The BioBeans Project

farrightSoftware and s/w Development

Aug 15, 2012 (4 years and 10 months ago)


The BioBeans Project: Motivation

During data analysis, biologists have to deal with several

identifying and locating computational tools that are
suitable for the task at hand

obtaining, understanding and managing these

transferring data between applications by copy
paste or saving files

transforming data files from one format to another in
order to allow applications to exchange data


A bioinformatics workflow tool based on the NetBeans

Allows users to discover and dynamically bind
components at runtime

Transfer of data between components is automated

Any Java based bioinformatics tool can be integrated as a

Java tools can be integrated through a Java front
end and a wrapper

Open source project coordinated by Tim Troup at
DCS/BRC Glasgow

The NetBeans Platform

= NetBeans IDE without the code
editing modules

a generic desktop application that
developers can add their own
modules to

developers inherit useful generic
features (dockable windows, menus,
file storage and file access)

may save a significant amount of
programming time

numerous projects have used this
model (see

BioBeans system architecture

instance of the infobus is created
and components join it

components connected to the bus
listen for events

data producers listen for data
requests, data consumers for
announcements of data being
published on the bus

data consumers are registered in the
Yellow Pages, where the Data
Controller locates them via Lookup
when data has become available on
the bus

Data Controller then provides a
pointer to the available data item and
instantiates the appropriate data
consumer module (user selects one
from list)

Current suite of BioBeans modules

ClustalW module

BioBeans module with GUI client to ClustalW web
service at DNA Databank of Japan

Connection to web service is hard

Future Work

Currently only 5 working modules

Open up CVS repository and encourage others to
contribute modules

Development time: 1
2 weeks (?) per module for
experienced developers

Modules are easy to distribute and install (via BioBeans
website or Sourceforge)

Workflow integration module

Under development (Iain Darroch, DCS/BRC)

Will allow recurring workflows to be preconfigured and
saved for future use

Graphical drag
drop interface for preconfiguration
of workflow/sequence of use of modules

Step A

Step B

Step C

My Workflow.file