Thermo Scientific appliedbiosystems SeqStudio Flex Series - Page 280

Thermo Scientific appliedbiosystems SeqStudio Flex Series

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5.

Tap Attributes.

6.

Select attributes, then tap Done.

For information on creating custom ﬁelds, see “Deﬁne custom ﬁelds” on page 262.

Chapter 11 Manage library resources on the instrument

File Name Conventions library

11

280

SeqStudio

™

Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Table of Contents

default chapter3
- Table of Contents3
CHAPTER 1 Product Information16
- Product Description16
- Precautions for Use17
- Instrument Components18
- Instrument Interior Components21
- Power and Communication Connections22
- Theory of Operation23
- Preparing Samples23
- Preparing the Instrument23
- During a Run24
- Results24
- Materials for Routine Operation24
- Instrument Consumables Handling, Usage Limits, and Expiration25
- Configuring the Instrument to Prevent the Use of Consumables Beyond25
- Expiration and Usage Limits25
- Important Notice Regarding Use of Consumables that Exceed Supported Limits25
- Buffer Storage, Usage, and Limits26
- Polymer Storage, Usage, and Limits26
- Conditioning Reagent Storage, Usage, and Limits27
- Capillary Array Storage and Usage27
- Hi-DI ™ Formamide Storage and Usage28
- About the Seqstudio ™ Flex Series Instrument Software V1.028
- Profile and Sign in Options29
- Parts of the Software35
- Companion Software49
- Secondary Analysis Software50
- Network Connection Options51
- Network and Password Security Requirements52
- Network Configuration and Security52
- Password Security52
CHAPTER 2 Get Started53
- Sign in53
- Profile and Sign in Options55
- Create a Local Profile (One Time Only)55
- Sign in57
- Switch User or Sign out59
- Sign in (if Another User Is Signed In)60
- Workflow: Create a Plate, Start and Monitor a Run, then View Results62
- Prepare the Instrument64
- Review Upcoming Maintenance64
- Check Consumables Status66
- Check Instrument Status67
- Preheat the Instrument Oven and the Detection Cell68
- Check for Leaks and Spills68
- Check Buffer Fill Levels70
- Replenish Consumables71
- Ensure Proper Installation of CBC Septa71
- Control the LED Light, Speaker Volume, and Screen Brightness72
CHAPTER 3 Prepare the Samples73
- Sample Preparation Guidelines73
- Plate and Strip-Tube Layout75
- Prepare and Assemble Sample Plates76
- Prepare Sample Plates76
- Prepare the Plate Assembly77
CHAPTER 4 Create a Plate File on the Instrument83
- Create, Copy, or Import a Plate File83
- Options for Creating Plate Files83
- Create a Plate File84
- Copy a Plate File85
- Import a Plate File86
- Enter Plate Properties88
- Enter Injection Properties89
- Specify Replicate Injections92
- Enter Sample Names, Sample Types, and Custom Fields93
CHAPTER 5 Create a Plate File in the Plate Manager Software95
- Options for Creating Plate Files in the Plate Manager Software95
- Get Started with the Plate Manager Software (Desktop)96
- About the Seqstudio ™ Plate Manager 2.0 Software (Desktop)96
- Access the Plate Manager Software (Desktop)99
- Parts of the Plate Manager Software (Desktop) Home Screen101
- Connect the Plate Manager Software (Desktop) to an Instrument103
- Get Started with the Plate Manager Software (Cloud)105
- About the Seqstudio ™ Plate Manager 2.0 Software105
- Connect)105
- Access the Plate Manager Software (Cloud)111
- Parts of Plate Manager Software (Cloud) Home Screen112
- Connect Plate Manager Software (Cloud) to an Instrument114
- Set up a Plate File115
- Create or Open a Plate File (PSM File)115
- Enter Plate Properties116
- Enter Sample and Injection Information116
- Save a Plate File119
- Keyboard Shortcuts and Examples121
- Set up Cloud Analysis in the Plate Manager Software (Cloud)124
- Print the Plate Layout125
- Send a Plate File to the Inbox on the Instrument126
- Additional Functions in the Plate Manager Software127
- Load or Download an Example Plate File127
- Specify Replicate Injections (Add Run Module Function)128
- Use the List View in the Plate Tab128
- Define Custom Fields129
- Save a Plate File in CSV Format129
- Export or Download a Plate File in PSM Format129
- Manage the Software131
- Load and Unload a Plate136
- Load a Plate into the Instrument136
CHAPTER 6 Start and Monitor a Run138
- Unload a Plate from the Instrument139
- Link a Plate File and Start a Run140
- Unlink a Plate File144
