User Manual
Contents
1. Instrumentation Group BioSAXS Sample Changer User Manual Author Alexandre Gobbo Revision 1 0 0 Date 22 02 2012 Table of Contents Functionality Introduction Plate Loading Commands Graphical User Interface Side Bar Control Bar Status Bar Tabs Samples Tab Commands Tab Temperature Tab Fluid Tanks Tab Logs Tab Alarms Tab Advanced Tab Menus File Menu Devices Menu Help Menu EMBL 10 10 u u 2 12 14 14 15 16 Functionality Introduction The BioSAXS Sample Changer is a machine conceived to Temporally store liquid samples in plates or strips Transfer the samples to a pod for them to be exposed to X rays and optionally recuperated Clean itself the needle tubings and capillary in order to load samples with no contamination Control the temperature of the samples in the storage plates and also on the exposure pod The user can set the sample viscosity low medium or high used for adjusting the machine parameters and type green yellow or red Yellow samples can be used but not recuperated Red samples are not acceptable for automatic transfer they must be handled manually All functionality can be remotely accessed by the beamline control but also commanded by the Sample Changer s own graphical user interface Plate Loading The first step for the user is to load their sample plates into the Sample Changer by clicking the Load Positio2. Save Animation 5 section o access ee User or Administrator requires password User Preferences Software Configuration changes the stare configuration or administrative purposes only EN anman The User Preferences dialog allows users to Change parameters typically set by the beamline such as the sample type and viscosity level These parameters are considered for remote commands Enable plate barcode scanning the checkbox should be set if the plates have barcode that should be read when plate table goes to park position Enable sample detection volume in wells always checked unless the liquid detection sensor shows a problem Enable spectrometer read during sample load if the information is not needed it should remain unchecked because it slows down the sample loading Disable the alarm monitoring The Allow Critical Alarms checkbox should always be unchecked In situations such as when there is a sensor problem and the software is blocked in Alarm status then the user can check Allow Critical Alarms to unblock the machine Attention in this case because no other relevant alarm will be monitored Disable interlocks The Enable Interlacks checkbox should be always kept checked If the software displays interlocked status and cannot move disabling the interlock may be a temporary workaround to unblock the machine 14 gi Var Peto 1 samc Tyne ena en aia
3. Loan ub 20967680 ventende enean sen piate beresdes Zl Detect samp velinin wale Elend pestmet dra scene 3 cra arne Flere inc Devices Menu 1D icsaNS Semple Chorger File Hep The Devices menu presents forms for tuning and configuring each individum device of the system Valves This menu is fr administrative Pumps purposes and should not be used by Light amp Focus at users Table X Tabie Y TebleZ Exposure Temperature Storage Temperature Spectrometer Plate Table Sample Path Cleaning Station 15 Help Menu TE BiosANS Sample Changer Help Contents Inspector Open the user documentation An ap lcation debugger or administrative purposes ony 16
4. change temperature setpoints and start stop the thermostat circulator 10 EMBL Fluid Tanks Tab Sapa commands rampen sd en Logs Aare Avance ud Level arms Hetory Chart Vater Level 100 ay Ox Wate Leet poten lavt Was Lovet This tab presents the level of the fluid tanks during the past 24 hours It can help to identify anomalies Logs Tab Sarp Caen Tenperatu Fran Les are advanced mme mme levd Ono Descipton un fe MFO onder terge 4 zamana 15 50 45 MeO contier nt Senge 202 12 sts MED Conroe set syne Va posten maut 5703 12 lisana MEO Conte fet Synge prance bedst 2102 12 255006 MFO Conrcler Set Over fon Venturi site true ziana isso eo Coneaer lntperetc vister Pure aaja fen MFO onder rit Perside Dicer Rap marte 55047 MeO Conealer PLC Ste RUNING ipaa 5502 meo Conoler set Overfon Verste aaja hisas NEO Concer Rese deena san morte fissa MFO Conraler rot spt py erdes Ret vaker OX zima sso mro Conroe stare ready Frans fs as jore font fem ache Gen vem Espe The Log Tab displays the application logs which are also written in daily log files Each log has a timestamp a level fine info warning severe an origin server interface controller and a description Color scheme Black normal logs informational Yellow warning level Red severe level 1 EMBL
