The BioBeans Project

farrightSoftware and s/w Development

Aug 15, 2012 (5 years and 2 months ago)

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The BioBeans Project: Motivation

During data analysis, biologists have to deal with several
problems:



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



obtaining, understanding and managing these



transferring data between applications by copy
-
and
-
paste or saving files



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

BioBeans


A bioinformatics workflow tool based on the NetBeans
IDE/Platform


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
module


Non
-
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 www.netbeans.org)

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
-
coded

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
-
and
-
drop interface for preconfiguration
of workflow/sequence of use of modules

Step A

Step B

Step C

My Workflow.file