DropSense Integration Manual
Contents
1. Page 12 of 28 DropSense Integration Manual v0 9 The data is organized as follows The user data is managed by the script on the control PC This includes the name of the samples source plates concentrations etc The script generates the experiment settings and processes the measurement results for example storing in his local LIMS system The instrument data is stored on the host PC and not accessible by the script This includes calibration data of the instrument parameters of the disposables such as path length of the reservoirs pump profiles etc There is no need to change this type of data except if the system needs recalibration or if the information of a new type of disposables must be uploaded Such interaction can be done in local mode only requiring service interaction The raw data of the measurement is stored in a user defined path The script can set the path for storing these raw data This data includes all details of the measurement including all spectra measured during pumping of the DNA in the measurement wells etc The set of the DropSense instrument DropQuant software and the location for storing the raw data can be seen as one virtual instrument Power up DropSense start DQ close _tray DropQuant Post processing done on DropQuant Login as remote DQ get_results Use measurement results DQ _request_access equalise concentration storein LIMS etc Fetch data from2. the robotic arm has to move the DropFrame to a specific X Y Z position relative to the instrument The robot must know the exact position of the instrument in order to put the DropPlate in the centre of the in out tray To achieve this there is a mechanical reference at the bottom side of the instrument defining the exact position of the instrument on the workbench This allows to define the X Y Z position of the DropFrame to put the DropFrame In the in out tray The mechanical reference for positioning the DropSense instrument on the workbench consists of 2 10 mm holes matching 10mm diameter pins By placing the instrument on a plane with the 2 pins the position of the instrument and the in out tray is defined relative to these 2 pins Page 10 of 28 DropSense Integration Manual v0 9 425 25 Figure 7 features for defining the position of the in out tray of the DropSense instrument the indexing holes have 10mm diameter the holes in the bottom plate are 12mm and act as a pre alignment The X Y and Z coordinates of the DropPlate are defined on the figure If the tray is open then the disposable must be positioned at next position relative to the two pins in the workbench see figure 7 Height the ground plane of the 96 well disposable must be at 158mm relative to the reference plane Front position distance from the line between
3. DropQuant program on the controller PC the communication over USB between DropSense and controller program is initialized Login as Remote user After login as remote user the screen of the DropQuant software looks like figure 10 At that moment the DropQuant software is monitoring the TCP port for receiving commands Page 15 of 28 DropSense Integration Manual v0 9 System is in Remote Mode No user interaction possible IP address of this computer 10 0 0 43 current port number 6300 no remote connection is made ABORT REMOTE MODE Figure 11 DropQuant screen when logged in as a remote user The control PC making connection to the host PC needs the IP address of the host PC and the TCP port e The IP address can be found running the ipconfig command on the host PC In case the script and the DropQuant program are running on the same PC then the localhost keyword can be used e The standard value for the port is 6300 Note bioth IP address and port number are visible on the user screen see figure 11 4 2 Definition of the interface files To start a measurement the host PC needs crucial information such as the number of samples required results export format etc The control PC must send this information to the host PC This is done via a number of text files or strings These are e Sample Definition String text file or string describing the samples position name reference to the dropframe refe
4. LIMS to Tine Eze nea DQ_release_access DQ_define_experiment a Te 0 Close the DropQuant DQ_open_tray Place dispo i DQ_close_tray i 4 egend User interaction on host PC Script on control PC DropQuant API functions Script on control PC other functions DQ_measure i DQ_get_status until measurement done DQ_open_tray Remove dispo i Figure 9 example of a measurement algorithm To perform a measurement the control PC acts as a master and controls the host PC The control PC asks the host PC to load unload DropPlates to read the plate in the DropSense instrument and to send the measurement results back to the control PC The control PC uses the results of the measurement the concentration OD quality checks for further processing for example communicate with the liquid handling robot for cherry picking the good bad samples from the plate calculate the dilution factors and performing the dilution etc Page 13 of 28 DropSense Integration Manual v0 9 We defined a complete set of functions allowing writing scripts and routines for controlling the instrument initialization loading and unloading a frame starting a measurement getting the status of the instrument A typical algorithm is summarized in figure 7 These functions are available through an API application programming interface and by executables The executables have a limited functionality and can be us
