A graphical user interface (GUI) consists of a set of buttons, menus and other graphical elements to allow the user to parameterise and run the applications. GUIs are controlled with a mouse and keyboard, for example to set options and name files.
Available GUIs include:
Jemboss (Chapter 9, Using EMBOSS under JEMBOSS) is a java-based interface to EMBOSS. The software is free and part of the EMBOSS distribution. It has the advantage of providing sensible default values on-the-fly for a given sequence or for a given input parameter. Jemboss can run the EMBOSS applications interactively or as a batch process. The progress of the batch processes are monitored by a job manager.
Jemboss can be set up to work with a local EMBOSS installation or one installed on a remote server. It provides file managers for data transfer between the local machine and a remote machine running the EMBOSS applications. Local and remote files can be used directly.
There is also a project manager responsible for maintaining the details of each run and the input and output files. These can be called up at any time, annotated or deleted.
Its main features are:
Launched by a script or via the web (Java Web Start).
Communicates with EMBOSS via SOAP (client-server) or directly (standalone installation)
Optional user authentication (Unix)
Presents programs as group listings & as a scroll list. Parameters are displayed with pop-up help & help links
Local and server file management systems
Stores results on the server, along with the run information.
Provides direct access to the Jemboss Alignment Editor (though this can be run independently of the main Jemboss GUI).
Dynamically calculates default parameters based on the users input (as EMBOSS does from the command line).
Interactive or batch submission of EMBOSS applications to job queues (NQS, OpenPBS or just the background).
Installation scripts provided to set up client-server installations. One for installing EMBOSS and Jemboss server as an Axis based web application on Tomcat; another one for preparing a web-launch page for launching Jemboss clients using Java Web Start.
Under Microsoft Windows this interface is automatically installed and configured for a single user by the mEMBOSS package.
The Staden package provides a fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows, free of charge to academic users. External applications can be included through tcl/tk scripts. Interactive graphics are included.
Rodger Staden's group was working with EMBOSS on integrating EMBOSS more closely with the Staden package. Unfortunately, funding for Staden was terminated.
COLIMATE (command line mate) is a utility for building interfaces for command line programs. A Colimate-generated menu helps you to fill all parameter values such that you can launch the command line without having to write and remember a tedious command line structure.
Kaptain is a universally applicable graphical front-end based on context-free grammars. It is a KDE2 application, but you can run it also from Gnome if the QT libraries are installed. It now supports the complete set of command line options of all applications in EMBOSS.
You will find a compressed tar archive for download, additional information, and a few screenshots at http://userpage.fu-berlin.de/~sgmd
The kemboss interface is based on the
emboss.kaptn scripts by Thomas Sigmund and was developed using the
Qt libraries. But in contrast to the
kaptn scripts the application is a compiled binary file. As such, kemboss for example is able to save and load individual EMBOSS program configurations. It also allows to paste some data into an input text field and after execution of the EMBOSS program, automatically displays the generated output. Therefore, when simple analyses are done, the user doesn't have to care about input and output files.
kemboss has been developed and tested using SuSE Linux, Windows XP, Mac OS X, OpenSolaris and PC-BSD. But as the program is based on the multi platform
Qt libraries, the sources should also compile on a variety of other 32- and 64-bit operating systems, including many other Unix Systems.
The current kemboss release 0.9 includes graphical user interfaces for all programs of the EMBOSS main package, version 6.4.0, as well as the phylip EMBASSY package.
Some screenshots, the source code, as well as binaries for the above-mentioned operating systems are available at:
Please report all problems, bugs and suggestions to:
Geneious combines EMBOSS and other leading DNA and protein sequence analysis tools into a single interface. Its ease of use makes bioinformatics accessible to any biologist. It is commercial software that runs on all major operating systems.