Drosophila Activity Monitoring System User`s Guide
Contents
1. 32 Rotation sensor count magnitude only Troubleshooting First verify that the rotarod unit is communicating properly with the host computer status code 1 Then rotate the brass flywheel by hand and verify that all tubes spin properly on their respective hubs and that the motor pulley spins via the rubber drive band Then command motor rotation via the Preferences tab and verify that rotation is smooth and constant Select Live and nnn Monitor tab and verify that the channel 32 rotation sensor increments once per turn If the motor and tubes turn properly then remove all tubes and carefully clean them with their end plates Then install the empty and clean tube sections and command a motor rotation Verify that all 30 channel counts 5 per tube read 0 after the next data collection and remain at 0 indicating that the tube sections are clean and ready for flies Note that any dirt or foreign matter on the tube end plates or inner walls will be detected as a fly if it blocks an infrared beam with sufficient opacity 20 DAMSystem User s Guide LC3 LC6 Light Controller The Light Controller allows the DAMSystem soft ware to directly schedule incubator light timing on up Rp to 6 independent light channels By bypassing the re simple internal timers that many incubators have the m Light Controller hardware and DAMSystem software combination makes available a wide array of pulse patterns for both entrainment and stimulus resp2. Computer to Power Supply Unit Blue Box Serial Cable The Power Supply Unit contains an RS 232 standard DB 25 female connector which must mate to the cable from the computer The pinout for the DB 25 is as follows Pin 1 Earth ground Pin 2 Transmit to computer Pin 3 Receive from computer Pin 7 Signal ground If the computer has a hardware serial port then the cable to the Power Supply Unit is as follows Macintosh legacy 8 pin Mini Din to DB 25 male Modem Windows PC DB 9 female to DB 25 male Modem If a USB Serial adapter is to be used then the USB end will connect to any USB port on the computer The serial port end will connect to the Power Supply Unit using one of the above cables usually the PC modem cable DB 9 female to DB 25 male Power Supply Unit to Monitor Cable The activity monitors are connected to the Power Supply Unit with conventional 4 wire modular tele phone cable and the 6 position RJ 11 connectors are identical to those of domestic telephone extension cables The same normal or straight wiring polarity is used as the telephone system opposite color sequence on the 2 ends so that any telephone wiring accessories or cables which would work at home will also work to connect activity monitors to the Power Supply Unit At least 3 telephone jacks are provided on the front of the Power Supply Unit so a system with 3 or fewer monitors may simply connect each monitor to a jack with a cable Wi
3. Activity counts Last line of file The DayLight file contains the date and time for each reading of the data files The file begins with the same 4 line header as the channel files but instead of activity data the data lines contain the date and time of the reading Also included on each line are the states of the lights as reported by the power sup ply unit at the time of the reading 0 Off 1 On 2 Unknown Status error from light controller Note that these light states are taken immediately prior to any change in them which may be due at the time of the reading and so indicate the state of the lights over the preceding reading interval File Header Line 1 MyRunDayLight 28 Mar 2002 Line 2 94 Line 3 30 Line 4 1330 File Data Line 5 20020328 1330 100 Line 6 20020328 1400 100 Line 7 20020328 1430 000 Line 8 20020328 1500 000 Line nn 23 DAMSystem User s Guide File Name First Date Number of Readings Reading Interval MM SS First Reading HHMM SS First Reading Lights On Off Off 1 3 Lights Off Off Off Last line of file Cables All cables and wiring accessories are standard items and should be available locally almost anywhere from a retail computer or electronics supply store Computer catalog retailers are also good sources for these supplies Computer to PSIU USB Cable The USB cable is of type A B male and cannot be substituted by another type Any available length will serve
4. Extra readings combined into output Preview reports as Save but produces no output files 9 Save Log adds this log to file DAMFileScanLog txt Input data is contained in readings which may or may not be periodic and sequences of which may contain gaps Output data is produced in bins which are guaranteed to be periodic and sequentially complete Hints 1 Skipped and Extra readings are not associated with specific monitors or even the Power Supply Unit but instead with the time sequence of the readings as they are collected by the DAMSystem3 pro gram If the output file Bin Length in DAMFileScan is set differently from the input file Reading Interval used by DAMSystem3 to collect the data then Skipped or Extra readings will be generated in the output files even if such errant readings do not exist in the collected data Such skips or extras are strictly arti facts of the modified bin length and are not malfunctions of the data collection system 2 If an unexpected number of skipped or extra readings is reported reduce the number of readings and repeat Preview to determine when the readings were added or dropped Extra readings will be pro duced if the Reading Interval is shortened in the middle of an experiment and readings will be skipped if the data collection process is interrupted by a power failure or program termination 3 Separate groups of monitors may be saved into the same RunName folder even though a warning mess
5. Keyspan Systems using the PSIU will connect to the computer by USB cable and the Serial Port will be synthe sized by the USB driver software In the case of the Macintosh the synthesized port will be labeled Triki netics PSIU and in the PC case will usually be the highest numbered COM port listed To select or change the active port simply click an entry in the Serial Port list If the selected port acti vates the selection will turn dark but if the port is already in use or otherwise unavailable it will remain light in color and an error message will display To refresh the list of available ports click the Serial Port list header Note that a serial port search will take place automatically if no port is available when a reading occurs as when a USB cable is inadvertently unplugged The system will try to reconnect with the lost port to re store communication with the monitors Data File Location This column shows the absolute file path to the DAMSystem3Data folder on the hard drive where col lected data is written to the Monitor files As multiple copies of the DAMSystem3 program may be operat ing concurrently from different folders this path information identifies the specific location of the data for this particular copy of the application Lights tab The light timing system allows the host computer to independently control the On Off timing of up to 6 external lights often installed in incubators The DAMSystem software
6. TriKinetics web site and installed If the drivers have already been installed and they still do not properly recognize the PSIU then the machine should be rebooted If connecting the PSIU still generates a New Hardware Found message the drivers have been corrupted and should be removed and reinstalled see instructions with downloaded drivers Communication Errors Status codes other than 1 indicate a failure of the computer to successfully acquire data from the ad dressed monitor Any break in the communication chain between the DAMSystem program and the hardware monitor will result in such a failure If the Status Code is 50 color black then the program is unable to communicate with even the PSU PSIU and either it is unplugged from the serial port or its power is off Check under Preferences that the selected communication port is as it should be and then follow the checkout procedure under Power Supply Interface Unit or Power Supply Unit Or choose the Live Monitors mode and watch the status boxes while tracing the connections Note that a short circuit in the network telephone wiring may prevent any communication so the first step should always be to disconnect all monitor telephone cables Then 25 DAMSystem User s Guide plug them back in one at a time while watching the status boxes and in this way track down the offending cable or connection If the status code is 51 color red then the PSU PSIU is connected proper
