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EMBOSS Interfaces

Contents

What are interfaces?

An interface is something that comes between you and the raw horror of any computer's operating system. An EMBOSS interface provides access to the applications and and their options, including their input and output files.

EMBOSS is designed to make it relatively easy to automate the process of defining interface to the applications. This includes graphical user interfaces (GUI) which are controlled with a mouse, for example to set options. EMBOSS may also be interfaced via perl and python script modules, making it easier to run the programs and process the results.

The current status of the interfaces we are aware of is given below, and highlights the usa of EMBOSS in different contexts.

Jemboss

Jemboss is a java based interface to EMBOSS. It provides the advantage of being able to provide sensible EMBOSS defaults 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. Jemboss provides file managers for data transfer between the local machine and the remote machine that runs the EMBOSS applications. Local and remote files can be used in Jemboss.

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 and deleted by the user. The user can also add notes for each run.

Jemboss is part of the EMBOSS ditribution. This means that sites can download the code and set up Jemboss locally using a script. There is on-going development of this project and your feedback is encouraged.

Some details:

Other GUIs

The interfaces we have seen so far are:

Staden

The Staden package provides sequence analysis free to academic users. External applications can be included through tcl/tk scripts. Interactive graphics are included.

Rodger Staden's group was working with us on integrating EMBOSS more closely with the Staden package. Unfortunately, funding for Staden was terminated.

CoLiMate

COLIMATE (command line mate): a utility for building interfaces for command-line programs. COLIMATE was developed by Carlos Oscar at the Spanish EMBnet node.

Kaptain

A KDE GUI for EMBOSS applications from Thomas Siegmund, Institute of Biology, Genetics, at the Free University of Berlin

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

EMBOSS kaptn needs

  • kdelibs 2.0 - 2.2.2
  • kaptain 0.6
  • nedit 5.0 - 5.2

embossRUNNER

embossRUNNER is an interface for EMBOSS on MacOS X. It is available for download at the MIT Mac Hyperarchive. 

Author: Rudi & Suksiri Grams
Department of Biology
Mahidol University
Bangkok, Thailand

SeqPup

SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems that support the Java 1.1 runtime environment, including Macintosh, MS-Windows and X-Windows.

Arka

Not much is known about this project. It is rumoured to be able to incorporate EMBOSS.

Web interfaces

Most web interfaces to EMBOSS provide a form for setting options and running applications. Difficulties can arise because of 'dependencies' in the application input. These include where the value of one parameter depends on the value or property of another, for example sequence length, or where the available options depend on the input, for example whether a sequence is DNA or Protein. Some web interfaces handle dependencies better than others.

To use a web interface, all you need are a web broswer and internet access. Some of these interfaces run 'anonymously' so any user can run the applications. In most cases however you will be expected to register with the site before you can use their services.

The interfaces we have seen so far are:

WebLab

WebLab collect provide easy web access to the most popular bioinformatics programs. It is task-oriented instead of tool-oriented. It provides pre-defined protocols to guide biologists to work step by step through the entire analysis procedure.

Pise

PISE (french pronunciation like the english word 'peas') was developed by Catherine Letondal at the Institute Pasteur. Using an XML definition for each application, PISE generates a Web interface and other common interfaces automatically.

For EMBOSS, the ACD files were converted with scripts to generate the XML definitions. Where ACD files caused problems, we simply fixed the ACD files.

EMBOSS Explorer.

An extremely popular web interface to EMBOSS from Luke McCarthy at Plant Biotechnology Institute, Canada

W2H

W2H is a free web interface to sequence analysis software packages including EMBOSS. W2H is developed in a collaborative project between the German EMBnet node (DKFZ) and EMBL-EBI by Peter Ernst and Martin Senger.

wEMBOSS

An EMBOSS web interface from Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node.

Features:

  • Each user has a separate and private workspace.
  • Organize your work by creating projects and subprojects.
  • Results saved for easy recover & review.
  • On-line help.
  • Keyword search for programs and documentation.
  • Administrator can exclude EMBOSS programs from wEMBOSS.

You can download wEMBOSS from http://wemboss.sourceforge.net/

wEMBOSS is a joint effort between BEN & AR (Belgium and Argentina EMBnet nodes).

AppLab

Applab was developed by Martin Senger at EBI. It is now part of SoapLab but not independently supported.

The present version is in Java and uses CORBA IDL definitions for applications.

SRSWWW

SRS is the most widely used biological database indexing and query system worldwide. Originally developed by Thure Etzold at EMBL and EBI, it was further developed by Lion Bioscience in Cambridge in collaboration with the EBI.

In addition to the database query capabilities, SRS includes external application definitions written in the Icarus language.

