Mapping Honeycomb Networks into Different ...

Send Orders for Print-Reprints and e-Reprints to [email protected] Recent Patents on Computer Science 2013, 6, 000-000

1

DroLIGHT-2: Real Time Embedded and Data Management System for Synchronizing Circadian Clock to the Light-Dark Cycles Zeeshan Ahmed* and Charlotte Helfrich-Förster Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany Received: September 2, 2013; Revised: October 25, 2013; Accepted: November 7, 2013

Abstract: Synchronizing the endogenous clock of animals to artificially created light-dark cycles in the laboratory is a challenging task, because it needs a fully controllable, automatic lighting system that produces various light-dark cycles with changing spectral composition of high quality and fidelity. Here, we focus on the development of such a system for the model species Drosophila melanogaster. Meeting the technological objectives of this research, we introduce a user friendly, real time embedded, distributed, data management and multi-threading based system i.e. DroLIGHT-2, which is capable of controlling and automating an LED-based lighting system. In this manuscript, we briefly explore what DroLIGHT-2 is, its features, advancements, hardware, usage and pitfalls. We validate the software application with two and three dimensional presentation of the obtained results generated by DroLIGHT-2 and compare them with existing, our previously published solutions. We also discuss followed software engineering’ paradigm, used development life cycle, some designed application’ models with implementation and graphical user interface’ details. Moreover the paper also discusses few patents relevant to circadian-rhythm and real time embedded systems.

Keywords: Drosophila, circadian-rhythm, diurnal rhythm, embedded systems, light-dark cycles, neurobiology, neuroinformatics. INTRODUCTION Like other highly correlated fields in natural sciences and medicine (e.g. Bioinformatics, Health-informatics etc.), computer science has potentially contributed and played a vital role in the development of Neurobiology as an interdisciplinary methodical initiative that builds and systematizes the biological facts in the form of testable details and predictions about the nervous system. In last two decades, neurobiology has excitingly progressed and become significant especially in the fields of Genetics, Gene Environment Interactions, Brain Plasticity, Imaging and Brain Development. Neurobiologist together with the help of computer scientists and engineers (electrical, mechanical etc.), have produced different analytical tools towards genetics, molecular biology, systems anatomy, psychology and behavioral biology. Light is of major importance for all living systems: it is used as energy source for photosynthesis, as heat source for temperature sensitive processes, as directional cue for phototactic behavior, and as the basis of image forming vision in animals. In addition, the regular 24-hour light-cycles are the most important Zeitgeber for synchronizing the endogenous clocks of all organisms to the environmental rhythms on earth. In the northern and southern hemispheres, the daylength changes over the year and serves as a cue to induce physiological changes that prepare the organisms to the coming winter or summer. *Address correspondence to this author at the Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany; Tel: +499313181917; Fax: +499313184452; E-mail: [email protected] 2213-2759/13 $100.00+.00

Over 24h, the amount of light, its spectral composition and its direction change in a regular way. In theory, all of these features could be used for clock synchronization, but each would be subject to considerable variation or `noise’ [1]. Especially the daily irradiance can vary largely from day to day due to the weather. Despite this high degree of environmental noise, entrained organisms show remarkable precision in their daily activities. It is assumed that organisms use early dawn and late dusk for synchronizing their endogenous clocks, because at that time of the day day-to-day fluctuations in irradiance are smallest and the spectral composition of light changes very systematically [1]. Organisms possess multiple photoreceptors to detect these systematic changes, but it is still unknown how they do so [2]. One major difficulty is that the light changes during dawn and dusk are hard to simulate in the laboratory. Here we propose an intelligent software system to control irradiance and wavelength of light designed for the photoreceptor system of fruit fly Drosophila melanogaster. The fruit fly has been successfully used as model organism to unravel basic mechanisms in genetics, development and neurosciences for about 100 years [3]. This includes research on photoreception, behavioral biology and circadian clocks [4-6]. Drosophila’s circadian clock consists of about 150 interacting clock neurons of which some are photoreceptive on their own (reviewed [7]). In addition, five rhodopsins in the eyes with distinct absorption spectra contribute to synchronization of the activity rhythms to environmental light-dark cycles [810]. We try to understand how the different photoreceptors contribute to the precise daily timing of activity. The presented DroLIGHT-2 software system is the advanced form of an existing, recently implemented and pub© 2013 Bentham Science Publishers