7. cables couplers and 5 way splitters 7 Light Controller optional Software Installation The DAMSystem3 application is available for download from www trikinetics com Choose the correct version for your host computer and operating system DAMSystem3 for Windows 98 XP DAMSystem3 for Macintosh OSX Save the compressed file to the hard drive and UnZip or UnStuff it then move the program to any con venient folder and launch it USB Drivers The Power Supply Interface Unit PSIU uses a Universal Serial Bus USB hardware connection to the host computer and is activated by a one time installation of unique USB driver software for the PSIU These drivers simply synthesize in software a serial data link between the DAMSystem program and the PS U activity monitors which in the case of the PC will be a COM port and in the Macintosh a simple serial port The USB drivers are available for download from the TriKinetics web site and must be installed into the host computer prior to data collection Hardware Installation Connect the DC Power Supply to a line power outlet 100 240 volt 50 60 hz using the supplied Line Cord This power supply must be rated for a maximum output of 9 volts DC and no other voltage should be used lest the activity monitors be damaged Then plug the power supply output connector 5 5mm round with 2 5mm center cavity into one of the 2 mating PSIU jacks and verify that the adjacent green led illuminates Set t
8. increments with each one The tapping intensity may be adjusted by changing the number of flat washers between the top of the round post and the solenoid bracket More washers will raise the solenoid up providing a firmer down tap and softer return Fewer washers will lower the solenoid with contrasting results The units are ini tially adjusted to provide firm contact on both up and down strokes and if set right the flies will be nudged down through the funnel neck before they have a chance to take wing Silicone coating of the funnel interior will also help with this The counting electronics is quite sensitive and will count the taps of the funnel if specs of dirt on the funnel neck pass by the detectors as a fly would Keep the funnel neck clean to prevent such spurious counts Mounting holes are provided in the sides and bottom of the unit to hold it in place if necessary The holes in the bottom are especially useful for clamping the unit to an incubator shelf so that it does not walk during taps The tapping solenoid draws a substantial current from the Power Supply and if the total cabling dis tance between the 2 becomes excessive the resulting voltage drop will reset the unit To prevent this a maximum separation of 15 5m should be used 15 DAMSystem User s Guide DEnM Environment Monitor The Drosophila Environment Monitor continuously measures the temperature and relative humidity of its surrounding air and t
9. monitors and either will continue to provide power in the event of failure of the other Because of this failure possibility each supply must be rated to deliver the full current load of the system by itself USB Connection The PSIU connects to the host PC or Macintosh computer with an A B male USB cable Any free USB port on the computer may be used and if none are available a USB hub may be used to add ports Note that the DC Power Supply must be connected to the PSIU to enable the USB computer link Software Drivers All USB devices require drivers to inform the host system of their characteristics Drivers for the PSIU may be downloaded from the TriKinetics web site and must be installed for the PSIU to be recognized Checkout To verify that the PSIU is operating properly perform the following steps 1 Unplug the USB cable and all monitor data cables from the unit 2 Connect a 9 volt DC power supply to one of the PSIU power input jacks and connect the supply to the AC mains power Confirm that a green light on the PSIU is On and the yellow light is Off 3 Connect the USB cable from the PSIU jack to a computer USB port 4 Verify that the USB driver is loaded properly and that the USB port is activated To do this on a Mac intosh launch the System Profiler About This Mac More Info and verify that the Hardware USB De vice Tree contains TriKinetics PSIU On a Windows PC launch the System Control Panel Start Settin
10. of consistent long term performance and should be expected to produce it why settle for less Log File The DAMSystem3 program writes certain status and fault conditions to text file DAMSystem3Log txt and these are often useful in diagnosing performance issues This file is created in the same directory as the DAMSystem3 application 26 DAMSystem User s Guide
11. on each beam channel whereas flies which fall off part way around will regis ter counts on only some of the channels Tube Assembly Tube sections consist of a 25mm diameter glass cylinder and 2 end plates with integral mounting clips Wash the cylinder and end plates thoroughly being careful not to scratch them Install the cylinder onto 1 end plate load the flies and install the other end plate holding the assembly together with your hand Rotate the end plates about the cylinder axis to align the U shaped mounting clips in the same direction and verify that the opposing circumferential tabs are also aligned Stretch 3 8 natural rubber bands along the outside of the cylinder between the tab pairs to hold the tube assembly together Tube Insertion and Removal To install a tube assembly into the unit align the open ends of the U shaped clips over a pair of protrud ing trunnion hubs in one of the 6 tube positions and press down to snap the clips into place The tube should be securely held aligned with the axis of rotation and free to rotate with the other tubes and mo tor To remove a tube assembly first stop the motor rotation and then rotate the tube by hand until the open ends of the U shaped clips face upward Then while holding the tube push down on it to release the clips from the hubs and remove it from the unit Spin Rate Control The small motor spins the tube string through the large brass pulley using a single 14
12. on the nylon block when the plunger is all the way down else it may break Solenoid Timing Solenoid timing is controlled from the Preferences tab the number of taps and their frequency The Tap Now text will cause an immediate tap sequence for the selected monitor Note that the monitors tap in sequence so that only a single monitor taps at a time Monitor 1 will tap immediately after the time of day clock initiates the sequence and then each monitor will tap in turn To inhibit all tapping set the Tap Count to 0 and to inhibit the tapping from a single monitor unplug its sole noid cable Data Collection The unit counts all objects greater than 0 5mm in extent which fall down through the funnel neck and is quite adept at discriminating multiple objects in rapid succession The unit reports 32 channels of count ing activity to the host computer but all will be 0 save channel 1 which contains the count total Troubleshooting To verify that the unit counts properly remove the plastic disk from the funnel top and set the DAMSys tem Monitor tab to show Live data for the monitor in question Verify that the unit status is 1 and that the 14 DAMSystem User s Guide 32 channel numbers are displayed and updated If 1 is not the status check that the unit is plugged in to the DAMSystem network and consult Troubleshooting in the Reference section Drop some small ob jects down through the funnel and verify that the channel 1 count
13. protected against power failure to insure continuous data collection over an extended period of time A battery backup UPS can provide protection against short term 30 minute power outages and if a backup generator is available in the lab facility to provide standby power thereafter no power interruption to the computer should ever occur To minimize data loss in the event that the computer actually does lose power and stop the computer should be set to automatically restart when the power returns and then automatically relaunch the DAMSystem program This will allow data collection to resume on its own minimizing the number of skipped readings 10 DAMSystem User s Guide PSIU Power Supply Interface Unit The Power Supply Interface Unit and its companion DC Power Supply s provide 9 volt DC operating power to the activity moni tors One unit is required for each complete system which may include up to 120 individual monitors of various types DC Power Supply The PSIU and all activity monitors connected to it are powered from an external 9VDC power supply which connects to the PSIU through one of the two power input jacks These jacks accept a round 5 5mm OD by 2 5mm ID power plug with the center pin positive polarity Only 9V DC supplies must be used To provide redundancy the PSIU provides 2 input power jacks each of which may be connected to a 9V power supply In this case the 2 supplies will share the power load to the