5. washes rinses and dry the needle tubings and capillary The timings are automatically set according to the viscosity It is possible to execute this command with modified times for instance a drying operation can be performed by setting the wash and rinse times to zero Transfer The sample changer can realize pipetting operations A given volume of sample can be transferred from a well to another If the destination well contains sample then the depth of liquid is detected inside the destination well While releasing the pipetted sample the needle moves up in order to push all the transferred volume along the depth of the destination sample The purpose isto let the contents reasonably mixed Execute a thorough mixing typically after a transfer A given sample volume Is pipetted in and out the well a certain number of cycles EMBL Graphical User Interface The following picture presents the components of the Sample Changer main window These components are detailed in the next sections Gom sane EMBL The application interface can be used in the touch screen by the robot or remotely by a KVM or VNC solution The main uses for the touch screen are Assist the user loading plates inside the robot Load Position and Scan and Park buttons Display the overall machine state and alarms The Samples tab displays a representa
6. Alarms Tab a Tate Ams aad age eal onga Terpin unanaz 50 feonecter lnc te leves ZEZE sos EE concer iar Snare Hat pedig 270272 20 niste ero sem suter renga aed aT This tab shows the application alarms Alarms are unexpected events with a time span associated Some alarms can block the application and make the overall state change to Alarm or Error Color scheme Red Alarms still active not yet acknowledged by user Magenta Alarms still active already acknowledged by user Blue Alarms already inactive but not acknowledged Black Alarms inactive and acknowledged A blinking signal ALM on the Status bar is displayed if there is at least one active not acknowledged alarm Alarms are acknowledged by double clicking the alarm table Advanced Tab Sarees Corman Tepe rid Tanks Logs Ans Adon sep Con This tab allows the execution of advanced tasks 2 Panel Description Scripts Execution of scripts for administrative purposes only Control start stop the machine controller fr administrative purposes only Syringe Direct control of the syringe used for testing purposes Calibration Tasks normally done during beamline setup by the beamline responsible Auto focus Calibration of light Needle locating Full calibration calibration of focus light determination of tubings dead volume and image
7. ks can be triggered by drag and drop operations dragging a sample to the capillary will load it Dragging the capillary to a well will recuperated it in the respective well Dragging a sample to another will perform a transfer operation The sample volume and viscosity considered for these manual commands are those indicated on the command box on the right Color scheme Samples that were not loaded since last plate scan are drawn gray Samples that were already loaded are drawn blue The sample currently loaded is drawn in bright blue The selected sample is highlighted So it it s row and column EMBL Commands Tab Fo 555 renne Pal Ta 109s Arme Advance Saree toat sarpe uricad sampler mang Petra Dive gt BE Tine This tab presents the commands with a finer control of the parameters For example one can override the default setting for viscosity and Clean the tubings choosing different timings for washing rinsing and drying Fill or recuperate the sample at any speed Furthermore this tab contains the mixing command not present in the Samples tab Temperature Tab Sarake Cannan Tenpera Fiaa Taria Leos Aims Advanced Storage Tenceratre Expose Tenseratire semen Sapone in m frem TER vane Frasen serge terpet boere Tempore This tab displays a graph of the storage and exposure temperatures in the past 10 minutes It has controls to
8. r button on the application side bar and opening the cover once the plate table stops The plates or stripes should be loaded into the thermal supports The Sample Changer has three slots for plate supports 4x 843 PCR strip wells THERMO FAST 96 well plate SBS 96 Deep well plate NOTE Attention to use only standard consumables NOTE The plates should be inserted correctly in their slots The stripes should be inserted completely If they are not then the Sample Changer will refuse the loading when scanning for sample overlap After loading the plates the user must close the cover and press Scan and Park button Commands This is a list of the basic Sample Changer commands Fil Toad a given volume of sample from a well The loading speed is determined based on the current viscosity The liquid is detected when reach the pod and the syringe is stopped when the meniscus is just after the beam mark Flow Samples can be flowed during the data collection time to avid damage The speed is calculated in function of the loaded volume The meniscus at the end of the sample is detected and in case it is about to touch the beam mark the syringe is stopped not to let air into the beam mark Recuperate loaded sample can be recuperated to a given well The speed is determined based on the current viscosity Clean The sample changer must be cleaned before a new sample Is leaded The Clean command
