Poster: General neuroinformatics
P41 Butterfly: a paradigm towards stable bio & neuro informatics tools development Zeeshan Ahmed1,2,3,*, Saman Zeeshan2,3, Thomas Dandekar3 1. The Jackson Laboratory for Genomic Medicine, USA 2. School of Medicine, University of Massachusetts, USA 3. Department of Bioinformatics, Biocenter, University of Wuerzburg, 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” (1, 2), 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 work load 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 DroLIGHT (3–5), LS-MIDA (6), Isotopo (7), Ant-App-DB (8, 9), and Lipid-Pro (10). Keywords: Neuroinformatics, Bioinformatics, Butterfly Paradigm, Human Computer Interaction, Scientific Software Solutions
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Figure 1. Butterfly three layer model. Shown in grey is the abstract layer, the basis for design and development (yellow), followed by implementation and testing by the user (green) so that the software is released including installation and training. Acknowledgements The authors would like to thank German Research Foundation (DFG- TR34/Z1) for funding on this research. The authors thank to the University of Wuerzburg Germany, University of Massachusetts USA and The Jackson Laboratory 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. Conflict of Interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. References 1. Ahmed Z, Saman Z, Dandekar T. Developing sustainable software solutions for bioinformatics by the ‘Butterfly’ paradigm. F1000Research (2014). doi: 10.12688/ f1000research.3681.2 PMID:25383181 2. Ahmed Z, Zeeshan S. Cultivating software solutions development in the scientific academia. Recent Pat Comput Sci (2014) 7(1):54–66. doi: 10.2174/221327590766614061221 0552 PMID:NOPMID 3. Ahmed Z, Charlotte F. DroLIGHT: real time embedded system towards endogenous clock synchronization of drosophila. Front Neuroinformatics (2013) 7. doi: NODOI PMID:NOPMID
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Ahmed Z, Helfrich-Förster C. DroLIGHT-2: real time embedded and data management system for synchronizing circadian clock to the light-dark cycles. Recent Pat Comput Sci (2013) 6(3):191–205. doi: 10.2174/2213275906666131108211241 PMID:NOPMID 5. Ahmed Z, Helfrich-Förster C, Dandekar T. Integrating formal UML designs and HCI patterns with spiral SDLC in DroLIGHT implementation. Recent Pat Comput Sci (2013) 6(2):85–98. doi: 10.2174/22132759113069990005 PMID:NOPMID 6. Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Münch R, et al. Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinformatics (2013) 14(1):218. doi: 10.1186/1471-2105-14-218 PMID:23837681 7. Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Munch R, et al. ‘Isotopo’ a database application for facile analysis and management of mass isotopomer data. Database (2014) 2014(0):bau077–077. doi: 10.1093/database/bau077 PMID:25204646 8. Ahmed Z. Ant-App-Database towards neural, behavioral research on deserts ants and approximate solar estimations. Front Neuroinformatics (2014) 8. doi: NODOI PMID:NOPMID 9. Ahmed Z, Zeeshan S, Fleischmann P, Rössler W, Dandekar T. Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies. F1000Research (2014). doi: 10.12688/f1000research.5931.3 PMID:25977753 10. Ahmed Z, Mayr M, Zeeshan S, Dandekar T, Mueller MJ, Fekete A. Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics (2014). doi: 10.1093/ bioinformatics/btu796 PMID:25433698
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