2 Recent Patents on Computer Science, 2013, Vol. 6, No. 3

lished solution [11]. The previous version of DroLIGHT offered audio access to the connected hardware device and limited number of operations to manually control dark and light cycles. The recent developed version meets all future recommendations and provides diurnal cycles for multiple iterations with once set lights (LEDs) as well as with multiple lights at different timings. It offers a new file based experimental database management system, three dimensional visualization interface and new interface to refine the mechanism of human machine (direct) instructional communication. Furthermore unlike previous version, it not only allows user to set intensity values in Pulse-Width Modulation (PWM) but to choose the intensity mode in Watt per Square Meter (W/m^2) and set wavelength in Photon. The rest of the manuscript is organized as follows: starting from a more general overview, section DROLIGHT-2 presents the advanced real time embedded system, its modules (Controller, Diurnal, Simulation and Board Settings), internal activity flows, features, development details and installation procedure. Section 3, VALIDATION discusses the performed (two) experiments, provides their results individually as well as in comparison and validates the application with the presentation of two and three dimensional result summaries. Section 4, CONCLUSION summarizes and gives future recommendations.

Ahmed and Helfrich-Förster

simulate various light-dark cycles with high quality and fidelity. DroLIGHT-2 helps in analyzing the effect of different lights produced by the LEDs on Drosophila’s cyclic behaviors, with a uniformly controlled access to the hardware simulating natural-like light-dark cycles. It is a Multiple Document Interface (MDI) software application, developed following the principles of embedding children windows under a single parent window by creating nesting hierarchies, which benefits by allowing multiple instances to control one or multiple connected devices using one main interface. The Graphical User Interface (GUI) provides different functions for the COM port (serial baud rate, parity, number of data bits to send and stop) and line signal (data terminal ready, data set ready, request to send, clear to send, carrier detect, clear with DTR and clear with open) settings for the establishment of the connection to the hardware.

DROLIGHT-2

DroLIGHT-2 provides options to control the LEDs, one as well as all at once, manually and automatically. It requires user’s input for the desired intensity in Watt per Square Micro (w/m^2), which is then converted into PWM and executed at ARDUINO microprocessor board. Using DroLIGHT-2 it is also possible to produce one colored light as well as mixing different colored lights in both additive (turning on two or more different colored lights) and subtractive (fully or partly decreasing wavelengths or intensities of some lights) ways [12].

DroLIGHT-2 is a user friendly platform capable of controlling an LED-based lighting system to automatically

To efficiently take advantage of it, the DroLIGHT-2 application is divided into four components: Controller,

Fig. (1). DroLIGHT-2 Components. We present computer with the preinstalled DroLIGHT software application, controlling the special purpose Hardware (black box, right bottom) using in-house engineered Board (green PCB with several electronic components and ARDUINO, left top). Three produced sample lights are also shown (Sample Light 1, 2 and 3).

DroLIGHT-2 Towards Circadian Clock Synchronization

Recent Patents on Computer Science, 2013, Vol. 6, No. 3

3

Fig. (2). DroLIGHT-2, Controller’s updated activity flow demonstrate the basic flow of operation, which starts with successful connection establishment to the hardware, with given COM (port, baud rate, priority, bits, stop bits) and Line Settings (DTR, RTS, CTS, Clear DTR, DSR, CD, Clear on Open). Controller provides three different but integrated modules: 1. Configurations, 2. Control and 3. Experiment. Using Configurations, user can create set the value of each and all LEDs’ wavelengths, adjust the brightness mode between three provides states (low, middle and high), set the box ID (connected hardware) and refresh the established connections. Control offers user to switch ON &/ OFF LEDs and Experiment allows to schedule switching operations for user given date and time (only one cycle). Both scheduled and/or manual LED control instructions, prepared as the dataset to be sent to the connected hardware via USB serial communication mode, which then be first verified and transferred to the connected LEDs.

Circadian (Diurnal), Simulation and Board Status. The controller component manually runs multiple hardware devices with variable preliminary specifications (details given in section Controller), the diurnal is to schedule light operations for generating diurnal (or daily) rhythm (details given in section Diurnal), the simulation is to produce different kinds of simulations (details given in section Simulation) and the board status is to allow the user to directly instruct the hardware in string instructions (details given in section Board Status).