- Processes that the Instrument Performs During a Run144
- Pre-Run Check Messages and Plate Alerts During a Run146
- Pre-Run Checks When a Plate Run Starts or a Re-Injection or a Cancelled Injection Is Added to the Run Queue146
- Pre-Run Checks before each Injection or When a Paused Run Is Resumed146
- Run Plates with the Automated Barcode Workflow147
- Create the Plate Files before the Barcoded Plates Are Loaded into the Drawer147
- Pre-Run Checks and Plate Alerts in an Automated Barcode Run149
- View Alert and Notification Details149
- Auto-Spectral Calibration During an Injection150
- Auto-Spectral Calibration Overview150
- Auto-Spectral Calibration Requirements151
- Auto-Spectral Calibration Results152
- View Real-Time Results in the Home Screen153
- Pause the Instrument in the Home Screen157
- Use the Run Queue to Monitor a Run on the Instrument160
- Parts of the Run Queue Screen160
- View Real-Time Results in the Run Queue Screen162
- Change the Injection List Order163
- Cancel or Add Injections or Specify Re-Injections in the Run Queue Screen165
- Pause the Instrument in the Run Queue Screen166
CHAPTER 7 View Results on the Instrument169
- Options for Viewing Results on the Instrument169
- View Results for a Completed Run (Run History)170
- Export Results from the Instrument-Results and Data Files, Logs, and Reports171
- Sample QC and Quality Alerts172
- Use the Electropherogram Screen173
- Sequence Analysis Results175
- Parts of the Sequencing Electropherogram Screen175
- Sequencing Results and Well Details176
- Understanding Quality Values (Qvs)178
- Fragment Analysis Results179
- Parts of the Fragment Analysis Electropherogram Screen179
- Fragment Analysis Results and Well Details180
CHAPTER 8 Use the Remote Monitoring Software to Monitor Runs182
- View Results, and Use Cloud Analysis182
- Monitor a Run from the Remote Monitoring Software182
- Open the Remote Monitoring Software from the Plate Manager Software (Cloud)182
- Open the Remote Monitoring Software from the Instrumentconnect Software183
- Parts of the Remote Monitoring Software Home Screen184
- Plate File Requirements for Viewing Analyzed and Cloud Results187
- View Instrument Notifications in Your Thermo Fisher ™ Connect Account188
- Set up Email Notifications from the Instrument189
- View Real-Time Results in the Remote Monitoring Software190
- Sequencing Results192
- Fragment Analysis Results192
- Cancel Injections or Specify Re-Injections in the Remote Monitoring Software192
- Instrument Home Screen193
- Monitor a Run from a Mobile Device193
- Register the Instrument with the Instrumentconnect App193
- Monitor a Run from a Mobile Device195
- View Results in the Remote Monitoring Software198
- View Results for a Completed Run in the Remote Monitoring Software198
- History Tab)198
- Export a Results Report from the Remote Monitoring Software201
- Download Results from the Remote Monitoring Software201
- Viewing Spectral Calibration or Install Run Results in the Remote202
- Monitoring Software202
- Use Cloud Analysis in the Remote Monitoring Software202
- Automated Cloud Analysis with Secondary Analysis Software202
- Workflow: Cloud Analysis203
- Set up Cloud Analysis for a Completed Run in the Remote Monitoring Software205
- Access Cloud Analysis Results from the Remote Monitoring Software207
- Connect210
CHAPTER 9 Use the Instrument with Thermo Fisher211
- Overview of Thermo Fisher ™ Connect Features211
- Administrator Set up for Thermo Fisher ™ Connect211
- Overview of Thermo Fisher211
- User Set up for Thermo Fisher ™ Connect212
- Local Profile and Cloud Profile: When to Use, User Name, and User Initials213
- Sign in to Apps.thermofisher.com and Access the Instrumentconnect Software215
- (Recommended) Link Directly to Your Thermofisher.com Account217
- Link a Local Profile to Your Thermofisher.com Account (One Time)220
- Sign in to the Instrument with a Cloud Profile222
- Re-Link the Instrument to Your Cloud Profile223
- Disconnect the Instrument from Your Cloud Profile224
- Change Your Cloud Profile PIN225
- Set up Email Notifications from the Instrument226
- Tasks for the Cloud Administrator of an Instrument228
- Enable or Disable Thermo Fisher ™ Connect Access on the Instrument228
- (Administrator Only)228
- Thermo Fisher ™ Connect Cloud Administrator Functions229
- Manage the Users and Administrators of Your Instrument229