5. application programming interface API for communication between a third party program or script with the DropQuant software This manual describes the operation of the system in remote mode Liquic hancling robot and ocher periphery a virtual machine Host PC running DropQuant software DropSense instrument Lab control PZ o using the DropQuant inter ace functions library LIMS system for retrieving sample informatior and storing measurement results Raw data is stored in measurement database Any PC running the DropGvant software san browse meusuremen s storedin tae measure rent datubase Figure 8 organisation of the measurement 1 lab control PC asks the host PC to measure the plate the host PC stores the raw data in the measurement database and 2 send the measurement results back to the lab control PC for further processing and or storage of the results in customer LIMS system 3 any PC with desired access rights can look up old measurements on the measurement database for debugging system maintenance etc In remote mode the DropQuant is controlled by a script running on the control PC cfr figure 8 Note the script and the DropQuant software may run on the same PC or on a separate PC connected by a network The communication between script and controller program is organized over a TCP port In case the script and DropQuant run on the same computer this TCP port is bypassed
6. defined 14 Timeout for going to open tray position 20 Access free 21 Access and connection no measurement 22 Access and connection measurement failed to initialize 23 Access and connection measurement started 24 Access and connection measurement failed 25 Access and connection measurement succesfull 30 Access and connection measurement initializing 31 Access and connection measurement busy 31 Could not perform command measurement busy 32 Access and connection load next DropFrame 50 Access and connection tray is open 51 Access and connection tray is closed 52 Access and connection could not perform command tray is moving 52 Access and connection tray is moving 99 Timeout DropQuant not responding 100 Access interrupted by local user interface 102 Incorrect argument used DropFrame ID not valid 103 Incorrect argument used DropFrame ID is already measured 104 Results can only be exported if all DropFrames are measured 200 Could not connect over TCP 999 DropQuant Exit accepted Page 28 of 28
7. next table DropQuant_Remote ex c requestaccess a localhost 6300 out c result txt for f Si in c result txt do if i 0 echo i else echo i amp goto exit DropQuant_Remote ex c defineexperiment a localhost 6300 out c result txt e c expdef txt s c samples txt for f i in c result txt do if amp goto end ol ae ol H i 0 echo i else echo DropQuant_Remote ex c opentray a localhost 6300 out c result txt ae oe H Qfor f i in c result txt do if i 0 echo i else echo amp goto end DropQuant_Remote exe c closetray a localhost 6300 out c result txt o9 o9 H Qfor f i in c result txt do if i 0 echo i else echo amp goto end DropQuant_Remote ex c measur a localhost 6300 out c result txt d DropFrame 1 Qfor f i in c result txt do if i 0 echo amp goto end oe oe ol ol H i else echo statusloop DropQuant_Remote ex c getstatus a localhost 6300 out c result txt for f i in c result txt do if i 31 echo i amp goto statusloop else echo i DropQuant_Remote ex c opentray a localhost 6300 out c result txt for f i in c result txt do if i 0 echo i else echo i amp goto end DropQuant_Remote exe c closetray a localhost 6300 out c result txt for f i in c result txt do if i 0 ech
8. DropPlates in the instrument Measurement directory path to network drive for storing the raw data of the measurement Be sure to foresee sufficient disk space on this drive The Import samples section contains next fields column_source_plate column number containing the source plate ID this is a reference to the plate in the biobank in which the extracted DNA is stored typically this is a string with the plate name column_source_position column number containing the position in A1 H12 notation column_dropframe_ ID column number containing the ID of the DropFrame column_dropframe_position column number containing the column_sample_name column number containing the name column_blank_dropframe_ID column number containing the ID of the frame with blank column_blank_dropframe_position column number of the position of the blank blanking information O autoblank 1 single blank cfr 2 regeltjes hieronder 2 multiple blanks zoals defined in de kolommen blank_dropframe_ID definition of the frame ID of the blank in case of one blank for the complete experiment blank_dropframe_position definition of the blank position in case of one blank for the complete experiment May be empty in case An example is shown in table 1 Experiment definition experiment_name Experiment by remote samp material dsDNA label xperiment_description first DP16 U measurement le_Type Nucleic Aci