Real Time Embedded System A real time embedded system is a combination of software and hardware, designed and implemented with domain specific control functions [13]. DroLIGHT-2 is a smart and complex embedded pro-gram proficient in connecting (COM port [0…n]) and controlling associated hardware via an USB serial cable. The hardware is a noncommercial and in-house engineered device Fig. (1), a combination of different hard-


ware devices including microcontroller, memory unit, switching state system (e.g. it may have only little conceptually similarity to the patent [14], in having the concept of organizing different hardware devices, working together). It is based on a specially designed board, including an ARDUINO microprocessor, controlling Light Emitting Diodes (LEDs) of seven different wavelengths (375 nm, 405 nm, 420 nm, 470 nm, 530nm, 574 nm and 660 nm). The brightness of the LEDs is adjusted by switching them on and off at high frequency (370 Hz) with a resolution of 2^16 (0 = off; 2^16 = high). Three brightness ranges are available by setting the current to low, mid, and high. The ARDUINO microprocessor board establishes the communication with the software interface at a high serial baud rate (115200bd). DroLIGHT-2 has key properties, required for an intelligent application: Computational Power, Memory, Real-time, Communication and Dynamic Decisions [15]. It is capable of sending and receiving instructions to the hardware as well as responding to user input. Moreover it is also capable of taking dynamic decisions in trouble shooting and unexpected conditions. It shares the properties of both kinds of embedded system, it is both a Soft and Hard real time system. It


becomes soft real time system as it won’t cause any significant inconvenience to the user. Furthermore, the latest DroLIGHT-2 has implemented a multiplexed approach, capable of controlling more than one hardware device at a time. Additionally user can choose the intensity mode between W/M^2, Photon or PWM. Controller There are seven colors (Lavender, Slate Blue, Violet, Blue, Green, Yellow and Red) available to be used (manually as well automatically) separate, as well as in combinations (mixing) of different colors, at similar or different wavelengths and brightness, well demonstrated in given in Fig. (2) the activity flow diagram. The controller allows user to turn on the lights (one or more LEDs) manually by pressing green color button and with needed wavelengths or intensities from the provided control (with editable drop down control, for each colored LED) on the left side of the respective button Fig. (3). User can select and also enter a new wavelengths or intensities value in the same control. When user presses the button to turn on the

Fig. (3). DroLIGHT-2 Control Graphical User Interface (GUI). The top left-right part of the GUI contains settings to establish connection with the hardware. At successful (using top-right button with USB connection sign inside) connection the remaining GUI options will be enabled to control LEDs manually and automatically by scheduling the time. Currently GUI is mainly showing that the controller is at default state, hardware is connected at COM port 3 with 115200bd, no priority, 8 bits, no stop bits and none of line signals (DTR, RTS, CTS, Clear DTR, DSR, CD and Clear on Open) are used. All (seven LED) lights are set to the default intensity value (0 W/m^2), all switches are off, date and time is given in the all DateTime controls (to start and stop lights), no time is scheduled, no experiment is running, box is connected with its default ID (with no user assigned ID) and default brightness mode (high). User can switch on the light individually (by pressing respective light’s color with green light circle inside), set the time for on and off (using respective given DateTime control and then pressing gray color button with timer inside), run the experiment (using large sized button with three color lab tubes inside), refresh connection with hardware (using small button with cloud inside), change the connected hardware ID (using Box ID control), switch to the default setting (using gray colored button with switches inside) and turn on or off all light at once (using blue colored button with sending signals notation inside). Additionally user can choose the light wavelength or intensity mode (Photon or W/m^2 or PWM).



5

Fig. (4). DroLIGHT-2 Circadian Graphical User Interface (GUI). DroLIGHT-2 provides interface to create, edit, load (already created) and run circadian experiments. Currently GUI is mainly showing that the hardware is connected at COM port 3 at 115200bd, and at default circadian state. User can give experiment information using provided controls (down-bottom), add into list (using button with green colored plus sign inside) and start experiment (using large sized button with three color lab tubes inside). User can export experiment data (using blue button with folder and world sign inside), import already created experiment lists (using button with blue folder inside), clear all data (using gray colored button with arrow inside), select any particular data entry to only proceed (using button with hand sign inside), delete one particular data entry (using button with paper cracked inside), update data (using button with green-white arrow inside) and turn on particular entry before or after time (using blue colored button with sending signals notation inside). As one of the last steps, user has to transfer the experiment data (by copying using blue colored button with water drop sign, or by cutting using blue colored button with ‘X’ sign) from main list to the running mode list. Additionally, in case user wants to run two experiment lists, then he/she has to load immediate in running mode and the next in the main, and has to click the checkbox “Automatic Data Extraction” (after completing the data list from running mode it will automatically shift the control to the main list). Moreover likewise Control, user can chose the light wavelength or intensity mode (Photon or W/m^2 or PWM).