14. scanned using the DAMFileScan program to insure that the data records are complete with no gaps or duplicate readings This program produces a new set of output files from the input monitor files and in addition to cleanup allows for the extraction of data within a specified date time range as well as compression to a longer bin length if desired Thus for example activity data collected at 1 minute intervals may be converted to 30 minute intervals for analysis or plotting purposes The program also allows input monitor files to be converted to legacy Channel files as produced by the earlier DAMSystem2 program for compatibility with existing analysis procedures Data Analysis Outputs from the DAMSystem3 DAMFileScan software suite are essentially columns of numbers with each entry corresponding to an activity total recorded by a single monitoring channel over a short period of time collection bin These individual columns or files may be plotted or analyzed in various ways in cluding import into Excel ClockLab FlyTools or other software 2 DAMSystem User s Guide Installation A complete monitoring system includes the following components All are available from TrikKinetics save the computer 1 Macintosh or Windows PC with available USB port 2 DAMSystem3 Data Acquisition Software 3 Power Supply Interface Unit with USB cable 4 DC Power Supply with line cord 9 volt output 5 Activity Monitor s 6 Telephone type
15. settings are adjusted by clicking the mouse pointer on the upper half to increment and the lower half to decrement and some settings will move as long as the mouse is held down Click the Monitors tab and then the Live text immediately above and verify that the selected range of monitor status boxes is scanned in sequence All should be green for those monitors which are con nected and red otherwise To verify the performance of any single monitor select its number below the Ail text with Live still ac tive and see that real time data is displayed If a locomotor monitor for example pass a pencil point through a channel slot and verify that the corresponding channel count increments If an eclosion moni tor drop a fly down through the funnel and again verify that it counts up channel 1 4 DAMSystem User s Guide DAMSystem3 Data Collection Software At launch the program presents a single window which is locked in place on the screen No menus popups or other windows are used and the program will run until Quit Adjustments to settings are made by simply clicking on them in the upper half to increment and the lower half to decrement Settings are spread across 3 tab panels each of which may be seen in turn by clicking its tab text in the upper left part of the window Preferences Lights Monitors Data collection will occur automatically no matter which tab panel is visible Reading Box The Reading box upper cen
16. 15 16 25 minutes 17 18 26 minutes 19 20 27 minutes 21 22 28 minutes 23 24 29 minutes 25 26 30 minutes 27 28 31 minutes 29 30 32 minutes 31 32 16 DAMSystem User s Guide Light Measurement Incident light intensity is measured by the round silicon photodiode sensor on the top surface The green filter absorbs wavelengths outside of the visible band providing a sensitivity curve which approxi mates the photopic response of the human eye The sensor is calibrated to a fluorescent light as this is the dominant light type for incubators and will be accurate over the range of 1 2500 lux to 5 for any light of this type Incandescent lights will read higher because of their substantial infrared energy output and the imperfect attenuation of these wavelengths by the sensor filter The light sensor will not be damaged by illumination levels which exceed 2500 lux but the numeric out put will eventually saturate going no higher The wavelength of maximum sensitivity is 550 nm falling to 10 of maximum at 350 and 820 nm Linearity is 1 or better Note that the specified sensitivity is measured along the axis of the sensor directly perpendicular to the plane of the front surface Off axis sensitivity will be lower decreasing to 50 at 55 degrees away from the axis Temperature Measurement Ambient temperature is measured by a precision thermistor which sits just under the perforation holes in the top of the unit It is calibrated to 0 1 de
17. Drosophila Activity Monitoring System User s Guide v3 0 January 2007 Contents System Operation Installation DAMSystem3 Data Collection Software Monitors tab Preferences tab Lights tab Data file management Multiple systems on one computer DAMFileScan Software Hardware Host Computer PSIU Power Supply Interface Unit DAM2 Drosophila Activity Monitor MAN2 Gas Distribution Manifold DEM Eclosion Monitor DEnM Environment Monitor DPM Population Monitor DPR6 Rotarod LC3 LC6 Light Controller Reference Output File Formats Cables Troubleshooting TriKinetics Inc 56 Emerson Road Waltham MA 02451 USA 781 891 6110 www trikinetics com 1986 2007 TrikKinetics Inc All rights reserved comments to support trikinetics com Aoouaua4dcdksd WN MO wp OH NY HAH A A Baraat a d a A NN OBDWDDARWBNH COO O System Operation The TriKinetics Drosophila Activity Monitoring System consists of one or more Activity Monitors a Power Supply Interface Unit and Power Supply and a host Macintosh or Windows PC for data collection Each monitor uses an onboard microprocessor to independently detect and count activity events and at periodic intervals to upload the activity totals to the host computer The monitors are connected to the Power Supply Interface Unit by a network of conventional 4 wire telephone cables which supply operating power and lines for data transmission Monitors may be plugged and unplugged from the network at will wi
18. activity events a host computer is necessary to periodically ac quire this data from the monitors and hold it for the length of an experiment This computer may be either an OSX Macintosh or Windows PC and should be physically located ad jacent to the activity monitors As it will need to run reliably and untended for extended periods of time its software load should be minimized to avoid the potential for a software crash which might interrupt data collection If no other applications are active in the computer during an experiment and no network ac cess is allowed the likelihood of such a software crash will be diminished Macintosh Any model of Apple desktop or laptop Macintosh computer may be used to collect the monitor data as long as it has available a free USB port to connect to the PSIU If no such port is available a USB expan sion hub will be required available in any computer store Software versions of the DAMSystem pro gram and the requisite USB drivers are available under OSX for both the PowerPC and intel Macintosh families Windows PC Any PC model which runs the Windows98 or later operating system including WindowsXP and Vista may be used with this program as long as a USB port is available to connect to the PSIU As in the Mac intosh case a software driver will need to be installed into the computer to operate the USB link to the monitors Power Backup The computer and activity monitor Power Supply should be
19. age is displayed when the second group is attempted Simply click the Save button again and the save will occur into the existing folder Note that any existing files in the folder with the same names will be overwritten so be careful 9 DAMSystem User s Guide Hardware Acomplete DAMSystem installation must include a host computer a Power Supply Interface Unit and one or more activity monitors of any or all of the following types DAM2 DAM5 Activity Monitor 32 channels for 5 or 7mm tube DEM Eclosion Monitor with Tapper 1 channel for 100 mm funnel DPM Population Monitor 3 channels for single 25 mm vial DEnM Environment Monitor Temperature Humidity Ambient Light LC3 Light Controller 1 to 6 channels The computer connects to the Power Supply Interface Unit with a USB cable and the PSIU connects to the activity monitors with a network of 4 conductor flat telephone cables Monitor Addresses Each monitor on a DAMSystem network must be identified by a unique numeric address so that it may be individually accessed by the host computer As the maximum number of monitors on a single system is limited to 120 the range of valid addresses is 1 to 120 The address of each monitor is set at the time of manufacture and can only be changed if the unit is returned to the factory Host Computer A host computer is required to collect and store data from the activity monitors While the monitors themselves actually detect and count the
20. andard table lamp plug to one of the output receptacles Adjust the settings in the Lights tab to make the channel go on at the next col lection bin and verify that the lamp does indeed come on 4 Plug the incubator light cords into the output receptacles in place of the test lamp and adjust the Lights tab settings to control the lights as desired Notes Light pulses are initiated only at bin boundaries though they may terminate at any time according to the Duration setting The light status boxes are updated as each bin begins just prior to any command changes to the lights Thus the status box and status record in the LC file reflect the state of the lights in the bin just ended aligning itself with the data collected which similarly reflects activity in the bin just ended Fuses are provided in each of the relays to protect against overload In the event of fuse replacement the exact same size and rating must be used The light status boxes reflect the On Off state of the lights as commanded by the software and reported back by the controller If a fuse is blown or a cable unplugged the status will clearly be incorrect and only a direct measurement of the light level itself will tell the real story See DEnM Drosophila Environment Monitor or DAM2 Ambient Light Sensor 21 DAMSystem User s Guide Reference Status Codes Each attempt by the host computer to read data from an activity monitor results in a numeric status cod