9. E EAE ESERE 22 4 3 9 Abort Measurement ceecceesssceessecesceeeeeeeeeseeeeeaaeceeaaeeeaaesaeeeeaaeceeaaeseeaeeeesaeeeeaaeseeaaeenaees 23 43 10 Get ResultS iroi i secede a wile ao Gea a a a e a a 23 4 3 11 Eit gna a ia Geen eee a hea ee eee 23 5 MAPPeNdix Lexa ples cicsec si hsv ded ess cs sok ahaaeadec eas oa vase ds A E E TE E E 24 5 1 Example G program Using DLL wit ccet okie seta bickee hoi ee ore ee 24 5 2 Example2 script using CXECUTADIES cccccccccessessssececeeecessaeseeeeseesseseeaeeesesseeesseseaaeseeeeseesees 26 6 Appendix 2 list with status COC cccccsccccecesssssssaeeecesssessaeseeeescesseseaaeeeeeeeecessesssaeaeeeeeessesenaeess 28 Page 6 of 28 DropSense Integration Manual v0 9 1 Introduction The Trinean DropSense is a novel plate reader designed to read the Trinean DropPlate This DropPlate is a microfluidic disposable compatible with SBS standard allowing the measurement of the UV vis absorption spectrum of small liquid samples typically 1 3uL Applications are concentration measurements of biomolecules such as DNA or proteins and read out of colorimetric assays Throughout this manual the terminology DropPlate and DropFrame are used to describe the microfluidic chips The DropSense instrument is operated by the DropQuant software running on a host PC This host PC communicates with the instrument using a USB cable The system can operate in stand alone mode or integrat
10. NE ch ena cgcnncd AE N E dae vansetacdessch TE 7 2 Physicalint gration s OVervView a ceed eevee deeds vk hae r aa eae Ere aan aa 8 2 1 Compatibility with liquid handling robOts cccccccsssssscceceessesseaeeececeseesesneaeceeceessessessaaeeeeees 8 2 2 Mechanical references on the inStrUMeNt cceeccceesceceeeeeceeeecaeeeeaaeceeaeeceaeeeseaaeeteaeeseeeeess 10 3 Software integration overview and CONCEPTS ccccccccccessssessceccecessessaececececeesesssaaeaeeeeseeseessaaeas 12 4 Software integration details nsoni nren r a E E due veastacketes 15 4 1 Installation and initialisation of the integration ccccsesssececesessesssseeeeeesseessesseseeeesensees 15 4 2 Definition of the interface files eee ecceesseeesseeeesceceeeeceeeeeeaeeeesaeceeaaesesneeesaeeeeaaeceeaaettaneens 16 4 3 Overview of the COMMAMNAS 0 0 eeeeceeeteceeseceeneeceeeecaaeeeeaaeseaeeceaeeecsaeeeeaaeseaaeeeeaaeeseaaeeeeaeeenaees 19 4 3 1 CONStMUCKOR Hii ane oie ea ee A ee ee ieee Ao Ab 20 4 3 2 REGUESE ACCESS fecdis ex seciebeiadi E EE eebe ladies anes E Re est ha ese 20 4 3 3 REC ASE ACCESS inniinn neii a a i i aiia i paia 21 4 3 4 OPe i Tray AA E E A E esi eeaee le 21 4 3 5 COSC Tita E E re Sieh eth area E es Hae aod te RO Ped E eo are tuenes Svea 21 4 3 6 Get AA E e ROE E E eaten A E A E E T ceveuhi cl Seashell weve AE 22 4 3 7 Define Experiment e aaraa a E aE oaa beaded tea Gliese desea onde 22 4 3 8 Start Measurement soian Enee ees eed E
11. Sense Integration Manual v0 9 To minimize the number of responses return codes are used Appendix 1 gives an overview of these return codes If the command was successfully executed 0 is returned If not successfully executed the reason of failure is found in the code for example 1 if you don t have access because another remote user has access or the program is in local mode 2 if there is no connection to the DropSense If there is a need to give more details but no error has occurred positive number are used for example if you want to determine the status of the ongoing measurement with DQ_GET_STATUS more specific information is required In case of executables 3 arguments are always required e command there are a set of commands that can be used f e c opentray a address and port the address and port are given as address port f e a localhost 6300 out the location of the file where the status code will be written to f e out C DQ_result txt All arguments may be in random order but all are required before execution of the command 4 3 1 Constructor To create an object of the type DropQuant include the parameters address and port to specify the communication parameters Syntax1 DropQuant String address int port f e DropQuant DQ1 new DropQuant address port Return code is a reference to the DropQuant kind of handle Note there is no alternative function for the exec
12. charge for a period of one year provided that the products are utilized and maintained in accordance with the instructions in the applicable operating and servicing manual and provided further that the products have not as determined solely by TRINEAN been subject to misuse or abuse by the Customer or other parties unrelated to TRINEAN TRINEAN makes no warranty expressed or implied as to the fitness of any product for any particular purposes other than those purposes described in the applicable operating and servicing manual nor does TRINEAN make any other warranty whether expressed or implied including merchantability other than those appearing on the face hereof Where TRINEAN guarantees any product whether under this Warranty or as a matter of law and there is a breach of such guarantee the Customer s only and exclusive remedy shall be the replacement or repair of defective parts and materials as described above This shall be the limit of TRINEANS liability Furthermore TRINEAN shall not be liable for incidental or consequential damages Failure of the Customer to notify TRINEAN of a claimed defect by registered mail within thirty days of the discovery thereof shall constitute a waiver of any claim for breach of warranty When a product is required by TRINEAN to be installed by a TRINEAN engineer or technician the period of this Warranty shall begin on the date of such installation provided however that any use of the product pr