light, it will send the signal to the hardware (ARDUINO microprocessor board) to switch on the LEDs of that color and will also automatically (change the state) convert to the Red colored button, which represents the switch off state. User can switch off the same light by pressing the same button. The control section allows the user to schedule each light, as well as all lights, by selecting the date and time from provided calendars. Each light is provided with two calendars, one is to set the date and time for turning on the light and the other is to turn off. When the user selects a certain date and time, then he will have to press the gray color time button to set the timer (set time will appear in blue color). DroLIGHT-2 helps users in selecting the right date and time. The control section provides sub-sections i.e. experimentation, which allows the user to start a short time experiment (with previously scheduled Date and Time) by pressing the colorful button (with three color lab tubes). At the start of the experiment, same button will turn to Red emergency state to abort the running experiment (could be used, in case user needs to quit the experiment in between). ‘All Controls’ is another sub-section of the Control, which allows user to turn on or off all lights at once (by pressing blue button, which will turn to orange color, at on to

off state), reset the whole system to its default state (by pressing the gray button with three switches), refresh hardware (by pressing the button with white cloud) and set brightness (a cyclic process, High - Low – Mid by pressing a button with three colored bars). Diurnal The limitation of scheduling experiments using the control section is that the user can only schedule LEDs, once for an experiment (without circadian iterations). The third section offers enhanced experimental possibilities Fig. (4). DroLIGHT-2 Circadian (Diurnal) is the major advancement (in comparison to the previous version [11]), it offers a file based data management system (third party independent, system for embedded system, like e.g. patent [16]), which allows the user to create, edit, export, load and run multiple experiments. Each experiment is mainly based on the information about the wavelength or intensity, iteration, date and time of turning on and off the LEDs. It requires user to give the experiment ID/name, start time of turning on lights, end time of turning off lights, number of iterations (for how many days) and wavelengths or intensities for all seven lights (one for each set of LEDs).



Fig. (5). DroLIGHT-2, Diurnal's activity flow demonstrate the basic flow of operation, which starts (likewise Controller) with successful connection establishment to the hardware, with given COM (port, baud rate, priority, bits, stop bits) and Line Settings (DTR, RTS, CTS, Clear DTR, DSR, CD, Clear on Open). Using Data Management module, user can create new, edit existing, store and load experiments for the Diurnal Rhythm productions. During preparing experiments, user has to give information about the wavelengths (for each light), number of iterations (days; experiment will repeat the same operation), date and time of turning on and off of the LEDs. It requires user to give the unique (could also be similar, depends) experiment ID/name, start time of turning on lights, end time of turning off lights, number of iterations (for how many days) and wavelengths for all seven lights (one for each set of LEDs). Scheduled instruction will be prepared in the form of data set and transferred to the connected hardware. It is also possible to connect and control more than one hardware devices.


The diurnal section allows to run one experiment at a time as well as checking the sequence of multiple listed experiments (by clicking the check box ‘Process All’) on a particular day by pressing “Experiment” button. Furthermore, it offers a feature to repeat experimental cycles as well Fig. (5). To use Diurnal for the purpose of only creating experiments and editing existing ones, user needs not to connect to the hardware, as it allows the user to create experiments in time, which can be used or altered when needed. Another major advancement is the implementation of the concept of multiple split data set integration and usage. This allows user a multifunction experiment dataset preparation and automatic usage mechanism. In short and swift, the user is given with two list views: main and running mode. User can perform experimental data manipulation activities using the main list and then load the selected (copy or cut operations) or all data entries into the running mode list, and can run the experiment. At the same time, when DroLIGHT-2 is running the experiment list, the user can still use the main list and can prepare the second experimental data list. Furthermore, by clicking a provided option in the graphical interface (check box i.e. “Automatic Data Extraction”), user can instruct the DroLIGHT-2 system, to start using the provided 2nd experiment data list from the main, only when the running mode task list will be completed. Moreover likewise Control, user can chose the intensity mode e.g. W/M^2, Photon or PWM.


7

DroLIGHT-2 provides an option to restart or continue a scheduled experiment in case of an interruption caused by a default in the hardware during an experiment. DroLIGHT-2 provides an option, to restart or continue a scheduled experiment (in between or after interruption). In case of emergency (especially when hardware is reset), user only has to select the missed or next data entry to be used (from the running mode list) and press the blue colored button (in the right button list, at the bottom). This will not harm the running experiment but will turn the selected light settings ON and the experiment could be continued. Simulation DroLIGHT-2 provides interfaces for different kinds of two and three dimensional visual simulations and animation Fig. (6). This module automatically works, along with the running experiments as well as manual light operations. DroLIGHT-2 simulation offers user to select different modes of visualizations, including two and three dimensional line, spline, step line, point and bar charts, with different sized lines, rotation and inclination (only in 3D, automatic as well as by selected provided bars). It offers users to animate results (by selecting option to Animate) with preferred colors (which can help in result analysis and interpretation) and save results in image files (by pressing red and white button