21. be added to the On Time to form the new On Time for the next pulse This On Off cycle will continue at the Repeat Period for as long as the program is operating Several special cases are of interest If the Duration is 0 the pulse will never turn On If the Duration equals the Repeat Period the pulse will never turn Off If the Repeat Period is 0 only a single pulse will be output and it will not be repeated Changing the Settings To change a time setting place the mouse pointer over the number to be modified and hold down the left button If the tip of the pointer is above the centerline the number will increment and if below it will decrement Note that some settings are restricted to multiples of the Reading Interval On Time The On Time for each light pulse indicates the time of day at which the pulse either was or will be turned On The digit in front of the hour indicates the day of turn on with O for today 1 for yesterday and 1 for tomorrow As light pulses are turned on only at the Reading Interval the On Time is restricted to multiples of this interval Duration The Duration sets the length of time for which the pulse is to remain On after turn on The value may range from 00 00 00 never On to that of the Repeat Period always On If the Duration is set above the Repeat Period it will be set to the Repeat Period when the settings are saved The timing resolution is 1 second Repeat Period The Repeat Peri
22. calculates when the lights are to be turned on and off and then activates solid state relays within the Light Controller to perform the actual control These relays selectively apply AC power to receptacles on the unit to which the incubator lights are connected Light Channel Matrix The software generates 8 independent pulses each of which may be assigned to one or more of the physical light channels according to the matrix of check boxes A light channel with a single assigned pulse will be On when the pulse is On and Off when the pulse is Off When multiple pulses are assigned to a single light channel the logic to combine them will be deter mined by the x symbol displayed below the pulse column or logic will cause the light channel to be on when any of its assigned pulses is on and x and logic will turn on the output only when all of the assigned pulses are on 6 DAMSystem User s Guide When a light channel is configured to be On its corresponding outlet on the Light Controller will be en ergized with AC power Pulse Algorithm Each pulse is individually controlled by 3 parameters On Time Duration and Repeat Period A pulse will be turned On when the Day of its On Time parameter is today 0 and the H M S of its On Time equals the H M S of the computer clock The pulse will then stay On for the H M S of its Duration parameter after which it will go Off As it does so the Repeat Period parameter will
23. d below the base The funnel is Kimble 28950 100 and should not be replaced with any other type if the tapping mechanism is to be used If the tapping mechanism is not needed then any funnel whose stem is 9mm or less in diameter should work If the funnel is not installed loosen the large knob which holds the solenoid bracket to the post lift up the arm over the restraining pin and rotate the arm to the side Gently slide the funnel stem down through the coil spring and into the hole in the top of the nylon block lower it all the way down until the funnel bell rests on the top of the spring Note that in this position the end of the stem will protrude through the bottom of the unit by about 1 inch Place the thin plastic disk over the funnel mouth with the stepped edge to the inside of the funnel Push down on the center of the disk and verify that the funnel slides smoothly up and down in the nylon block compressing the spring Hold the funnel in its down position and rotate the solenoid bracket over the center of the funnel and disk Tighten the T handle to secure it in place insuring that the restraining pin goes through the align ment holes in the washers Release the funnel and verify that the spring pushes the funnel disk stack up and into the solenoid plunger which also moves up Press down and release the top of the solenoid plunger and verify that the stack moves smoothly down and up The funnel must not bottom out
24. e which indicates whether or not the read was successful The value of this code is also indicated by the color of the monitor status box as follows Code Color Status 1 Green Good data read 24 Yellow Monitor power on reset 50 Black No connection to Power Supply Unit 51 Red No monitor response 52 Red Communication fault Sync 53 Red Communication fault Address 55 Red Communication fault Checksum Any code other than 1 indicates that no data was received from the monitor Codes other than those listed above indicate internal monitor or system faults and should be reported to the manufacturer at support trikinetics com Output File Formats All data output files are text files and may be viewed or edited with any text editor Text lines are termi nated with CRLF on both Macintosh and Windows platforms for compatibility Monitor File Monitor files are produced by DAMSystem3 directly and are contained in folder DAMSystem3Data until moved elsewhere They are named MonitorNNN txt NNN 1 120 or MonitorLC txt for the Light Control ler and contain 1 line for each reading in 42 tab delimited columns Monitor files are also produced by the DAMFileScan application as selected and validated versions of the raw MonitorNNN files These processed files are contained in the MyRun folder and are named MyRunMNNN txt or MyRunLC txt where MyRun is the name selected in the DAMFileScan program The 42 tab delimited columns of the monitor file f
25. erate a single pulse today 0 H M S Pulse 2 could gen erate a single pulse tomorrow 1 H M S and so on up to 8 pulses A single long pulse may enable or gate a series of short pulses by using the x ana logic symbol Thus a 1 hour sequence of short 1 minute pulses would be generated by x combining on a single channel the 1 hour pulse with a repeating 1 minute pulse The channel output will only be On when both pulses are On If however the or symbol is used instead the channel will be On whenever either pulse is On negating any effect of the 1 minute pulse Data file management Monitor data is saved in the individual Monitor text files in the DAMSystem3Data folder This folder re sides in the same directory with the DAMSystem3 application as does the DAMSystem3Settings file and the DAMSystem3Log file All of these files are automatically generated by the program when necessary At the conclusion of an experiment the relevant Monitor files perhaps only a few of the total should be moved dragged or cut pasted out of the DAMSystem3Data folder and into another folder on the com puter This will effectively terminate the data collection for at the next reading the program will create new Monitor files for these monitors and begin writing new data into them Thus the files just moved will con tain the activity records for the experiment just ended and a new set of files will begin for the next one The moved m
26. es not represent a true standard deviation but instead defines the absolute limits of the uniform variation about the nominal value as a fraction of the nominal Off Time In all cases an immediate repeat may be generated but only at the conclusion of a pulse and thus no partial pulse repeats will occur Note that as long as the pulse duration is at least as great as the reading interval the MonitorLC or DayLight file will contain a record of the pulse times Note also that the pulses 7 DAMSystem User s Guide may only be initiated at the beginning of a bin so the Repeat Period must be substantially greater than the Reading Interval for the randomizer to be effective Examples 1 24hr light dark cycle On at 8 00 AM Off at 8 00 PM OnTime 0 08 00 00 Duration 12 00 00 Repeat Period 24 00 00 2 Single Pulse tomorrow at noon for 30 minutes OnTime 1 12 00 00 Duration 00 30 00 Repeat Period 00 00 00 In each case the check boxes in the row of the pulse must be checked at the column of the channel s it is to control if it is to have any effect on the hardware Hints Asingle pulse of the 8 may be used to control multiple light channels if all are to cycle On Off simulta neously Simply check the boxes for these channels in the row of the pulse and all will be controlled A finite string of pulses may be generated by combining several of the 8 pulses each of which is set to produce a single pulse Thus Pulse 1 could gen