13. definition and Import samples The Experiment definition section describes the general settings of the experiment The Import samples section describes the format of the sample definition file Next fields must be in the Experiment definition section e Experiment name user defined name e Experiment description user defined text e Sample type Nucleic Acids or Purified Proteins e Material the material name Note the name must be defined in the material database of the DropQuant program installed at the host PC Names that are defined standard are o incase of Nucleic Acids dsDNA ssDNA RNA Oligo gt If the string contains whitespaces then add a before and after the string Page 17 of 28 DropSense Integration Manual v0 9 o incase of Purified Proteins General BSA IgG or Multiple Labeled FALSE or TRUE in case labeled TRUE label1 name of the first label in case labeled TRUE label2 name of the second label omit when only one label Solvent 0 1 or 2 0 water based solvents 1 water glycerol 2 water DMSO High viscosity TRUE or FALSE Path length one of double pathlength single pathlength Dropplate type sets the type of disposable one of DP16 G DP16 U Use_barcode_check use this option to active the internal barcode reader this can be used as extra check to avoid error in order of inserting the
14. dropframes Length i if DQ1 DQ_Open_Tray lt 0 goto End load the DropFrame if DQ1 DQ_Close_Tray lt 0 goto End if DQ1l DQ Measure dropframes i lt 0 goto End do status DQ1 DQ_Get_Status if status 32 amp status 25 amp status 31 goto End while status 32 amp status 25 String results experiment_path do status DQ1 DQ_Get_Results result_parameters out results out experiment_path if status 0 write results to the location you want break while status 104 104 is send when not all dropframes are processed yet End status DQ1 DQ Release_Access Exit Next table is an example of the output file in text format DropFrame ID DropFrame Position Sample name Pump Concentration ng pl A260 A280 A260 A280 DropFrame 1 Al1 blank 0 00 0 00000 0 00000 DropFrame 1 Cl samplel 277 59 5 55176 3 24380 1 71 DropFrame 1 E1 sample2 281 40 5 62798 3 30268 1 70 DropFrame 1 G1 sample3 277 46 5 54911 3 26779 1 70 DropFrame 2 Bl sample4 277 40 5 54803 3 24143 1 71 DropFrame 2 D1 sample5 282 18 5 64369 3 30929 1 71 DropFrame 2 F1 sample6 282 49 5 64985 3 27086 1 73 DropFrame 2 H1 sample7 279 00 5 58007 3 29418 1 69 Page 25 of 28 DropSense Integration Manual v0 9 5 2 Example 2 script using executables An example script is defined in
15. ds ed TRUE label 1 Cy3 label 2 Cy5 solvent 0 high_viscosity FALSE dropplate_type DP16 U pathlength double pathlength measurement_directory C Measurements use_barcode_check TRUE In col co mport samples Lumn_source_plate 1 lumn_source_position 1 Page 18 of 28 DropSense Integration Manual v0 9 column_dropframe_ID 0 column_dropframe_position 1 column_sample_name 2 column_blank_dropframe_ID 3 column_blank_dropframe_position 4 blanking_information 2 blank_dropframe_ID blank_dropframe_position Table 2 example of experiment definition string The Results Definition String is a text file defining the output format for the results These are stored in a table based text file This Results definition string contains a number of fields followed by the column number If the field should not be included in the results file set the column number to 1 e column_names defines which columns need to be in the results make a selection of the following columns Source Plate ID Source Position DropFrame ID DropFrame Position Sample name Pump Concentration ng l A260 A230 A280 A260 A230 A260 A280 Material Date Time Conc factor Instrument ID Pathlength mode all OD values e separator determines the character that will separate the different columns in the results values that are all
16. e 1 41 DropFrame 1 B2 sample9 DropFrame 1 41 DropFrame 1 C2 sample10 DropFrame 1 Al DropFrame 1 D2 samplell1 DropFrame 1 Al DropFrame 1 E2 sample12 DropFrame 1 Al DropFrame 1 F2 amplel13 DropFrame 1 Al1 DropFrame 1 G2 sample14 DropFrame 1 Al DropFrame 1 H2 sample15 DropFrame 1 Al Table 1 example Sample Definition String with16 samples on one plate all samples using A1 as blank reference Note an experiment may contain multiple plates all samples of the plates defined in the experiment are collected in one large sample definition string After definition of the experiment an array with the DropFrame_ID s defined in the sample definition string is returned If the script tries to measure more plates than defined in the sample definition string or if the script asks the DropQuant to send the results without having measured all plates defined in the Sample Definition File then an error message is returned It is the responsibility of the script programmer to offer the exact number of plates to the DropSense instrument as defined in the sample definition string After defining an experiment the DropQuant software returns an array with names of the plates defined cfr paragraph 4 3 7 This can be used in the script to make sure the plate inserted to the DropSense instrument are the ones that are expected by the DropQuant software Experiment Definition String contains 2 sections Experiment