Fig. (6). DroLIGHT-2 Simulation Graphical User Interface (GUI). DroLIGHT-2 provides interface for different kinds of two and three dimensional visual simulations and animations. Currently GUI is mainly showing sample produced results. Shown three dimensional line chart consists of seven color (Lavender, Slate Blue, Violet, Blue, Green, Yellow and Red) bars and values. Each bar is representing respective color light, with value of each’s intensity and date time of light operation. The shown image’s view can even be altered by changing it rotation and inclination (using two vertical slide bars), color can be changed (using button with colored circle inside), cleared (using button with white dropper inside), changed to two dimensional view (using button with one cylinder and triangular objects inside) and saved (using button with camera inside). Moreover user can set the print page set setting (using the gray colored button with small size black printer), see the print preview (using the gray colored button with small size black printer, with one magnifying glass) and can print the results (using the gray colored button with big size black printer).



Fig. (7). DroLIGHT-2 Board Setting Graphical User Interface (GUI). DroLIGHT-2 provides interface for the direct user machine communication using string and hexadecimal instructions. Currently GUI is mainly showing that the hardware is connected at COM port 3 at 115200bd, and at default board state with no running communication, and providing help information. Using this interface user can type string instructions (in given text field), send them directly to the connected hardware (using black button with cursor inside), clear the instruction (using red button with C and brush inside), test hardware’s light performance (using button with color circle inside), get the board information (using button with blue information sign ‘i’ and green board inside) and ask for the help (using blue button with question mark symbol inside).

with camera). Furthermore, it is also possible to print (including print page set up, print view and direct printing) produced visual results. DroLIGHT-2 simulations interface categorizes visualization in two different options: Experiment Status and Experiment Details. First option, experiment status is about to visualize the results obtained showing the performance of each operation performed (turning on and off light) with respect to its time, date and intensity (in two and three dimensional mode). The second option, experiment details, is about to visualize the overall picture of the scheduled and run experiment, including details about experiment ID, Start Date Time, End Date Time but eliminating the iterations (e.g. one experiment has to run 5 days with same intensities and timing of the days and night, will be visualized once). Board Setting DroLIGHT-2 provides an interface “Board Setting”, which gives status updates of user machine interactions as well as provides direct instructional mode Fig. (7). It allows user to communicate with the hardware in hexadecimal and text (string) formats, which could be helpful especially when system is facing abnormal behaviors e.g. hardware’s electricity broken, fan out of function or needs to be restarted etc. DroLIGHT-2 Board Status allows user to test the connected hardware’s lightening functionalities (by pressing rainbow circle button). This is a recommended feature, espe-

cially when the new hardware is connected to be used. This feature will turn on all connected LEDs (one by one with little time difference) at all provided brightness modes. Additionally user can also get the board information, which includes information about used microcontroller, box ID, port, baud rate, idle frames, energy of photons, maximum intensity ranges, brightness modes, sensors and EPROM write cycles etc. Moreover, especially for the new users, DroLIGHT-2 Board Status provides a feature “Help” (by pressing the blue button with question mark sign). This will give all directional information, which user can use to directly communicate with the connected hardware (using ARDUINO microprocessor). The help gives the information about the in use hardware and provides instructional information which consists of following elements: Commands, Brightness, Reading Values, Toggling Brightness, Toggling Fan, Toggling debugmode, Toggling Calibrate-mode, Test-mode, Print etc. (details are given in Table 1). DroLIGHT-2: Design and Development DroLIGHT-2 implementation follows the principles of one newly proposed software engineering paradigm i.e. Butterfly (by the author: Zeeshan Ahmed at the University of Wuerzburg). Butterfly model helps in design, modelling and the development of user-friendly scientific software solutions. The current abstract model of the Butterfly model mainly consists of four different phases: Scientific Software


Table 1.