27. es to escape but not the flies Insert tubes into the manifold holes by wetting the tube ends prior to insertion Insure that the tube is perpendicular to the manifold face and spin gently if resistance is encountered Do not force the tubes into 5 the holes lest the O ring seals be damaged aU A large 84 rubber band serves to seal the manifold cavity against leakage between the halves Tape may also be used Disassemble the manifold halves be removing the rubber band seal and the 4 thumb nuts Clean as necessary and insure that any and all debris is removed from the mating surfaces prior to reassembly to prevent leaks Align the T indents for repeatability The inlet tube fitting accepts 3 16 ID flexible tubing 13 DAMSystem User s Guide DEM Eclosion Monitor The Drosophila Eclosion Monitor uses a glass funnel to collect emerging flies from pupae cases affixed to the un derside of a plastic disk Unable yet to fly the insects fall down through the funnel neck where an infrared beam ar ray detects and counts their passage As flies are sticky on eclosion some tend not to fall but instead remain adhered to the disk or funnel walls until able to fly To prevent this a solenoid periodically taps the spring mounted disk funnel stack to dislodge those flies which have not yet fallen Mechanical Setup The unit should be placed on an incubator shelf so that the funnel stem may protrude down through an
28. f this is of interest for added throughput or the study of social effects Tubes We supply tubes in Corning Pyrex glass 5 or 7mm diameter by 65mm length and polycarbonate plastic 5mm diameter by 65mm length Both materials are transparent and may be washed and autoclaved for cleanliness and sterility Alternate tube lengths and diameters are available on request Fly Food A food mixture must be placed into one end of each tube to sustain the fly over the course of a multi day experiment Many recipes are reported in the literature but a simple one which works is as follows 100 ml water 5g sucrose crystals 2g agar powder Combine the ingredients in a glass beaker and bring carefully to a boil using a hot plate or microwave oven When the solids are completely dissolved pour the solution slowly down the side of another glass beaker containing the glass tubes standing on end to a level of about 15mm deep Allow the mixture to cool and solidify Carefully remove the tubes from the agar matrix sealing the tops with a finger to retain the food and wipe them clean Then seal the food end of each tube with either a quick dip in melted par affin wax or a plastic cap to prevent desiccation The flies may now be loaded one into the open end of each tube and the tubes then plugged with cotton Monitor Setup Tubes containing flies must be the proper diameter and may have a wax coating or plastic cap on one end to seal the fly food I
29. grees Centigrade and should be accurate to this level over the range of 0 to 70 degrees The time constant of the sensor is largely determined by the thermal mass of the unit enclosure though any airflow through or over the unit will significantly speed up the response A large temperature change in still air will take over 1 hour to stabilize to 0 1 degC but smaller changes to less precision will occur much more quickly Negative temperature values are not output the lower limit being set at 0 0 degC and no damage will occur if the unit is exposed to lower temperatures than this Elevated temperatures above 70 degrees C should be avoided Humidity Measurement Relative Humidity is measured by an electronic sensor which is mounted under the perforation holes of the case top Its range of operation is O to 100 with a calibrated accuracy of 2 Its speed of re sponse is also determined by the diffusion rate into the unit interior measured in minutes The unit will not be damaged by condensation but its output will saturate at 100 until the surface moisture evapo rates Be aware that moving a unit to or from cold environments may precipitate condensation and the resulting saturated readings Temperature controlled incubators often use fans to circulate heated or cooled air into the interior chamber The temperature and relative humidity of such circulating air may be substantially different from the air of the bulk interior and will oscil
30. gs Control Panel System and ver ify that the Hardware Device Manager Ports COM and LPT list contains TriKinetics PSIU COMnh or CP210x USB to UART Bridge Controller COMnh 5 Launch the DAMSystem program and select the Preferences tab Verify that the Serial Port points to the PSIU TriKinetics PSIU on Macintosh COMn on Windows 6 Return to the Monitor tab click on Live and verify that the monitor status boxes are Red in color Status 51 and not Black status 50 7 Verify that the yellow light on the PSIU flashes as each status box is updated 8 Plug the monitor network cables into the PSIU telephone jacks and verify that both the green light stays On and the yellow light continues to flash If these steps are successfully performed the PSIU is operating properly and the computer should be able to acquire data from installed monitors 11 DAMSystem User s Guide DAM2 Drosophila Activity Monitor The DAM2 monitor measures the simultaneous indi vidual activity of 32 flies each in a separate tube As a fly walks back and forth from end to end its passage is detected and counted by an infra red beam which bi sects the tube and the accumulated count totals are reported to the host computer at the conclusion of each reading period Monitors are built for either 5 or 7mm tube diameter and should be selected according to the size of the fly It is possible to use even the 5mm size with multiple flies per tube i
31. he PSIU adjacent to the computer which is to be used for data collection and connect the USB cable between the USB jack on the PSIU and any available USB port on the computer Connect the activity monitors to the PSIU telephone jacks using the wiring and accessories provided If the system includes more than a few monitors the wiring network will necessarily take the form of a tree with 5 way splitters serving as nodes to connect multiple monitors to a single PSIU jack The configura tion of this network is largely unimportant as long as the total cable length is restricted and each monitor is connected to it In the case of large scale systems with multiple incubators wiring should include a separate cable di rectly from the PSIU to the interior of each incubator and then a daisy chain configuration of 5 way split ters inside with a single splitter attached to each incubator shelf Then short cables may be run from these splitters to the individual monitors 3 DAMSystem User s Guide System Checkout Launch the DAMSystem3 application and click on the Preferences tab Select the Serial Port to match the USB serial port to which the PSIU is connected In the case of the Macintosh the synthesized port will be labeled TriKinetics PSIU and in the PC will usually be the highest numbered COM port in the list Choose the desired Reading Interval as well as the Monitor Range to match the set of physical moni tors which will be used These
32. he host com puter as monitor channels 1 2 and 3 of 32 Channel 1 is derived from the bottom ring that closest to the stop washer at the vial bottom channel 2 is in the middle and channel 3 is at the top closest to the vial opening The balance of the 32 channels will always record 0 Flies are detected as they move through the infrared beam cross section and thus 2 flies which move simul taneously through the beam ring may be detected as one Such dropouts will begin to affect counting accu racy as the number of flies in the vial is increased Also the detection electronics is tuned for walking flies and may miss those which quickly jump or fly through the beam ring Mechanical The monitor may be placed in a horizontal or vertical position for operation The stop washer may be adjusted in or out with a nut driver or socket wrench to position the vial axially relative to the detector rings Such a stop provides a registration basis for repeated measurements at a consistent position along the vial axis 18 DAMSystem User s Guide DPR6 Rotarod The Drosophila Rotarod uses 6 rotating glass tubes to challenge the geotactic facility of one or more flies 5 infrared beams placed at 60 degree increments around from the tube bottom shine axially along the inner di ameter of each tube wall and detect the passage of flies on the wall Flies which hold the wall for a complete turn will break all 5 beams and register counts
33. he illumination of its top surface At the end of each reading interval the monitor re ports not only the current state of the 3 sensed pa Drosophila Environment Monitor rameters but also their respective minimum average TriKinetics Ine Waltham MA USA and maximum values during the interval In addition the average illumination level for a succession of 2 minute bins is reported in channels 17 32 as shown below Channel 17 reports the average light level meas ured during the first 2 minutes of the interval channel 18 reports the average level for minutes 3 and 4 and so on These 2 minute averages allow for detailed monitoring of the light level in an incubator where the door may be briefly opened or the interior lights cycled on or off during the bin period By comparing these 2 minute averages to the overall bin average channel 4 a good profile of the lighting activity may be obtained Data Format 32 channels 1 0 always Lnow current illumination level lux 3 Lmin minimum over the current bin 4 Lavg average 5 Lmax maximum 6 0 7 Tnow current temperature degC x 10 8 Tmin minimum over the current bin 9 Tavg average 10 Tmax maximum 11 0 12 Hnow current relative humidity percent 13 Hmin minimum over the current bin 14 Havg average 15 Hmax maximum 16 0 17 minutes 1 2 average illumination level 18 minutes 3 4 19 minutes 5 6 20 minutes 7 8 21 minutes 9 10 22 minutes 11 12 23 minutes 13 14 24 minutes
34. late over time as the incubator controller adds or removes heat from this air to maintain the temperature and or humidity setpoints If the Environment Monitor is placed in this airflow it will record these oscillations of the control air rather than the temperature and humidity of the bulk interior air To avoid these effects place the monitoring unit out of the circulating air path and consider using the average values rather than the now values if there is substantial variation in the lat ter Packaging The unit is packaged in a rectangular plastic enclosure of nominal size 110 x 60 x 30 mm and con nects to the monitoring system using the standard 4 wire telephone jack The case is perforated on the top and bottom to provide convection airflow over the temperature and humidity sensors which are inter nal to the box For this reason special care should be taken to insure that no liquids are spilled onto the box 17 DAMSystem User s Guide DPM Population Monitor This monitor is designed to measure the activity of drosophila in 25 mm diameter plastic or glass vials of 95 mm nominal length With a food mixture in the bottom of the vial and an air permeable plug or cap on the top the vial may be inserted into the unit until the bottom rests on the stop washer The 3 rings of infrared emitter detectors each detect the passage of individual flies through their respective ring and report the cumulative counts to t
35. ly and perhaps other moni tors as well but the monitor in question is somehow disconnected Plug it into a different network cable until a valid response is received Intermittent error codes are always the most difficult to track down If the error is common to a number of monitors in the same reading then the problem is likely systemic wiring or power supply and not specific to a particular monitor Try to correlate the time of occurrence with an external disturbance or some other factor which could cause such a widespread yet temporary failure If on the other hand the errors are confined to a single unit then its connection to the network should be carefully investigated or simply replaced Skipped Readings Readings which are actually skipped in the collected data with the red skip error are due to the inabil ity of the program to collect data at the appropriate time If for example the program is terminated and then relaunched or the computer goes to sleep for a time any intervening readings will be skipped Simi larly if the Reading Interval is set for more readings per hour than can be accomplished by the computer some will simply be skipped Reduce the number of monitors or increase the Reading interval Power Outage A status code of 24 color yellow indicates that a monitor performed a power on reset since its last communication with the computer This error code supersedes any data output and indicates that the m
36. natural rubber band The band should be centered in the grooves of the 2 pulleys and smoothly transmit the motor power from one to the other The speed and direction of rotation are set in the Preferences tab of the DAMSystem program and are reported back from the unit in channel 16 Positive rotation is defined as up from the bottom and toward the label side or front of the unit Channel 32 reports the output of a shaft rotation sensor which is located in the final tube support out board of tube 6 This sensor increments its count once per revolution and indicates the number of ac tual turns of the tube string which may be slightly different from that commanded due to variation in the drive belt Data Format 32 channels Tube 1 SensorA 60 deg Tube 1 Sensor B 120 deg Tube 1 Sensor C 180 deg top Tube 1 Sensor D 240 deg Tube 1 Sensor E 300 deg Tube 2 Sensor A Tube 2 Sensor B Tube 2 Sensor C top Tube 2 Sensor D 0 Tube 2 Sensor E S gt OOND OFWND 19 DAMSystem User s Guide 11 Tube 3 Sensor A 12 Tube 3 Sensor B 13 Tube 3 Sensor C top 14 Tube 3 Sensor D 15 Tube 3 Sensor E 16 Command RPM 100 minus direction 17 Tube 4 Sensor A 18 Tube 4 Sensor B 19 Tube 4 Sensor C top 20 Tube 4 Sensor D 21 Tube 4 Sensor E 22 Tube 5 Sensor A 23 Tube 5 Sensor B 24 Tube 5 Sensor C top 25 Tube 5 Sensor D 26 Tube 5 Sensor E 27 Tube 6 Sensor A 28 Tube 6 Sensor B 29 Tube 6 Sensor C top 30 Tube 6 Sensor D 31 Tube 6 Sensor E
37. nsert the tubes through the 32 holes in the monitor and leave them centered so that the detection beam will bisect the tube If captivation of the tubes is necessary to prevent sliding use 14 rubber bands stretched first over the 4 corner tubes of 2 adjacent rows and pressed up against the monitor surface Then remove the tubes from columns 3 and 6 and reinsert them from above and below the bands as shown to place them into frictional contact ase a ee CO000000 OC oo OA0 O ia ae ee OU 0 60 Goo o oo 0o00 o With the tubes installed the monitor may be plugged into the DAMSystem network 12 DAMSystem User s Guide Ambient Light Sensor Each unit contains an ambient light sensor which may be seen adjacent to the hole for tube 1 This sensor is set to discriminate light from dark at a nominal threshold of 10 lux and will report its output with the count data at each collection bin With the Monitor tab set to Live and nnn the sensor output will be displayed in real time and may be used for diagnostic purposes When File data is retrieved from the monitor at the end of each bin the light sensor will report dark 0 only if dark for the entire preceding bin If the sensor measures light above its threshold at any point during the bin it will report light 1 for the bin serving to detect door openings or other lights on transients The sensor output is reported in column 10 of the MonitorNNN file Incande
38. od sets the rate of pulse cycling and with the Duration controls the duty cycle or On fraction of the pulse The pulse will be On for Duration Repeat Period fraction of the time If the Repeat Period is set to 0 only a single pulse will be output and it will not be repeated The maximum setting is 99 hours or just over 4 days at 24 hours each Random Repeat Period The Repeat Period may be randomized to vary the stimulation from pulse to pulse To activate this func tion for any pulse click in the space to the right of the Repeat Period toggling through 3 options Rn ran domize normal Ru randomize uniform and blank no randomness Operation is as follows For any pulse with its flag set to Rn the Repeat Period becomes a normally distributed random vari able with a mean equal to the nominal displayed value and a standard deviation equal to the Sigma fraction of the nominal Off Time Repeat Period Duration All Repeat Period values will be within the range of Repeat Period Off Time The Sigma parameter Preferences tab will adjust the width of the distribution with 1 providing little variation in the Repeat Period and 100 providing wide variation over the allowed range For any pulse with its flag set to Ru the Repeat Period becomes a uniformly distributed random vari able with a mean equal to the nominal displayed value and a maximum deviation equal to Sigma times the nominal Off Time Thus in this case Sigma do