17. e in the report what is used as separator and where the results can be stored leave blank to choose the default path If you enter a DropFrame_ID only the results of that DropFrame will be given if you leave it blank all results will be given Syntax1 DQ _Get_Results String results_parameters String dropFrame_ID out String results out String experiment_path Syntax2 c getresults a lt address port gt out lt output_path gt p lt result_parameter_path gt r lt result_store_path gt d lt dropframe_ID gt d is optional if omitted all results will be exported 4 3 11 Exit Closes down the DropQuant program Syntax1 DQ_Exit Syntax2 cC exit a lt address port gt out lt output_path gt Return status code see appendix 2 Page 23 of 28 DropSense Integration Manual v0 9 5 Appendix 1 examples 5 1 Example 1 C program using DLL A simple example of the script is shown in next table in C using System using System Collections Generic using System Text using DropQuant_Remote class Program static void Main string args String address localhost set the IP address int port 6300 set the TCP port add the experiment definition or read it from a file String exp_def Experiment definition experiment_name Experiment by remote experiment_description example sample_Type Nucleic Acids material dsDNA labeled FALSE J abe
18. ed in automated lab systems This manual describes the integration of the DropSense instrument including the DropQuant software in automated lab setups for example integration with liquid handling robots This includes e Physical integration description of the mechanical references for integration the instrument on the work bench e Software integration the application programming interface API for controlling the DropQuant software from another programming or scripting environment Note that the user aspects of the DropQuant software are described in detail in the user manual this includes settings up experiments and retrieving the measurement results This manual concentrates purely on the integration aspects Page 7 of 28 DropSense Integration Manual v0 9 2 Physical integration overview The Trinean DropSense instrument is designed for integration with liquid handling robots e The disposable is designed for automatic sample dispensing by liquid handling robots o dimensions are compatible with SBS standard input wells at 9mm pitch o self filling of the sample in the microfluidic meander reduces evaporation allowing longer storage times of the filled DropPlate without influencing the concentration measurements e The mechanical design of the disposable and the in out tray of the instrument are compatible with the grippers of liquid handling robots e The instrument has mechanical features for indexing the position o
19. ed in case the user script cannot access DLL functions In case of executables the communication set parameters and returned re sults is organized via text files The syntax of the executables is DropQuant_Remote exe c command a address port out output txt The functions from the DLL are executed in foreground this implies the script is frozen during a call of a function until the answer from the DropQuant is received indicating the command is executed successfully Notable exception is the measure command when starting a measurement the DropQuant controller sends an answer at the start of the measurement During the measurement the script may execute other tasks The script can use the get status function to follow up the status of the measurement and take further actions as soon as the measurement of the plates is finished for example deloading the old plate and loading a new plate This is shown in figure 10 User script DropQuant program DropSense instrument j a me startmeas E Oo ooon e H starimess i H i S Meas start OK i 1 i 1 StartMeas Meas start OK Get Status i __ i 1 i i H GetStatus m MeasBusyistatus X Get Status Se f 1 1 i _ a _ 1 1 GetStatus MeasRiisy status Maas dene Get Saatus _____ 1 ee 1 1 GetStatus p _ r Status OK Figure 10 communication during measurement Page 14 of 28 Dro
20. ey ee en DropSense96 System Integration Manual and API Reference Guide DropSense Integration Manual v0 9 Revision History Revision Date April 2010 Page 2 of 28 DropSense Integration Manual v0 9 Revision April 2010 This manual is published by TRINEAN NV SA Questions or comments regarding the content of this manual can be directed to the address below or to your TRINEAN representative TRINEAN NV SA Dulle Grietlaan 17 3 B 9050 Gentbrugge Belgium Tel 0032 9 2727535 Fax 0032 9 2727539 info trinean com www trinean com DropSense 96 and DropPlate16 96 are trademarks of TRINEAN NV SA Page 3 of 28 DropSense Integration Manual v0 9 This document is the copyright of TRINEAN and must not be copied or reproduced in any form without prior written consent TRINEAN reserves the right to make technical improvements to this equipment and documentation without prior notice as part of a continuous program of product development This manual supersedes all previous editions Page 4 of 28 DropSense Integration Manual v0 9 Warranty and Special Provisions Limited Warranty TRINEAN products are fully guaranteed for one year against defects in parts materials and workmanship Defective parts and materials will be replaced or at the discretion of TRINEAN repaired at no charge for a period of one year and labor required for such replacement or repair will be provided at no