9

DroLIGHT 2, Board Status Help. DroLIGHT – 2, Board Status Help

No. Instructions

Descriptions

1

i

set boxID [0..2^16]

2

p

set serial port [0..n]

3

b

set serial baud rate

4

d

set idle frame time in chars

5

t

User (1 Actor)

6

e ,

set energy in W/m^2 on channel

7

g ,

set energy in photons/(s m^2) on channel

8

c , ,

set pwm on channel

9

1

set pwm on status1

10

2

set pwm on status2

11

x

set ledTestPWM value

12

y

set ledTestPWM delay in ms

13

n

set ledTestPWM nr of test-loops

14

R , ,

set max IE for brightness on channel

15

S

read values [button, lock, temp, light]

16

B

toggle brightness

17

F

toggle fan

18

D

toggle debug-mode

19

C

toggle calibrate-mode

20

T

LED test-mode

21

f

print last received frame

22

A

print current settings

23

H

print this help

Engineering (SSE), Scientific Methodology (SM), Human Computer Interaction (HCI) and Scientific Application (SA) Fig. (8).

handling, processing and analysis. SA helped in resulting with a user friendly, quickly learned and easily deployed scientific application.

SSE helped in gathering and finalizing functional and non-functional requirements, choosing the best suited software development model and technology (best available, recommended, recent, affordable and transferable technologies e.g. programming languages, database etc.), programming testing and installing application. HCI helped in the design and implementation of the graphical user according to the end user background, psychology, and working (deployment) environment. SM helped in understanding the mathematics and process to be implemented, defining logic, data

DroLIGHT-2 developed following the Spiral software development life cycle [17], integrating formal Unified Modelling Language (UML) [18] perspectives: use case, design, process and implementation views, and incorporating Human Computer Interaction (HCI) design patterns: direct manipulation, conversational text, ephemeral feedback and step-by-step instructions [19]. It is the composition of many components with bonded as well as independently specified interfaces and context dependencies.



Fig. (8). Butterfly; abstract paradigm towards scientific software solution modelling and implementation.

Initially all the functional and non-functional requirements were finalized, which is then turned into the design and implemented using Microsoft Dot net platform. While designing the graphical user interface of the application, major concern was the availability of the user friendliness in deploying (see section Installation) and using it. The expected end users are the scientist (neurobiologist and photobiologists), with not much informatics background. DroLIGHT-2 uses Pulse-Width Modulation (PWM) technique for the low level hardware access, on the basis of switching frequency and hardware complexity. It implements exceptional handling approach to handle the unidentified run time errors, and applies multi-threading concepts for the parallel executions of several tasks and to avoid deadlocks. It is developed using C-Sharp (managed code) programming language [13]. Major developmental benefits are: it requires lower hardware cost, with much smaller memory foot print, faster execution time, with no heap effect and secure access to the connected hardware. The developed version of DroLIGHT-2 has the wider scope in its usage, which means it can also be used to take benefit in controlling any other hardware device using ARDUINO microcontroller [20]. Now it could be used for similar (controlling lights etc.) or different systems. Moreover, it is flexible and has the room for future improvements to have even better results and experiment’ performance.

but without any cross compiler to produce machine code understandable by connected hardware [14]. The overall process of deployment is simple (unlike running MATLAB, Perl, R and C etc. scripts, which requires additional user’ attention, knowledge, expense, time and compiler), as the user has to only run the DroLIGHT-2 installer; a simple six step process Fig. (9) which provides all kinds of immediate information and automatically configures software settings in the operating system. User just needs to follow the provided instructions and has to give the memory location for the software to be installed. To run DroLIGHT-2, user needs to observe following guidelines: click on the main menu “Product  DroLIGHT Ver 2 DroLIGHT” or double click on provided icon (white icon with black Drosophila inside) at the desktop. To have full functionality test, the hardware has to be properly connected at COM port via serial link and should be in proper running conditions (especially, without any identified problem). Similarly, to uninstall the DroLIGHT-2 software application, an uninstaller is by default provided, it can be accessed from stored location or from main menu “Product  DroLIGHT Ver 2 Uninstall”. A very simple two-step process, which automatically and safely removes installed DroLIGHT-2 application. It is recommended to uninstall DroLIGHT-2 application, rather than deleting installed files manually from stored location.

DROLIGHT-2: INSTALLATION DroLIGHT-2 is a Component Based System (CBS) [21], its process of deployment takes place on a host machine with an integrated environment (Microsoft Windows, 7 preferred with Dot NET Framework SDK 4.5 at 32 or 64 bit machine)

DROLIGHT-2: VALIDATION The software application has been tested with different ex perimental datasets. The validation procedure of DroLIGHT-2 starts with the input (I/O) of experiment information (e.g.



11

Fig. (9). DroLIGHT-2 Installation; a simple six steps process.

