GenBeans is build on top of BioBeans and StarBeans:
All 3 layers are written in java; Starbeans and BioBeans are open-source. StarBeans is based on the NetBeans platform and serves as a foundation for the entire project. BioBeans is an intermediate module suite which contains only biology-related modules; BioBeans can be either integrated in a separate application or serves an independent development platform when integrated with StarBeans.
Current release: StarBeans 7.0 - May 26 2011
What is StarBeans?
StarBeans is a fully branded application build on NetBeans generic platform. All bundles.properties have been branded to create a consistent application; all menus have been properly organized; all items more or less related to code development have been removed. StarBeans contains its own explorer located on the left side of the main window for the management of files in a project-independent manner (including opening and creation of files through wizards). StarBeans also contains part of NetBeans editor; as such, files with defined mimetypes can be edited in the Editor window with all the facilities found in NetBeans including syntax highlighting and various bars located in the four cardinal directions, editor toolbar, status bar, etc.
StarBeans contains the following specific modules:
Corelite. This modules brings additional functionalities to the platform, mainly file management in a project-independent manner and classes to manipulate menus dynamically.
DJ Native Swing. Support for an embedded web browser based on the DJ Native Swing project.
HTMLite. A simplified version of NetBeans HTML module for opening HTML files in web browser. HTML editing is possible but syntax highlighting is not functional.
Starcore. The branding module.
Upgrader. A simplified version of NetBeans upgrader module to handle the license during manual installation.
What's new in this version?
Version 7.0: The implementation of DJ Native swing embedded browser has been rewritten with a better integration within NetBeans.
Version 6.1.9c: conf files have been reformatted to allow proper launching on Linux and Mac OS X.
Version 6.1.9b:All biomodules have been transferred into the BioBeans suite. Support for embedded browser based on the DJ Native Swing project has been added. This is the implementation described by Geertjan Wielenga on The NetBeans Zone. Support for OS ions has been added. Unrecognized file types can be presented with their original OS icon in the Explorer with the default action set to open-in-system action. This result in cool effects on selected MIME types for which editors are only available outside the platform environment. The upgrader module was added for license check in absence of specific installer. This is a copy of o.n.upgrader with only the license part without settings import.
FAQ
Why a separate explorer component? The code of the Favorite module is duplicated to allow 1) The OpenDir action to mount a new directory from the main menu rather than through a counterintuitive right-click in the Favorite window; 2) The ability to open children nodes to make the Explorer more interactive; implementation of a navigator would most likely supersede this function; and 3) Expand folders in new Explorer windows (not-persistent). Remove the explorer code and enable the Favorite module to go back to the Favorite window.
Building StarBeans
StarBeans version number is identical to the version number of NetBeans it was build upon. Download the source and follow the instructions in the readme text. If you want to build on a more recent platform, you are very much on you own but you can try the following (some menus might be missing and new one appear): open the sbbuid project in StarBeans source; remove the HTMLite and HTMLite Lexer modules; in the project properties, libraries tab, set the platform to platform coming with your NetBeans distribution and make sure that Favorite and RCP Platform modules are not included in the platform cluster; also remove all dependencies to editor modules in the Starcore module and launch.
Current Release: BioBeans 1.1
What is BioBeans?
BioBeans 1.1 is a module suite which contains the following modules:
Biocore. Support for basic biofunctionalitites regarding MIME type, sequence cookies, biooptions; still a work-in-progress.
BioToolbar. Create a toolbar to access bioinformatic resources over the internet.
Biojava1. This module exposes BioJava1 1.8.1 libraries.
Biojava3. This module exposes BioJava1 3.0.1 libraries.
Biojava demo. A demo module containing a few demos from both BioJava1 and BioJava3. This module exposes a few Netbeans platform capabilities such as TopComponent, Output window, etc.
Bistro. This modules enables online and offline biology services. The source code for this module is in part derived from the Taverna project.
Seqformat. A module to handle file parsing in the editor.
BioBeans can be either imported in an application as an extra cluster suite, or used as a host platform for module development. In this case, use the BioBeans platform, which is nothing else that the StarBeans platform plus the BioBeans module suite.
BioBeans modules and libraries are all open source.
Building BioBeans
Building BioBeans within NetBeans. Download and unpack BioBeans 1.1 source and StarBeans 7.0 binary. Open the bbbuid project in BioBeans source; in the project properties, libraries tab set the platform to NetBeans IDE 7.0, add the sib and the nb ex clusters from Star Beans and launch.
Building Bio Beans all from sources. First build Star beans from sources as described above, open the bibbed project, set the platform to the extended platform and add Star Beans cluster (found in the build folder, Star Beans must be build first).
Files |
NetBeans |
Size |
|
|---|---|---|---|
6.8 |
4.54 MB |
||
6.9.1 |
4.54 MB |
||
6.9.1 |
18.8 MB |
||
6.9.1 |
23.5 MB |
||
6.9.1 |
5.4 MB |