Bioinformatics process management: information flow via a computational journal.
This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread-ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.
Feagan
Lance
L
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Rohrer
Justin
J
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Garrett
Alexander
A
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Amthauer
Heather
H
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Komp
Ed
E
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Johnson
David
D
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Hock
Adam
A
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Clark
Terry
T
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Lushington
Gerald
G
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Minden
Gary
G
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.
Frost
Victor
V
Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA.