this time select the Locked check box.
4. 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 :: 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

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

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

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

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."