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Butterfly: A Paradigm towards Stable Bio & Neuro Informatics Tools Development

Zeeshan Ahmed1, 2, 3*, Saman Zeeshan3 and Thomas Dandekar3
  • 1 The Jackson Laboratory for Genomic Medicine, United States
  • 2 University of Massachusetts, Department of Quantitative Health Sciences, School of Medicine, United States
  • 3 University of Wuerzburg, Department of Bioinformatics, Biocenter, Germany

Particularly in life science, with the front runner fields Bioinformatics and Neuroinformatics, the world has been changed by small, efficient, fast, logical, embedded and intelligent software, databases and management systems. Software design and its engineering are essential for bio and neuro Informatics software impact. We propose a new approach ‘Butterfly’ (Ahmed et al., 2014a; Ahmed and Zeeshan, 2014b), for the betterment of modelling of scientific software solutions by targeting key developmental points: intuitive, graphical user interface design, stable methodical implementation and comprehensive output presentation. The focus of research was to address following key points: 1) Differences and different challenges required to change from traditional to scientific software engineering. 2) Scientific software solution development needs feedback and control loops following basic engineering principles for implementation. 3) Software design with new approach, which helps in developing and implementing a comprehensive scientific software solution. Conscious adaptation of Scientific Software Engineering (SSE) principles as exemplified here by the suggested butterfly design and its multilayered architecture (Figure 1) might look like an increase in developmental workload in comparison to many current bioinformatics programming methods. However, on the long run, it will reduce the burden by making the scientific application well designed, flexible, structured and reusable. It allows a product line development, is analytical and allows qualitative software improvement. Furthermore, Human Computer Interaction (HCI) concepts make it user friendly, easy to learn and to deploy. We validated the approach by comparing old and new bio and neuro informatics software solutions. Moreover, we have successfully applied our approach in the design and engineering of different well applied and published Bioinformatics and Neuroinformatics tools including Lipid-Pro (Ahmed et al., 2015a; Ahmed et al., 2015b), Ant-App-DB (Ahmed et al., 2015c; Ahmed, 2014d), Isotopo (Ahmed et al., 2014c), DroLIGHT (Ahmed and Foerster, 2013a; Ahmed and Foerster, 2013b; Ahmed et al., 2013c), GenomeVX and LS-MIDA (Ahmed et al., 2013d).

Figure 1
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Acknowledgements

Funding: The authors would like to thank German Research Foundation (DFG-CRC-SFB-1047 to ZA and DFG-CRC-TR34/Z1 to SZ, TD) for funding on this research.

Support: The authors thank to the University of Wuerzburg Germany, University of Massachusetts USA and The Jackson Laboratory for Genomic Medicine USA for support in this publication. Authors also thank to all interested colleagues for critical input on the approach and anonymous reviewers for helpful comments.

References

Ahmed, Z., Michel, M., Saman, Z., Dandekar, T., Mueller, M J., Fekete A. (2015a). Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics 31, 1150-1153.
Ahmed, Z., Dandekar, T., Mueller, M J., Fekete A. (2015b). Lipid-Pro: A Bioinformatics Tool towards Lipid Identification. In the proceedings of 11th Annual International Conference of the Metabolomics Society, the University of California, Davis, San Francisco Bay, USA.
Ahmed, Z., Saman, Z. Dandekar, T. (2015c). Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies. F1000Research 3, 311.
Ahmed, Z., Saman, Z., Dandekar, T. (2014a). Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm. F1000Research 3, 71.
Ahmed, Z., Saman, Z. (2014b). Cultivating Software Solutions Development in the Scientific Academia. Rec Pat Comp Sci 7, 54-63.
Ahmed, Z., Saman, Z., Huber, C., Hensel, M., Schomburg, D., Muench, R., Eylert, E., Eisenreich, W., Dandekar T. (2014c). ‘Isotopo’ a database application for facile analysis and management of mass isotopomer data. Database 2015.
Ahmed, Z. (2014d). Ant-App-Database towards Neural, Behavioral Research on Deserts Ants and Approximate Solar Estimations. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014.
Ahmed, Z., Foerster, CH (2013a). DroLIGHT-2: Real Time Embedded and Data Management System for Synchronizing Circadian Clock to the Light-Dark Cycles. Rec Pat Comp Sci 6, 191-205.
Ahmed, Z., Foerster, CH. (2013b). DroLIGHT: Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013.
Ahmed, Z., Foerster, CH. Dandekar T. (2013c). Integrating Formal UML Designs and HCI Patterns with Spiral SDLC in DroLIGHT Implementation. Rec Pat Comp Sci 6, 85-98.
Ahmed, Z., Saman, Z., Huber, C., Hensel, M., Schomburg, D., Muench, R., Eisenreich, W., Dandekar T. (2013d). Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinf 14, 218.

Keywords: neuroinformatics, bioinformatics, Butterfly Paradigm, human computer interaction, Scientific Software Solutions

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Poster, to be considered for oral presentation

Topic: General neuroinformatics

Citation: Ahmed Z, Zeeshan S and Dandekar T (2015). Butterfly: A Paradigm towards Stable Bio & Neuro Informatics Tools Development. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00009

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Received: 31 Mar 2015; Published Online: 05 Aug 2015.

* Correspondence: Dr. Zeeshan Ahmed, The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States, zahmed@ifh.rutgers.edu