Limits...
Bioinformatics process management: information flow via a computational journal.

Feagan L, Rohrer J, Garrett A, Amthauer H, Komp E, Johnson D, Hock A, Clark T, Lushington G, Minden G, Frost V - Source Code Biol Med (2007)

Bottom Line: These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment.Extensive features facilitate sharing data, computational methods, and entire experiments.We illustrate the use of our implementation of the BCJ on two domain-specific examples.

View Article: PubMed Central - HTML - PubMed

Affiliation: Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA. frost@ittc.ku.edu.

ABSTRACT
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.

No MeSH data available.


Complete Experimental Workflow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2228283&req=5

Figure 2: Complete Experimental Workflow.

Mentions: Experiments are defined with simple block diagrams in a hierarchical fashion. Each block represents a program, or sequence of programs, to be executed. Input and output connections are made between blocks. In the BCJ environment, a block diagram is called a workflow. Figure 2 is an example of a simple workflow. Workflows provide a convenient and intuitive way for any user to define a customized task. Users are not required to be familiar with programming languages to define complex tasks. Once defined, a workflow may be reused. Workflows are just another entry content type, so they can be shared among all BCJ users. Experiments can be joined by connecting resources to form workflows. A data source can be used as an input to one BCJ resource with the output directed to another resource. The BCJ also provides a mechanism to annotate workflows. Figure 3 provides an example of a simple workflow definition.


Bioinformatics process management: information flow via a computational journal.

Feagan L, Rohrer J, Garrett A, Amthauer H, Komp E, Johnson D, Hock A, Clark T, Lushington G, Minden G, Frost V - Source Code Biol Med (2007)

Complete Experimental Workflow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2228283&req=5

Figure 2: Complete Experimental Workflow.
Mentions: Experiments are defined with simple block diagrams in a hierarchical fashion. Each block represents a program, or sequence of programs, to be executed. Input and output connections are made between blocks. In the BCJ environment, a block diagram is called a workflow. Figure 2 is an example of a simple workflow. Workflows provide a convenient and intuitive way for any user to define a customized task. Users are not required to be familiar with programming languages to define complex tasks. Once defined, a workflow may be reused. Workflows are just another entry content type, so they can be shared among all BCJ users. Experiments can be joined by connecting resources to form workflows. A data source can be used as an input to one BCJ resource with the output directed to another resource. The BCJ also provides a mechanism to annotate workflows. Figure 3 provides an example of a simple workflow definition.

Bottom Line: These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment.Extensive features facilitate sharing data, computational methods, and entire experiments.We illustrate the use of our implementation of the BCJ on two domain-specific examples.

View Article: PubMed Central - HTML - PubMed

Affiliation: Information and Telecommunication Technology Center, University of Kansas, Lawrence, Kansas, USA. frost@ittc.ku.edu.

ABSTRACT
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.

No MeSH data available.