39. onitor files now disconnected from the data collection process by being out of the DAMSystem3Data folder may be transferred to another computer for archival storage FileScan and analysis or plotting See Reference for the format of these 42 column monitor files Multiple systems on one computer The DAMSystem3 application allows multiple copies to run concurrently on one computer each con nected to a separate PSIU and monitor network This facilitates large systems where monitor numbers may overlap or wiring concerns mandate simplification To use this option duplicate the DAMSystem3 application and place each copy in a separate folder This will keep separate the settings and log files and monitor data files for each system Then launch each in turn and note how the windows are staggered on the screen and labeled in the upper right corner with a sequence number 1 5 The Preferences tab for each window shows the path to the particular folder which contains the application copy and monitor data for the system In all respects the systems are independent each with its own settings and files and there should be no deleterious in teraction between them Serial port assignments however must be monitored carefully especially at pro gram launch and restart to insure that the correct port is assigned to the correct system 8 DAMSystem User s Guide DAMFileScan Software This program scans DAMSystem3 Monitor data files and produces
40. onitor was inoperative for some or all of the preceding reading interval If the code is specific to a par ticular monitor then its wiring should be examined as perhaps its connection to the monitor network is intermittent If on the other hand the 24 code applies to all monitors for a specific reading then the power for all monitors failed even if momentarily Perhaps the PSU PSIU was inadvertently turned off or perhaps the monitor cables were unplugged from it for a brief instant Sporadic power interruption to the computer and Power Supply Unit may result in significant loss of data if it occurs in the middle of an experiment and goes undetected A good preventive measure against such loss is a battery backup Uninterruptible Power Supply UPS which can supply line power to the computer and monitor power supply for a short time in the event of an outage If a backup generator in the lab facility is available to come online within a few minutes then with such a system no loss of data should occur System Reliability The DAMSystem program and its attached Power Supply and Activity Monitors should reliably gener ate and collect data for hour upon hour without error of any kind If errors do occur their cause should be identified and corrected rather than simply accommodated so that the system may operate to its full po tential Wiring may fray and connectors may corrode in high humidity environments but the overall sys tem is capable
41. onse purposes Each light channel is switched on off by a solid state relay within the LC3 LC6 enclosure The relays are rated for up to 240VAC 50 60 hz operation at 3 am peres and each is fuse protected against overload An input AC line cord provides power to the relays and output cords provide switched power from the te GLa relays to the lights to be switched The connectors for Sea ee AC input and output are the North American stan dards IEC60320 C13 for input and NEMA 5 15 for output To use these controls for incubator lighting the lights must be disconnected from the internal incubator timers and connected instead to conventional line cords with plugs suitable for connecting to wall power Make sure that the ballast transformers for the lights are included in the circuit with the line cords test each cord by plugging it into a wall outlet If the lights work properly in this case the cord may be plugged into the LC3 LC6 for DAMSystem control NOTE electrical connections to the incubator lights must be made by trained electricians only Installation 1 Launch the DAMSystem program and enable at least one of the light control channels Checkbox matrix in the Lights tab 2 Connect the Light Controller to the DAMSystem network with a phone cable and verify that the light status boxes upper right of DAMSystem window turn orange on or blue off in Live mode 3 Connect an AC cord to the input power receptacle and a st
42. operates erratically in any way this part of the system must be diagnosed before reliable data collection can be expected to occur Once the program is operating consistently then the Power Supply Unit may be connected to the com puter and the communication link verified Then and only then should the monitor network be connected and finally the monitors themselves Computer Software Errors Both the Macintosh and Windows platforms should provide reliable operation of the DAMSystem pro gram If the program either fails at launch or quits unexpectedly some condition within the machine has interfered with its ability to execute and the troubleshooting challenge is to unmask this conflicting condi tion and then remove it Terminate all other applications which may be operating unplug any network cable and then reboot the computer Relaunch the program and if it still does not run well transfer it to a similar machine if avail able By comparing its performance in this way the offending operating system or hardware configuration may be identified and rectified USB Driver Problems If the USB drivers are installed properly the PSIU should generate no message or error window when it is first connected to a computer USB port If a message such as New Hardware Found pops up and does not resolve itself then the drivers have not loaded properly and the PSIU has not been recognized In this case the drivers should be downloaded from the
43. ormat are as follows with all being numeric except columns 2 and 3 Index at reading from 1 with each program restart Date of reading 9 Dec 06 Time of reading 19 09 30 Monitor status 1 valid data received Extra readings included in this bin DAMFileScan outputs only unused 0 unused 0 unused 0 unused 0 DAM2 Light Status 1 On 0 Off Channel 1 activity counts Channel 2 OOND ARWND oO mi hw Channel 32 fi Ph 22 DAMSystem User s Guide Light Control outputs are reported as Channels 1 6 of the MonitorLC or MyRunLC files with 1 On and 0 Off Skipped bins filled in by the DAMFileScan program will have the correct Date and Time but all other columns will be O including index monitor status and activity channels Legacy Channel File Each Channel File contains the data for a single channel from a single monitor The file begins with a 4 line header after which follows the sequential data from the monitor Readings with errors status code not 1 will appear as the negative of the status code unless the error has been corrected for example File Header Line 1 MyRunM001C01 28 Mar 2002 Line 2 94 Line 3 30 Line 4 1330 File Data Line 5 O Line6 3 Line 7 51 Line 8 12 Line nn Legacy DayLight File File Name First Date Number of Readings Reading Interval MM SS First Reading HHMM SS First Reading Activity counts Error status minus
44. ors at 0 10 20 30 40 and 50 minutes past each hour generating 6 x 24 144 readings per day 5 DAMSystem User s Guide Monitor Range These 2 numbers 1 120 specify the range of monitors which is assumed to be connected to the sys tem and which is interrogated for data at each reading If a system includes a single monitor 1 then the monitor range should be set for 1 to 1 Likewise if monitors 10 19 are active the range should be set accordingly Monitors within the selected range which are not present will simply be recorded in the data folder with a reading status code of 51 and data values of 0 Eclosion Monitor These parameters control the periodic tapping of the solenoids on any and all Eclosion Monitors which are present on the network Tap Now will cause the selected monitor to immediately tap Light Controller Sigma This parameter 1 to 100 controls the range of variation which is applied to the repeat period when the randomizer function is enabled see Lights tab Rotarod The DPR6 Rotarod spins at an RPM which is controlled by this setting Use the mouse pointer to select the desired RPM or and then click Set to transmit the command to the device Serial Port The Serial Port defines the input output connection between the computer and the activity monitors Legacy systems using the Blue Box Power Supply will be connected by an RS 232 serial cable to either a physical computer port or a USB Serial adapter
45. oxes indicating lack of communication with the PSIU itself Select Live and All to view the status of each monitor in turn as it is interrogated by the system This mode is useful when monitors are first connected for it allows a quick verification that all connections are proper and that all monitors which should be reporting data can do so To verify a single monitor select the Live text and use the mouse to increment decrement NNN to the monitor s number 1 120 If the monitor is connected it will be repeatedly interrogated for its current or live count totals and all 32 will be displayed In addition the DAM2 monitor will display the status of its on off ambient light sensor Similarly the File and NNN selections will display data for a single monitor from the most recently stored reading Preferences tab All Preferences are saved automatically in the DAMSystem3Settings file and are reloaded at startup after a shutdown Default values are used if the file is not present To change a setting left click the mouse pointer on the upper half to increment and the lower half to decrement Some settings will change as long as the mouse is held down Reading Interval The Reading Interval specifies the time between successive readings by the computer of monitor data The readings will occur on submultiples of the hour according to the computer time of day clock Thus a 10 minute setting will cause readings to be taken from all monit
