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Developing sustainable software solutions for bioinformatics by the " Butterfly" paradigm.

Ahmed Z, Zeeshan S, Dandekar T - F1000Res (2014)

Bottom Line: User feedback is valued as well as software planning in a sustainable and interoperable way.A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently.We validated the approach of our own software development and compared the different design paradigms in various software solutions.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany ; Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany.

ABSTRACT
Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (" Butterfly" paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.

No MeSH data available.


Lipid-Pro’s main graphical user interface.Scientific software solution towards lipidomics and pharmaceutical biology (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/).
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f12: Lipid-Pro’s main graphical user interface.Scientific software solution towards lipidomics and pharmaceutical biology (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/).

Mentions: Lipid-Pro (Figure 12) is a scientific software (computational) solution towards lipidomics and pharmaceutical biology (Department of Pharmaceutical Biology Department of Neurobiology and Genetics and Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany). It is a new solution towards the lipidome analysis including retention time (RT), mass to charge ratio values (m/z) of precursor and fragment ions, chemical compositions and peak intensities. Moreover, it provides comprehensive spectral data management, sharing and integration features.


Developing sustainable software solutions for bioinformatics by the " Butterfly" paradigm.

Ahmed Z, Zeeshan S, Dandekar T - F1000Res (2014)

Lipid-Pro’s main graphical user interface.Scientific software solution towards lipidomics and pharmaceutical biology (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4215756&req=5

f12: Lipid-Pro’s main graphical user interface.Scientific software solution towards lipidomics and pharmaceutical biology (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/).
Mentions: Lipid-Pro (Figure 12) is a scientific software (computational) solution towards lipidomics and pharmaceutical biology (Department of Pharmaceutical Biology Department of Neurobiology and Genetics and Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany). It is a new solution towards the lipidome analysis including retention time (RT), mass to charge ratio values (m/z) of precursor and fragment ions, chemical compositions and peak intensities. Moreover, it provides comprehensive spectral data management, sharing and integration features.

Bottom Line: User feedback is valued as well as software planning in a sustainable and interoperable way.A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently.We validated the approach of our own software development and compared the different design paradigms in various software solutions.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany ; Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, 97074, Germany.

ABSTRACT
Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (" Butterfly" paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.

No MeSH data available.