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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.


Isotopo Data Analyzer’s main graphical user interface.Scientific software solution towards bioinformatics and biochemistry, with the ability of performing quantitative mass spectrometry to mixtures of materials labeled with stable isotopes. It provides internal database management system, third party independent file based experimental data management system and intelligent data format parser for data extraction and conversion of different data formats. (http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/).
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f11: Isotopo Data Analyzer’s main graphical user interface.Scientific software solution towards bioinformatics and biochemistry, with the ability of performing quantitative mass spectrometry to mixtures of materials labeled with stable isotopes. It provides internal database management system, third party independent file based experimental data management system and intelligent data format parser for data extraction and conversion of different data formats. (http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/).

Mentions: Isotopo software74,83 (Figure 11) is a published scientific software (Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany), a bioinformatics solution with the ability of performing quantitative mass spectrometry in isotope labeling experiments. It is an extended version of the earlier software LS-MIDA with a well-optimized mathematics implementation. It not only provides the graphical interfaces for gas chromatography-mass spectrometry (GC-MS) experimental data analysis, visualization and management, but also provides an intelligent data parser to automatically transform the machine’s pre-processed data into the processable format of the Isotopo software (reducing both time and labor). It also provides a complete database management system as a simple, well sustainable version of a middleware between data storage and GUIs.


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

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

Isotopo Data Analyzer’s main graphical user interface.Scientific software solution towards bioinformatics and biochemistry, with the ability of performing quantitative mass spectrometry to mixtures of materials labeled with stable isotopes. It provides internal database management system, third party independent file based experimental data management system and intelligent data format parser for data extraction and conversion of different data formats. (http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f11: Isotopo Data Analyzer’s main graphical user interface.Scientific software solution towards bioinformatics and biochemistry, with the ability of performing quantitative mass spectrometry to mixtures of materials labeled with stable isotopes. It provides internal database management system, third party independent file based experimental data management system and intelligent data format parser for data extraction and conversion of different data formats. (http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/).
Mentions: Isotopo software74,83 (Figure 11) is a published scientific software (Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany), a bioinformatics solution with the ability of performing quantitative mass spectrometry in isotope labeling experiments. It is an extended version of the earlier software LS-MIDA with a well-optimized mathematics implementation. It not only provides the graphical interfaces for gas chromatography-mass spectrometry (GC-MS) experimental data analysis, visualization and management, but also provides an intelligent data parser to automatically transform the machine’s pre-processed data into the processable format of the Isotopo software (reducing both time and labor). It also provides a complete database management system as a simple, well sustainable version of a middleware between data storage and GUIs.

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.