httpFileManager.com - Home - Remote administration of files over HTTP

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: "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."

PHP - Smarty

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

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

NEBC Software Documentation Pages

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

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

Dynamic Drive: .htaccess password generator

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

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

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

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

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 - 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 - 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!, 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

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

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

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 :: 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. "

Eclipse SQLExplorer plugin

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 )"

1. Download the SQLExplorer file net.sourceforge.sqlexplorer_2.2.3.zip.
2. Extract the SQLExplorer .zip file to the /eclipse directory. is the directory in which Eclipse is installed
3. 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

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

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.

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.
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: "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

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 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

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

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: "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: "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

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

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."