- Change the Instrument Name in the Instrumentconnect Software230
- Administrator Only)230
- For more Information on Using Thermo Fisher ™ Connect231
- Connect231
- Use Voice Commands231
- Enable (Register) the Voice Command Function231
- Disable the Voice Command Function232
- Use Voice Commands232
- Basic Voice Commands234
- Interactive Voice Command-Start Run234
- Microphone Icon235
CHAPTER 10 Use the Instrument with the Security, Auditing, and E-Signature (SAE) V2.1 Module238
- Overview of the Security, Auditing, and E-Signature (SAE) V2.1 Module Components238
- Configuring the SAE Module and Setting Permissions239
- Functions that Are Not Available When the SAE Module Is Enabled240
- Enable SAE Mode on the Instrument and Specify the SAE Server (Administrator Only)240
- Disable SAE Mode on the Instrument (Administrator Only)243
- Sign in to the Instrument with SAE Enabled244
- Audit Reason Requirements245
- E-Signature Requirements for Starting a Spectral, Install, or Regular Run245
- Signing an Object before a Regular Run Is Started246
- Signing an Object When a Regular Run Is Started247
- Signing During an Automated Barcode Run249
- Displaying Signatures249
- Use the Instrument When the SAE Server Is Offline250
- SAE Error Messages and Actions251
CHAPTER 11 Manage Library Resources on the Instrument252
- Overview of Libraries253
- General Library Procedures255
- Create a New Entry from a Factory-Provided or Locked Entry255
- Lock or Unlock a Library Entry255
- Copy a Library Entry255
- Edit a Library Entry256
- Import a Library Entry256
- Export a Library Entry256
- Filter Library Lists257
- Delete a Library Entry258
- Plate Files Library258
- Plate File Definition258
- Create a Plate File259
- Define Custom Fields262
- Export or Delete a Plate File264
- Import a Plate Setup from a CSV or PSM File264
- Plate File Properties Tab265
- Plate File Plate Tab267
- Plate File Edit Injection Properties Screen268
- Plate File Edit Well Properties Screen (Sample Name Entry)271
- Run Modules Library272
- Run Module Overview272
- Run Module Provided272
- Create a New Run Module272
- Run Module Settings273
- Size Standards Library275
- Size Standard Overview275
- Size Standard Definition Files Provided275
- Create a New Size Standard276
- Modify a Factory-Provided Normalization Size Standard277
- Size Standard Normalization Feature278
- File Name Conventions Library278
- File Name Convention Overview278
- Create a New File Name Convention279
- File Name Convention Settings282
- Injection Protocols Library283
- Injection Protocol Overview283
- Create a New Injection Protocol283
- Injection Protocol Settings284
- Dye Sets Library285
- Dye Set Overview285
- Create a New Dye Set285
- Create a Custom Dye Set286
- Dye Set Settings286
- Analysis Settings Library288
- Analysis Settings Overview288
- Create a New Analysis Settings289
- Analysis Settings-Sequencing291
- Analysis Settings-Fragment Analysis295
- Results Groups Library301
- Results Group Overview301
- Create a New Results Group302
CHAPTER 12 Run Calibrations and Install Checks304
- Run a Spatial Calibration304
- Spatial Calibration Overview304
- When to Perform a Spatial Calibration304
- Perform a Spatial Calibration305
- Evaluate the Spatial Calibration Results306
- Example Spatial Profiles308
- Export Spatial Calibration Results or Report309
- Run a Spectral Calibration310
- Overview of Spectral Calibration310
- When to Perform a Spectral Calibration311
- System Dye Sets Versus Custom Dye Sets312
- Using Bigdye312
- Estimated Spectral Calibration Run Times313
- Prepare for Custom Dye Set Spectral Calibration314
- Prepare for Spectral Calibration314
- Perform a Spectral Calibration316
- View Spectral Calibration Results317
- Example Spectral Calibration Data324
- Export Spectral Calibration Logs or Report325
- View and Export the Spectral Calibration History326
- Perform an Install Run328
- Overview of Install Run329
- When to Perform an Install Run329
- Estimated Install Run Times330
- Prepare for the Install Run330
- Perform an Install Run333
- View Sequencing Install Run Results334
- View Fragment Analysis Install Run Results347
- View, Export, or Delete an Install Run History352
CHAPTER 13 Maintain the Instrument354
- Maintenance Schedule354
- Review Upcoming Maintenance355
- Daily Instrument Maintenance Tasks356
- Monthly Instrument Maintenance Tasks357
- Annual Planned Maintenance Tasks358