46. scent Light The light detectors used in the counting beams are sensitive to ambient light in the infrared band as would be emitted from a hot incandescent bulb Such external light will normally not prevent the counting circuits from detecting fly movement but may cause false counts if the level of such light changes rapidly as when the light turns on or off or is shadowed Fluorescent lights emitting principally in the visible band will not cause such transient counts Data Collection To verify that the monitor is operating properly return to the Monitor tab and show Live data for the sin gle monitor nnn in question The status box should be green status 1 and the 32 channels of real time count activity should be displayed If a thin object such as a pencil point is moved through one of the tube cavities the count total for that channel should increment The monitor will accumulate activity counts for as long as it has operating power and will uplink its ac cumulated counts and then reset to 0 whenever commanded to do so by the host computer Counts will be accumulated as the flies are active in both total darkness and bright ambient light MAN2 Gas Distribution Manifold This accessory for the DAM2 activity monitor pro vides for controlled gas flow through the tubes with a common inlet port and individual Oring sealed exit ports to each of the 32 5mm tubes Small exit holes in the tube sides near the opposite ends allow gas
47. ter of window indicates the date and time at which the most recent data collection from the monitors was made The index simply counts up from 1 with each reading and along with the date and time is stored in each monitor file with its monitor data Above the reading box is the countdown timer which indicates when the next reading will occur Read ings take place at the interval specified in the Preferences tab Lights Box The Lights box upper right of window shows the status of each light channel as reported by the Light Controller if connected The colors of the boxes indicate the same status conditions as those of an ac tivity monitor with the exception that instead of green for valid data the light boxes indicate orange for On and blue for Off Boxes which are visible have been activated in the Lights tab by selecting at least one pulse in the appropriate column of the selection matrix Quit If the DAMSystem program is terminated no periodic data collection from the activity monitors will oc cur The monitors themselves will continue to count events as long as they have operating power but these events will remain uncollected until the program is relaunched in the host computer Monitors tab This tab panel shows the status of all monitors connected to the system Select File and All to view the most recent reading status with green boxes indicating monitors reporting data red boxes indicating monitors not present and black b
48. th more than 3 monitors 5 way splitters are used which allow 5 monitors to be connected to a single jack These in turn may be cascaded in a tree fashion plugging the cable from one into the next so that ultimately any number of monitors may be connected to a single Power Supply jack For custom cable lengths or wiring configurations it may be more convenient to make the cables from scratch and this is readily done Purchase a roll of 4 conductor flat modular telephone cable a box of 6 position RJ 11 connectors and the appropriate hand crimp tool from a retail outlet or catalog Cut the cable to length and crimp a connector onto each end insuring that the color sequence of the 4 wires is reversed between the 2 ends and that the 4 wires are centered within the 6 positions Then test the ca ble All monitors and all Power Supply jacks are essentially connected in parallel so any monitor may be plugged into any jack or cable in the network Incubator Wiring If activity monitors are to be used within incubators it may be convenient to install the telephone wiring permanently within the incubator interior Attach a 5 way splitter to the side of each shelf with cable ties and then route 4 short cables from it along the front of the shelf Secure these cables to the shelf and leave each with a dangling end for connection to a monitor Then connect the splitters one to the next in daisy chain fashion using their attached cables pl
49. thout disturbing the activity of other monitors Data Collection At periodic intervals ranging from 1 second to 60 minutes the DAMSystem program in the host com puter transmits a command to all monitors to simultaneously freeze their current count totals The moni tors set aside these frozen counts reset the totals to zero and begin counting again for the next meas urement period Meanwhile the host begins a sequence of requests from each monitor in turn by address number to transmit its frozen counts to the computer for storage and later output This data collection or reading sequence requires about 2 3 second per monitor placing a lower limit on the reading interval if multiple monitors are used Data Storage The DAMSystem3 program stores the retrieved monitor data in a folder on the hard drive which is automatically created DAMSystem3Data Individual text files for each monitor accumulate successive readings for as long as the program operates and these files may grow without limit to the capacity of the disk drive At the conclusion of an experiment perhaps covering several weeks of continuous data collection these monitor text files containing the captured data should be moved out of the DAMSystem3Data folder for processing and analysis The DAMSystem3 program will create new files as necessary to store addi tional data as it is collected File Scan Prior to processing and analysis the data files should be
50. ugging each cable into the unused 5th jack on the next splitter in line Run the cable from the last splitter out 24 DAMSystem User s Guide through a hole in the rear of the incubator and connect it to the Power Supply using a coupler and exten sion cable if necessary If each incubator is connected to a separate Power Supply jack in this way the voltage drops in the ca bles are minimized and isolation of wiring network problems is more straightforward Light Controller to Lights Cable The Light Controller switches On and Off the AC power outlets on the unit s rear panel These outlets are the conventional US 117VAC type NEMA5 15R and accept a grounded 3 prong plug from a line cord The other end of this cord must be connected to the lights to be controlled and will supply up to 3 Amps fuse limited at the line voltage The internal solid state relays are rated for 240VAC operation making the unit suitable for line power in most parts of the world Troubleshooting The Drosophila Activity Monitoring System is made up of a number of interconnected components and the key to efficient troubleshooting is to isolate which component is not performing as it should The first troubleshooting step should be to verify that the host computer and its DAMSystem software can operate smoothly and continuously over an extended period of time The Power Supply Unit need not be con nected for this test and if the program halts for any reason or
51. validated output files at any bin length Use it as follows 1 Select Input Data Folder to choose the location of the DAMSystem3 data files File names must be of the form MonitorNNN txt where NNN 1 to 120 or LC for Light Control Files must consist only of 42 tab delimited columns 2 Choose the monitor range to be scanned 3 Click Scan to initiate read and review of the input files Results include the earliest and latest read ings for each file number of readings with errors and total number of readings Uncheck the Verify Data box to speed up scanning if the input files are known to be good 4 Choose the first and last bins to be saved and the output bin length 5 Choose the File Type Monitor files are of the same format as the input files and Channel Files are of the legacy DAMSystem2 format 32 per monitor 6 Multiple input readings within the time frame of a single output bin are combined either by sum or average The number of these extra readings is reported for each bin in column 5 of the output monitor file 7 RunName specifies the name of the output data folder which will be created alongside the input folder The individual output files will be named with the RunName prefix 8 Click Save to produce the output files Results for each monitor are reported as follows R Input readings included in output E Input readings with errors output as 0 S Skipped output bins with no input data output as 0 X
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