We have collaborated with Lion to develop Icarus definitions for many of the EMBOSS applications.

Biomanager

BioManager is a web interface developed by eBioinformatics Inc (now defunct), hosted by ANGIS (www.angis.org.au), the Australian EMBnet node. BioManager integrates EMBOSS and a number of other freeware analysis programs, as well as the major genetic databases. It is available on subscription.

Workflows

These include applications for combining more than one application together into a workflow or pipeline.

Taverna

The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community. As a component of the EPSRC funded myGrid project, Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL).

Pipeline Pilot

Commercial workflow software. From their website: Pipeline Pilot(tm) is a new high-throughput data analysis and mining system for drug discovery informatics. With this package, a user may define and perform a complex series of operations on extremely large data sets in real time. The result is unprecedented flexibility in processing the growing volume of data being generated in modern automated laboratories.

BioWBI (Bioinformatic Workflow Builder Interface) and WsBAW (Web services for Bioinformatic Analysis Workflow)

Bioinformatic Workflow Builder Interface - A Web-based working environment from which one can build and execute bioinformatic workflows and share analysis processes.

Web Service for Bioinformatic Analysis Workflow - An application that automates Bioinformatic Analysis Workflow by deploying a Web service.

These two pieces of software allow their users to design and execute complex bioinformatic analysis processes. They at present wrap about 40 EMBOSS algorithms, besides other algorithms that do not belong to this package.

Download: BioWBI WsBAW

G-Pipe

G-Pipe is a graphical pipeline generator that allows the definition of pipelines, and parameterisation of its component methods using Pise web interfaces. The entire analysis protocol is stored in XML and a complete bioinformatic experiment (linked set of methods and parameters) can hence be reproduced or shared among users. A Perl macro making use of Pise/Bioperl and implementing the pipeline can also be downloaded (for developers).

GPIPE is available at http://kun.homelinux.com/Pise/5.a/gpipe.html) .

Download: ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz

Ports and packages

These include applications for combining more than one application together into a workflow or pipeline.

EMBOSS for Windows

There is a port of EMBOSS to Windows by from André Blavier, France.

See http://www.interactive-biosoftware.com/embosswin/embosswin.html

Live DVD with Emboss/Jemboss

Live DVD with Emboss/Jemboss from NERC Environmental Bioinformatics Centre

See http://envgen.nox.ac.uk/live_dvd.html

Another Live CD with Emboss

Live DVD with Emboss/Jemboss from vigyaancd.org

See http://www.vigyaancd.org/

Another Live CD with Emboss

Live DVD with Emboss/Jemboss from vlinux

See http://ftp.bioinformatics.org/pub/vlinux/

Another Live CD with Emboss

Live DVD with Emboss/Jemboss from dnalinux.com

See http://www.dnalinux.com/

Bio::Emboss perl module version 1.0

This module is an interface to the libraries of the EMBOSS package (European Molecular Biology Open Software Suite).

With this module you can access EMBOSS databases and use EMBOSS functions to manipulate your data. You can write perl programs that look like any other EMBOSS program (command-line, web interface).

Bio::Tools::Run::EMBOSSApplication
The EMBOSS factory class encapsulates access to EMBOSS programs. A factory object allows creation of only known applications.

If you want to check command line options before sending them to the program set $factory->verbose to positive integer. The value is passed on to programs objects and the ADC description of the available command line options is parsed and compared to input.

NetBSD package

EMBOSS from the NetBSD package collection.

FreeBSD port

FreeBSD port of EMBOSS

BioLinux RPM for EMBOSS/JEMBOSS

The BioLinux RPM for EMBOSS/JEMBOSS.

Other interfaces

These include sequence and alignments editors, and other packages and interfaces on non-Unix operating systems.

CINEMA

CINEMA is a Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences.

In Version 2.0, the functionality was extended to include split-screen editing, and applet customisation through the use of "pluglets". The Pluglet menu allows customisation of CINEMA by allowing users to import their own pluglets. Clicking on the Load pluglets option causes the menu bar to be updated with a new menu relating to the imported applet, and a new icon to appear in the icon bar. Clicking on the icon invokes the new applet.

Pluglets include BLAST, ClustalW and other external applications.

AbiVIEW

Sebastian Bassi has written a web interface to the EMBOSS application AbiView. It's written in Python and consists of an HTML form.

Acedb

Acedb can be configured to start applications from a pop up menu.

emnu

This character-based menu program is distributed as an EMBASSY add-on to the EMBOSS package.

MolTalk

MolTalk: a computational environment for doing Structural Bioinformatics. Uses EMBOSS for handling of sequences and alignments.