Fig. (10). DroLIGHT-2 Validation: Two datasets are loaded, each consists of 15 light instructions with different timings and intensities. First running mode ‘Experiment’ will finish all loaded data and then the control will automatically switch to the main list and complete other list.

unique IDSs, start and end time, wavelength or intensity of lights etc.). We have shown the created, saved, managed and used datasets during validation Fig. (10). On the whole it consists of two experimental datasets, where each consist of 15 different data entries (attached in supplementary material).

Before starting the experiments, the especially designed and engineered hardware was properly connected to the COM port 3 with 115200bd, no priority, 8 bits, no stop bits and no line signals (DTR, RTS, CTS, Clear DTR, DSR, CD, Clear on Open). Moreover, the lights operations, colors and


a). Dataset 1.




13

Fig. (11). Contd….

b). Dataset 2. Fig. (11). DroLIGHT-2 validation, two and three dimensional presentation of system’s results of both datasets (1 and 2).

a). Results produced in line chart with given values, using Dataset 1.

b). Results produced in line chart with given values, using Dataset 2. Fig. (12). DroLIGHT-2 experiment status, two dimensional result presentation of system’s results of both datasets.

Send Orders for Print-Reprints and e-Reprints to [email protected] Recent Patents on Computer Science 2013, 6, 000-000

14

brightness were tested using the test button present on the Board Status section.

We would like to thank workshop (especially Konrad Öchsner) at Biocenter, University of Wuerzburg Germany, for their services in building the hardware.

At first stage, experiment dataset was loaded (previously created) and entered into the system. After this the second experiment list is loaded and checked for the automatic data extraction from the main list. System proceeds to loaded experiments and one after another, successfully completes both.

We would like to thank the scientific team members (especially Rudi Grebler, Matthias Schlichting, Pamela Menegazzi) at the Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg Germany, for their help in testing and evaluating the DroLIGHT-2.

Experiments were run properly and produced results were obtained. Using DroLIGHT-2 simulation, we generated different visual kinds of obtained results, without changing any useful information but here in this paper we are only discussing two of all. We have presented both experiments’ detailed results in both two and three dimensional modes (step line bar charts Fig. (11a) and spline bar charts, Fig. (11b) and individual results drawn in two dimensional bar charts Fig. (12a and 12b). The presented results are differentiated with seven different colored lines, values and points. DROLIGHT-2: CURRENT & FUTURE DEVELOPMENT Circadian rhythm can also be observed with this approach in other animals, plants, fungi and bacteria. DroLIGHT-2 is not only beneficial in synchronizing the circadian clock of Drosophila but the software can also be used for other laboratory experiments, as it is capable of controlling (using command line interface, provided in the GUI) any hardware board embedding the ARDUINO microcontroller. The embedded output produced by the DroLIGHT-2 relies on the capability of the hardware device in correctly producing the lights, as required. If more than one custom made hardware devices are carrying similar color (wavelengths) LEDs with different frequencies in different devices, then it might be possible to have little disturbed light effects (very minute). The best option would be to have same hardware component specifications (e.g. LEDs, Microcontroller etc.) for all connected hardware devices. The most recent available version of DroLIGHT-2 is in use (testing in academic labs) and we are focusing on the future research and development objectives by enhancing the capabilities of DroLIGHT-2 with more features to advance the experimental processes and improve the hardware control. CONFLICT OF INTEREST The authors confirm that this article content has no conflicts of interest. ACKNOWLEDGEMENTS We would like to thank Deutsche Forschungsgemeinschaft (DFG, Collaborative Research Centre, SFB 1047 / Z Project) for funding.

2213-2759/13 $100.00+.00

AUTHOR’S BIBLIOGRAPHY Zeeshan Ahmed is the Post Doc. and Scientific Software Engineer and in the central computation support administration and project coordination of the collaborative research center of DFG project i.e. SFB 1047 at the Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg Germany. Charlotte Helfrich-Förster is the Chair of the Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg Germany. AUTHOR’S CONTRIBUTIONS Zeeshan Ahmed proposed, designed and implemented the DroLIGHT 2, software application. Charlotte Helfrich-Förster guided the study. Both authors participated in writing of the manuscript. ABBREVIATIONS ADLs

=

Architecture Description Languages

CBS

=

Component Based System

CTS

=

Clear to Send

CD

=

Carrier Detect

C-DTR

=

Clear with DTR

CO

=

Clear with Open

COM

=

Communication

DTR

=

Data Terminal Ready

DSR

=

Data Set Ready

GUI

=

Graphical User Interface

HCI

=

Human Computer Interaction

LED

=

Light Emitting Diodes

MDI

=

Multiple Document Interface

PWM

=

Pulse-width modulation

PDM

=

Pulse-duration modulation

PLA

=

Product Line Architecture

RTS

=

Request to Send

SDLC

=

Software Development Life Cycle

SA

=

Scientific Application

SSE

=

Scientific Software Engineering

© 2013 Bentham Science Publishers


SM

=

Scientific Methodology

UML

=

Unified Modelling Language

W/m^2

=

Watt per Square Meter

Recent Patents on Computer Science, 2013, Vol. 6, No. 3 [10]