9. scaling Tools Scan Supports should be executed only by the beamline responsible when the type of sample supports changes NOTE IF f the support changes and is not scanned or properly configured then collision may occur Scan Plates repeat the scan for plate barcodes If this option is selected in User Preferences plate barcode are always scanned when Scan and Park is pressed This command can be used if a barcode is hard to read and have not been detected in the first try Light Allows controlling the light there are 10 predefined levels but the ideal one is the middle of the range for which we have more contrast NOTE In normal operation should be set to the middle of the range Focus There are three predefined positions Near Middle and Far Middle focus the middle of the capillary and is ideal for liquid detection Near and Far focus both capillary walls and is useful to check ifthe walls are dirty NOTE In normal operation should be set to Middle 13 EMBL Menus In normal operation the access to menus is not required It is important mostly to administrative tasks and tests File Menu Access Level F Th SAAS Sample henge pen yo Fie Devices Hep m ESSEN Open Log Fil go Opens sert hle lr administrative purposes ony Open Alarm File _ z m Open Script File Opens an image fe Open Image File TJ el age Save Snapshot As J saves vide animation
10. te the table position Yellow i the machine cover it open it must be closed after loading the plates spay the sample type law green or red EMBL Control Bar estat button ck to restart the machine contrat Abort the ongoing task am stops ali maters sr put the devices back somes tus md ove henge on Sam taian ened speed for manual Regulate gud postion In the case the miarat ig won t stay fue after loading due to thermal effects press ths button to keep it in postien he meniscus must be visitis NOTE The contemation dislag pes the choice to restart also the hardware I may be needed flowing a power ft the hardware is also ented then the sample Inthe tubing wil be lost en Status Bar m ETA The machine status a textual representation ofits overal state Gray if machine isin error state stoped it ready for commande Moving if currently exciting tsk EMBL Tabs Samples Tab Sans Commande Free Pud Tarka toge as area ots ske samde latin LETE 000 Ss vane FBE are Gon se 00000 00000 Z 00000 00000 The Samples Tab presents simplified access to most common user operations Each sample well is drawn as a circle having indication of row and column A sample can be selected by clicking over it or touching it in the touch panel A selected sample then can be loaded recuperated or flown using the litle command box on the right Tas
11. tion of the existing sample supports In order to make it easier the visualization of a plate it can be maximized by double clicking its name see figure below All three plates are shown back by double clicking again the plate name This is useful for drag and drop operations see Samples Tab section TI EIE ss en mere Terese os me oe 419800 rene Side Bar EMBL This bar presents the main indications of the machine state Machine errors will be displayed with red The only commands in the side bar are the positioning of the table to the plate load position and back to the parked position the only operations that should be done inside the experimental hutch lid Tarke Gad ar 50 20 Storage Tenperstire raw Brpoaure Temperaire Tatie Postion Ore cover sae Qo EE PES Overal status ofthe robot tis displayed in redi here an error exposure eal vacuurn stati not ok displays then red This ia ene signal nok ak the beamline commanded the The current leve ot Mud tanks Display red i empty in the case ot detergent and water or full inthe case of waste The current storage temperature Displays yellow Idd not reach The current exposure temperature Displays yellow dit nat reach the desrd setpoint vet Move the table t the plate load position Scan the plates and move the table 10 parked position under the cover Indica
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