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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.


DroLIGHT’s main graphical user interface.It is a scientific software solution towards neurobiology and photobiology, capable of controlling and automating the hardware that produces different colors of lightsvia Light Emitting Diodes (LEDs). It provides experimental data management system, circadian and diurnal rhythm generation, 3D visualization of system’s performance and experimentation details (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/drolight/).
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f10: DroLIGHT’s main graphical user interface.It is a scientific software solution towards neurobiology and photobiology, capable of controlling and automating the hardware that produces different colors of lightsvia Light Emitting Diodes (LEDs). It provides experimental data management system, circadian and diurnal rhythm generation, 3D visualization of system’s performance and experimentation details (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/drolight/).

Mentions: Case study. We have successfully applied the Butterfly model in the implementation of newly proposed applications i.e.DroLIGHT71–73, scientific computational solution towards neurobiology and photobiology (Figure 10). The engineering processes started with the initial scientific software solution planning, the involvement of the members of a scientific group (Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany). The desired end product was a system towards the behavioral biology of the fruit fly. The overall requirements were about to implement a domain specific, intelligent, distributed, real time, embedded, data management system capable of controlling hardware devices, proficient in producing different colors of lights and monitoring the movements ofDrosophila melanogaster. Moreover, it should be capable of generating circadian and diurnal rhythms, experimental data management system and visualize experimentation’s output in two and three dimensional graphics formats.


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

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

DroLIGHT’s main graphical user interface.It is a scientific software solution towards neurobiology and photobiology, capable of controlling and automating the hardware that produces different colors of lightsvia Light Emitting Diodes (LEDs). It provides experimental data management system, circadian and diurnal rhythm generation, 3D visualization of system’s performance and experimentation details (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/drolight/).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f10: DroLIGHT’s main graphical user interface.It is a scientific software solution towards neurobiology and photobiology, capable of controlling and automating the hardware that produces different colors of lightsvia Light Emitting Diodes (LEDs). It provides experimental data management system, circadian and diurnal rhythm generation, 3D visualization of system’s performance and experimentation details (http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/drolight/).
Mentions: Case study. We have successfully applied the Butterfly model in the implementation of newly proposed applications i.e.DroLIGHT71–73, scientific computational solution towards neurobiology and photobiology (Figure 10). The engineering processes started with the initial scientific software solution planning, the involvement of the members of a scientific group (Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany). The desired end product was a system towards the behavioral biology of the fruit fly. The overall requirements were about to implement a domain specific, intelligent, distributed, real time, embedded, data management system capable of controlling hardware devices, proficient in producing different colors of lights and monitoring the movements ofDrosophila melanogaster. Moreover, it should be capable of generating circadian and diurnal rhythms, experimental data management system and visualize experimentation’s output in two and three dimensional graphics formats.

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.