[11]

REFERENCES [1] [2] [3] [4] [5] [6] [7] [8]

[9]

T. Roenneberg and R. G. Foster, “Twilight times: light and the circadian system”, Photochem. Photobiol., Vol. 66, pp. 549-561, 1997. R. Foster and C. Helfrich-Förster, “Photoreceptors for circadian clocks in mice and fruit flies”, Phil. Trans. R. Soc. Lond., Vol. 356, pp. 1779-1789, 2001. H. J. Bellen, C. Tong and H. Tsuda, “100 years of Drosophila research and its impact on vertebrate neuroscience: a history lesson for the future”, Nat. Rev. Neurosci., Vol. 11, pp. 514-522, 2010. S. Benzer, “Behavioral mutants of Drosophila isolated by countercurrent distribution”. Proc. Natl. Acad. Sci., Vol. 58, 1pp. 112-119, 1967. S. Benzer, “Genetic dissection of behavior.” Sci. Am., Vol. 229, pp. 24-3, 1973. R. J. Konopka and S. Benzer, “Clock mutants of Drosophila melanogaster”, Proc. Natl. Acad. Sci. USA, Vol. 68, pp. 2112-2116, 1971. T. Yoshii, D. Rieger, C. Helfrich-Förster, “Two clocks in the brain - an update of the Morning and Evening oscillator model in Drosophila”, Prog. Brain. Res., Vol. 199, pp. 59-82, 2012 C. Helfrich-Förster, C. Winter, A. Hofbauer, J. C. Hall, and R. Stanewsky, “The circadian clock of fruit flies is blind after elimination of all known photoreceptors”, Neuron., Vol. 30, pp. 249-261, 2001. C. Helfrich-Förster, T. Edwards, K. Yasuyama, B. Wisotzki, S. Schneuwly, R. Stanewsky, I. A. Meinertzhage and A. Hofbauer, “The extraretinal eyelet of Drosophila: development, ultrastructure and putative circadian function”, J. Neurosci., Vol. 22, pp. 92559266, 2002.

[12] [13] [14] [15] [16] [17] [18]

[19]

[20]

[21]

15

D. Rieger, R. Stanewsky and C. Helfrich-Förster, “Cryptochrome, compound eyes, Hofbauer-Buchner eyelets, and ocelli play different roles in the entrainment and masking pathway of the locomotor activity rhythm in the fruit fly Drosophila melanogaster”, J. Biol. Rhythms, Vol. 18, pp. 377-391, 2003. Z. Ahmed, C. Helfrich-Förster, T. Dandekar, “Integrating Formal UML Designs and HCI Patterns with Spiral SDLC in DroLIGHT Implementation”, Rec. Pat. Comp. Sci., Vol. 6, pp 58-98, 2013. R. S. Berms, Balmier and Saltzman's Principles of Color Technology, Wiley, 3, New York, 2000. D. Thompson and R. S. Miles, Embedded Programming with the Microsoft®. NET Micro Framework, Microsoft Corporation, 2007. Beijing Lenovo Software LTD., "Methods and systems for state switching", U.S. Patent 20130179667A1, August 13, 2013. S. V. Ayer and P. Gupta, Embedded Real Time Systems Programming, Tata McGraw-Hill Publishing, 2004. Siemens Product Lifecycle Management Software Inc., "System and method for data management of embedded systems", U.S. Patent 8510752, August 13, 2013. B. W. Boehm, “A spiral model of software development and enhancement”, Computer, Vol. 21, pp. 61-72, 1988. N. Medvidovic, D. S. Rosenblum, D. F. Remixes and J. E. Robbins, “Modeling software architectures in the Unified Modeling Language”, ACM Trans. Software Engines. Method, Vol. 11, pp. 257, 2002. S. R. Klemmer, and B. Lee, “Notebooks that Share and Walls that Remember: Electronic Capture of Design Education Artifacts”, In ACM Symposium on User Interface Software and Technology, 2005. Z. Ahmed, C. Helfrich-Förster, “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. C. Szyperski, D. Gruntz and S. Murer, Component SoftwareBeyond Object-Oriented Programming, Addison-Wesley, 2002.