21. f the instrument on the work bench 2 1 Compatibility with liquid handling robots The handling of the DropPlate in a liquid handling robot and the filling of the reservoirs by such robots is shown in figures 1 and 2 Figure 1 liquid handling robots moving the DropFrame in Figure 2 A liquid handling robot filling the 96 input wells the workbench of the DropPlate The DropPlate is loaded into the instrument by the in out tray The in out tray of the DropSense instrument allows pick up and put down by most common robotic arms Note the alignment mark at the A1 corner of the frame this defines the orientation of the DropPlate in the instrument The outer dimensions of the DropPlates are compatible with standard 96 well plates width and length of the plate is 85 5x128mm The height of the DropFrame is 10mm and on top of the DropFrame the 1 4mm thick microfluidic disposable is mounted Multiple variants of the DropPlate are available e Analuminum frame with six DP16 disposables mounted on the frame The end user has to mount the DP16 disposables on the aluminum frame matching the hole sleeve of the DP16 on the pins on the frame In this case the DropFrame includes 6 DropPlates Page 8 of 28 DropSense Integration Manual v0 9 e Amoulded frame with the DP16 chips pre assembled on the moulded frame the end user must not assemble the small DP16 disposable chips on the frame In this situation the DropPlate and the Dr
22. ior to such installation shall at sole election of TRINEAN void this Warranty When installation by TRINEAN personnel is not required the period of this Warranty shall begin on the date of shipment from TRINEAN The period of this Warranty shall begin as described above whether or not the product has been installed pursuant to a purchase order and any trial period shall be deducted from the Warranty period that would otherwise apply under a subsequent placed purchase order for that product Limitation of Liability Notwithstanding anything to the contrary contained herein the Seller whether by reason of breach of warranty breach of contract tort or otherwise including without limitation under any indemnification provision contained herein shall be limited to replacement of goods returned to TRINEAN which are shown to TRINEANS reasonable satisfaction to have been nonconforming or to refund the purchase price or if not paid to a credit amount of the purchase price therefore THE FOREGOING WARRANTIES ARE EXCLUSIVE AND A RE GIVEN AND ACCEPTED IN LIEU OF ANY AND ALL OTHER WARRANTIES EXPRESS OR IMPLIED INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTY OF MECHANTABILITY AND THE IMPLIED WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE NEITHER PARTY SHALL BE LIABLE TO THE OTHER FOR ANY INCIDENTAL INDIRECT SPECIAL OR CONSEQUENTIAL DAMAGES Page 5 of 28 DropSense Integration Manual v0 9 TABLE OF CONTENTS Le MACFOGU CH ON A T E
23. l Les J abel Qa wws solvent 0 high_viscosity FALSE dropplate_type DP16 U pathlength double pathlength Measurement directory C DS_measurement Import samples column_source_plate 1 column_source_position 1 column_dropframe_ID 0 column_dropframe_position 1 column_sample_name 2 column_blank_dropframe_ID 3 column_blank_dropframe_position 4 blanking_information 2 blank_dropframe_ID blank_dropframe_position N n add the samples or read them from a file String samples DropFrame 1 A1 blank DropFrame 1 A1 DropFrame 1 C1l samplel DropFrame 1 A1 DropFrame 1 E1 sample2 DropFrame 1 A1 DropFrame 1 G1 sample3 DropFrame 1 A1 DropFrame 2 Bl sample4 DropFrame 1 A1 DropFrame 2 D1 sample5 DropFrame 1 A1 DropFrame 2 F1 sample6 DropFrame 1 A1 DropFrame 2 H1 sample7 DropFrame 1 A1 add the result parameters or read them from a file String result_parameters m Export results Page 24 of 28 DropSense Integration Manual v0 9 column_names DropFrame ID DropFrame Position Sample name Pump Concentration ng ul A260 A280 A260 A280 separator String dropframes int status create DropQuant object DropQuant DQ1 new DropQuant address port if DQ1 DQ_Request_Access lt 0 goto Exit if DQ1 DQ Define_Experiment exp_def samples out dropframes lt 0 goto End for int i 0 i lt
24. n status code 1 no access status code 2 host computer not connected to DropSense status code 3 could not open tray status code 52 tray is moving status code 200 could not connect over TCP 4 3 5 Close Tray Closes the tray Syntax1 Syntax2 Return codes DQ_Close_Tray c closetray a lt address port gt out lt output_path gt status code 0 success status code 4 tray already closed status code 1 no access status code 2 host computer not connected to DropSense Page 21 of 28 DropSense Integration Manual v0 9 e status code 52 tray is moving e status code 200 could not connect over TCP 4 3 6 Get Status This command can be send at all times and will return information about access connection to DropSense tray is moving open closed measurement succeeded failed ongoing If this command is executed during a measurement extra information can be obtained Syntax1 DOQ_Get_Status out String measurement_info Syntax2 c getstatus a lt address port gt out lt output_path gt Return status code see appendix 2 measurement info 4 3 7 Define Experiment Defines the experiment based on two inputs ExperimentDefinition and SampleDefinition These two inputs have specific syntax and give information about experiment name type of measurement material type of disposable samples blanks sample names Syntax1 DQ _Define_Experiment S
