Title |
A graph-based approach for designing extensible pipelines
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Published in |
BMC Bioinformatics, July 2012
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DOI | 10.1186/1471-2105-13-163 |
Pubmed ID | |
Authors |
Maíra R Rodrigues, Wagner CS Magalhães, Moara Machado, Eduardo Tarazona-Santos |
Abstract |
In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest implementation of pipelines involves hardcoding the execution steps into programs or scripts. This approach can lead to problems when a pipeline is expanding because the incorporation of new tools is often error prone and time consuming. Current approaches to pipeline development such as workflow management systems focus on analysis tasks that are systematically repeated without significant changes in their course of execution, such as genome annotation. However, more dynamism on the pipeline composition is necessary when each execution requires a different combination of steps. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United Kingdom | 1 | 33% |
Unknown | 2 | 67% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 2 | 67% |
Scientists | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 3 | 7% |
United Kingdom | 2 | 4% |
Germany | 2 | 4% |
Brazil | 1 | 2% |
Unknown | 37 | 82% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 18 | 40% |
Student > Ph. D. Student | 6 | 13% |
Student > Master | 5 | 11% |
Student > Bachelor | 4 | 9% |
Other | 4 | 9% |
Other | 7 | 16% |
Unknown | 1 | 2% |
Readers by discipline | Count | As % |
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Agricultural and Biological Sciences | 23 | 51% |
Computer Science | 6 | 13% |
Medicine and Dentistry | 4 | 9% |
Engineering | 4 | 9% |
Biochemistry, Genetics and Molecular Biology | 2 | 4% |
Other | 3 | 7% |
Unknown | 3 | 7% |