DroLIGHT: Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila
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1
University of Wuerzburg, Neurobiology and Genetics, Biocenter, Germany
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2
University of Wuerzburg, Department of Bioinformatics, Biocenter,, Germany
It’s been more than 100 years since the Drosophila melanogaster species is well used in the neurobiological studies (especially after mid 1960s), the past research had well contributed in the key findings towards nervous system development and function (Bellen et al., 2010). We are interested in research on photoreception, behavioral biology and circadian clocks (Benzer, 1967; Konopka and Benzer, 1970; Roenneberg and Foster, 1997; Helfrich-Förster et al., 2001) of Drosophila. Here, we briefly present a new solution, might be helpful in synchronizing the endogenous clock of Drosophila to natural-like light-dark cycles.
Meeting the technological research objectives, we introduce a new computational software solution towards neurobiology and photobiology i.e. DroLIGHT (Ahmed et al., 2013); a user friendly, domain specific, intelligent, distributed, real time embedded and data management system. It is capable of controlling and automating the hardware that produces different colors of lights via Light Emitting Diodes (LEDs). The hardware used is a non-commercial, in house and custom engineered device, integrating seven combinations of different colors of LEDs with three brightness ranges.
DroLIGHT is a desktop Multiple Document Interface (MDI) application (Fig. 1), capable of doing several tasks: manually controlling multiple hardware devices with variable preliminary specifications, making combinations of different colors with similar and/or different wavelengths, scheduling light operations, generating circadian rhythm, producing different kinds of simulations and allowing user to directly instruct the hardware in string instructions. Moreover, the major developmental benefits of DroLIGHT are: it requires lower hardware cost than other high end platforms, with much smaller memory foot print, faster execution time, based on preprocessed managed object oriented source code, with no heap effect, secure access to the deployed and connected hardware.
DroLIGHT is implemented following spiral software development life cycle, integrating formal unified modelling language to scheme from different perspectives and incorporating human computer interaction guidelines, principles and patterns. Looking at the future perspectives and focusing own scientific system requirements, it is programmed (managed code) in C-Sharp programming language within Microsoft Dot Net Framework 2012. Unlike most of the traditional neuroinformatics and bioinformatics applications or scripts, the deployment procedure of DroLIGHT is very simple. User has to only run the 6 steps installer which provides all kinds of immediate information and automatically configures software settings in the operating system, without requiring any additional third party compilers or interpreters. It is compatible to the Microsoft Windows platform (preferably, 7 or higher).
The most recent, available version of the DroLIGHT is in use (in academic labs) and we are focusing on the future research and development objectives by further enhancing the capabilities of DroLIGHT with the addition of more features to advance the neurobiological experimental processes and improve the hardware control.
Fig. 1: DroLIGHT Graphical User Interface (GUI).
(A) Control; the top left-right part contain settings to establish connection with the hardware, at successful connection the remaining GUI options will be enabled to control LEDs manually and automatically by scheduling the time (example: currently the hardware is connected at COM port 4 at 115200bd, two LEDs are producing lights and all rest are scheduled in an experiment). (B) Circadian; provides interface to create, edit, load and run circadian experiments (example data set is loaded and in editing mode). (C) Simulation; produces visualizations in different styles (example line chart is shown). (D) Board Status; gives the board’s operational status as well as the direct access to test and control the hardware with string and hexadecimal instructions.
Acknowledgements
We would like to thank Deutsche Forschungsgemeinschaft (DFG, grant SFB 1047/Z) for funding.
References
Ahmed, Z., Helfrich-Förster, C., Dandekar, T. (2013). Integrating Formal UML Designs and HCI Patterns with Spiral SDLC in DroLIGHT Implementation. Recent Patents on Computer Science. [Accept, notified 7th June 2013]
Bellen, H. J., Tong, C., Tsuda, H. (2010). 100 years of Drosophila research and its impact on vertebrate neuroscience: a history lesson for the future. Nat Rev Neurosci., 11, 514-522.
Benzer, S. (1967). Behavioral mutants of Drosophila isolated by counter-current distribution. Proc. Natl. Acad. Sci., 58:3, 1112-1119.
Helfrich-Förster, C., Winter, C., Hofbauer, A., Hall, J.C., Stanewsky, R. (2001). The circadian clock of fruit flies is blind after elimination of all known photoreceptors. Neuron, 30:1, 249-261.
Konopka, R.J., Benzer, S. (1971). Clock mutants of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA, 68:9, 2112-2116.
Roenneberg, T. and Foster, R.G. (1997) Twilight times: light and the circadian system. Photochem. Photobiol., 66:5, 549-561.
Keywords:
Drosophila,
Light-dark cycles,
Circadian Clocks,
embedded systems,
neuroinformatics
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Demo
Topic:
General neuroinformatics
Citation:
Ahmed
Z and
Förster
CH
(2013). DroLIGHT: Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00053
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Received:
22 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Zeeshan Ahmed, University of Wuerzburg, Neurobiology and Genetics, Biocenter, Wuerzburg, Bavaria, 97074, Germany, zahmed@ifh.rutgers.edu