25. o i else echo i amp goto end DropQuant_Remote ex c measur a localhost 6300 out c result txt d DropFrame 2 for f i in c result txt do if i 0 echo i else echo i amp goto end statusloop2 DropQuant_Remote ex c getstatus a localhost 6300 out c result txt Page 26 of 28 DropSense Integration Manual v0 9 for f S i in c result txt do if i 31 echo i amp goto statusloop2 else echo i resultsloop DropQuant_Remote ex c getresults a localhost 6300 out c result txt r c results csv p for f resultsloop c result txt else do if amp 6G 2 SSi in Ooa ool echo end c resultparameters txt Si 104 echo i amp goto DropQuant_Remote ex c releaseaccess c result txt do echo a localhost 6300 out c result txt e ool Page 27 of 28 DropSense Integration Manual v0 9 6 Appendix 2 list with status code 0 Successful 1 No access 1 Access already achieved 2 Not connected to DropSense 3 Could not open tray 3 Tray was already open 4 Could not close tray 4 Tray was already closed 5 Tray not in right position 9 Error reading experiment definition 10 Error reading samples 11 No pump profiles found 12 No pump profiles found 13 No samples
26. opFrame refer to the same object All variants are compatible and interchangeable outer dimensions and shape of the input reservoirs is the same The input wells are on same position as the input wells of a standard 96well plate as defined in the SBS standard The shape of the input well is shown in detail in figure 5 Page 9 of 28 DropSense Integration Manual v0 9 Good dispensing of the sample in the input well requires e Avoid contact of the needle with the input well during dispensing e Bring the droplet in contact with the input well during dispensing With these guidelines the 3uL sample will be transferred directly into the input meander The height position of the input well relative to the ground plane is 11 4mm 10mm height of the DropFrame and 1 4mm thickness of the DP16 The instrument includes an internal barcode scanner for reading the barcode This requires that the barcode label is positioned at a specific location on the skirt of the DropFrame the barcode is attached on the longest side of the plate as shown in figure 6 The scanner can read CODE39 and CODE128 codes 4imm 2 mm Figure 6 definition of location for barcode that can be read by the internal barcode scanner in the instrument 2 2 Mechanical references on the instrument In most lab setups the instrument will be mounted on the workbench of a liquid handling robot When loading and unloading the DropFrame to and from the input tray
27. owed are and tab Note if some fields are not defined in the sample definition file then empty string will be in the results file Export results column_names DropFrame ID DropFrame Position Sample name Pump Concentration ng yl A260 A280 A260 A280 separator Table 3 example of results export format file 4 3 Overview of the commands Next is an overview of all functions defined in the API to interact with the DropQuant software All functions return a response to the script with at least the status of the system after executing the requested command Receiving the response from the system does not always mean that the system is ready for accepting new commands For example with DQ_Open_Tray the response is sent when the tray is open after the action After this the system can execute new commands However with DQ_Start_Measurement the measurement is first initialized and a response is sent if the measurement is successfully started or not This way the script is not frozen during the measurement The end of the measurement can be detected using the command DQ_Get_Status In case of using functions through the DLL parameters are sent to the function using arguments In case of the executables the parameters are sent to the executable using text files the path of the text files is part of the prompt Thus the communication is through files Page 19 of 28 Drop
28. pSense Integration Manual v0 9 4 Software integration details 4 1 Installation and initialisation of the integration The API is installed via a separate installer After installation next files are available on the system default installation path is C Program Files Trinean DropQuant API The DLL with the functions for communication with the DropQuant software An executable DropQuant_Remote exe offer a simple interface in case the user script cannot access the DLL functions Note this executable offers a reduced functionality compared to the DLL functions Documentation and examples System requirements The DropQuant program must be running on the host computer There must be at least DropQuant user of type remote When installing the DropQuant software there is standard a login remote with empty password The user with level lab manager can create more logins of type remote A user of type remote must be created on the DropQuant software This can be done by labmanager The NET environment must be installed on the control computer version 2 0 or higher A network connection between host PC and control PC note host PC and controller PC can be same computer then a TCP connection to localhost is used Next start up sequence must be followed to set up a remote connection 4 Power up the instrument and the controller PC Connect the instrument to the controller PC with USB cable Start up
29. rence to the source plate etc e Experiment Definition String text file defining the settings of the experiment such as name of the experiment type of the disposable etc e Results Definition String text file defining the format of the results file The Samples Definition String is a text file with the definition of the samples This file format is the same as used by the import feature of the DropQuant when operated in manual mode It is a table with columns and rows Each row represents one sample in the columns the name position This can be changed in the DropQuant software from settings menu requires service access String in case of DLL functions text file in case of exectuable Page 16 of 28 DropSense Integration Manual v0 9 dropplate type etc of the sample is defined The columns may be random order the Experiment Definition Settings file defines the meaning of the column see next section An example of a sample definition string is shown in table 1 DropFrame 1 Al blank DropFrame 1 A1 DropFrame 1 Bl samplel DropFrame 1 Al1 DropFrame 1 Cl sample2 DropFrame 1 41 DropFrame 1 D1 sample3 DropFrame 1 41 DropFrame 1 E1 sample4 DropFrame 1 41 DropFrame 1 F1 sample5 DropFrame 1 Al DropFrame 1 G1l sample6 DropFrame 1 Al DropFrame 1 H1 sample7 DropFrame 1 Al DropFrame 1 A2 sample8 DropFram
30. the two reference pins to the projection of the middle of the disposable on the reference plane is 425 25mm Lateral position projection of the centre of the disposable on reference plane is in middle of the two reference pins Page 11 of 28 DropSense Integration Manual v0 9 3 Software integration overview and concepts The Trinean DropSense instrument is operated by the DropQuant software running on a host PC This host PC communicates with the instrument using a USB cable The DropQuant software can be used in two modes e inlocal mode the operator defines a measurement starts and analyses the experiment with a few mouse clicks using the integrated graphical user interface The use of the DropQuant software in local mode is explained in detail in the user manual e in remote mode typically if the DropSense instrument is integrated with liquid handling robots in an automated lab environment a script communicates with the DropQuant software and controls the measurement Once the script is running no further user interaction is required for example no need to click to start button to load a new disposable instead the script sends commands to the DropQuant software to open and close the tray The user sets the operation mode of the DropQuant software by choosing remote as login if the software is in remote mode the user interface is disabled and incoming messages will be processed Trinean offers an
31. tring experimentdefinition String sampledefinition out String dropframe_IDs Syntax2 c defineexperiment a lt address port gt out lt output_path gt lt experiment_definition_path gt s lt sample_definition_path gt Return status code see appendix 2 DropFrames returns a string with the list of DropFrame ID s that are defined by the sample definition This list can be used to start the measurement of the DropFrames Note during measurement the system assumes the plate are inserted in the instrument in the order defined in the dropframe_ID string 4 3 8 Start Measurement Starts the measurement based on the DropFrame_ID Every DropFrame should be started by a command To know when the previous measurement is finished use Get Status Syntax1 DQ Measure String DropFrame_ID Syntax2 c measure a lt address port gt out lt output_path gt d lt dropframe_ID gt Return status code see appendix 2 Page 22 of 28 DropSense Integration Manual v0 9 Note if available in the system the internal barcode scanner checks the DropFrame_ID 4 3 9 Abort Measurement Stops the measurement The ongoing measurement will be interrupted by this command Syntax1 DQ _ Abort_Measurement Syntax2 c abort a lt address port gt out lt output_path gt Return status code see appendix 2 4 3 10 Get Results Returns the results of the measurement ResultParameters determines what columns ar
32. utable interface 4 3 2 Request Access Requests the access to the DropQuant program running on the host PC If DropQuant is in Remote mode logged in as a remote user and no other computer has already access then the access will be granted the Remote mode can be interrupted by a local user by clicking on Abort Remote mode no other actions can be taken by a local user Syntax1 DQ1 DQ_Request_Access Syntax2 DQ ex c requestaccess a lt address port gt out lt output_path gt Return codes e status code 0 successful e Status code 1 access already active e Status code 1 no access DropQuant is not in local mode or DropQuant is connected to other computer e Status code 200 could not connect over TCP Page 20 of 28 DropSense Integration Manual v0 9 4 3 3 Release Access Releases the access to the DropQuant program so other remote users can request access Note the DropQuant program remains in remote mode Syntax1 Syntax2 Return codes DQ Release_Access c releaseaccess a lt address port gt out lt output_path gt status code 0 success status code 1 no access status code 200 could not connect over TCP 4 3 4 Open Tray Opens the tray if the tray is not moving Syntax1 Syntax2 Return codes DQ_Open_Tray c opentray a lt address port gt out lt output_path gt status code 0 success status code 3 tray already ope
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