- As-Needed Instrument Maintenance Tasks358
- Maintenance Wizard Overview359
- Clean the Instrument361
- Export Consumables Log Files363
- Install Buffers (Wizard)363
- Install the Anode Buffer Container (ABC)364
- Install the Cathode Buffer Container (CBC)367
- Replenish, Change, Flush, and Store Polymer (Wizards)370
- Precautions for Use370
- Replenish Polymer or Change Polymer Type (Wizard)370
- Store Partially Used Polymer371
- Change and Store a Capillary Array (Wizards)371
- Parts of the Capillary Array372
- Install or Change the Capillary Array (Wizards)374
- Store a Capillary Array375
- Maintain the Pump (Wizards)376
- Parts of the Polymer Delivery Pump376
- Avoiding Damage to the Pump Assembly377
- Remove Bubbles from the Polymer Pump (Wizard)377
- Wash the Pump Chamber and Channels (Wizard)379
- Flush the Water Trap (Pump Trap)379
- Shut Down, Move, and Reactivate the Instrument381
- Shutdown the Instrument (Wizard)381
- Move and Level the Instrument381
- Reactivate the Instrument (Wizard)382
- Maintenance Wizard Procedures382
- Change Capillary Array Maintenance Wizard382
- Change Polymer Type (with Change Array Option) Maintenance Wizard394
- Fill Array with Polymer Maintenance Wizard409
- Remove Bubbles Maintenance Wizard409
- Spatial Calibration Maintenance Wizard412
- Replenish Buffers Maintenance Wizard413
- Wash Pump and Channels Maintenance Wizard415
- Replenish Polymer Maintenance Wizard417
- Shut down Instrument Maintenance Wizard420
- Reactivate Instrument Maintenance Wizard427
CHAPTER 14 Manage the Software (Instrument)439
- Connect the Instrument to a Computer or Network (Hardware Connections)439
- Wired and Wireless Network Options439
- Wired and Wireless Network Connections on the Instrument440
- Antivirus Recommendations for Direct Connection of the Computer to440
- The Instrument440
- Connect the Instrument Directly to a Computer441
- Connect the Software to a Network Drive (Software Settings)443
- Determine the IP Address for a Computer on a Network443
- Create Folders and Enable Network Folder Sharing444
- Connect the Instrument to a Network Drive (Software)445
- Manage Sign-In Profiles446
- Local Profile Roles (Standard and Administrator) and Functions446
- Change the Role of a Local Profile (Administrator Only)447
- Edit Your Own Local Profile447
- Delete a Local Profile or a Cloud Profile from an Instrument (Administrator Only)447
- Create a Local Profile (One Time Only)448
- Change Your Own Local Profile PIN451
- Manage Settings452
- Display Instrument Hardware and Software Information452
- Configure Consumables Usage and Warnings (Administrator Only)453
- Set up Email Notifications from the Instrument454
- (Administrator Only)455
- Enable and Set up Demo Mode457
- Enable/Disable the Internal Barcode Reader (Administrator Only)459
- Set the Power Save Duration (Administrator Only)459
- Connect Access on the Instrument460
- (Administrator Only)460
- Manage Instrument Settings461
- Change the Instrument Name (Administrator Only)461
- Manage Date and Time Settings462
- Update the Software (Administrator Only)462
- Manage the Network Configuration (Administrator Only)464
- Select a Language465
- Configure, Check Status, and Cancel Background Exports and Backups465
- Set the Default Save Location for Results468
- Manage Storage Space468
- Automatic File Cleanup (Autopurge)468
- Export Results from the Instrument-Results and Data Files, Logs, and Reports469
- Delete a Run History469
- Back up User Data (Instrument Settings, Library Items, and Results)470
- (Administrator Only)470
APPENDIX A Troubleshooting471
- Troubleshooting Workflow472
- Troubleshooting Resources473
- Use Smart Help to Request Assistance from Technical Support or Instrument Service473
- Start a Remote Support Session475
- Inspect the Data-Troubleshooting Procedures476
- View the Raw Data and the EPT Plot476
- Check Size Standard Quality (Fragment Analysis)476
- Monitoring Software478
- Inspect the Instrument -Troubleshooting Procedures480
- View the Instrument Sensor Details and EPT Plot480
- Check the Pump for Bubbles or Debris480
- Additional Troubleshooting Procedures482
- Export Troubleshooting Logs482
- Check the Position of the Cathode Buffer Container (CBC)483
- Use the Manual Commands Function to Move Instrument Components483
- Proximity Sensor485
- Power off or Power on the Instrument485
- Instrument Interior Components487
- QC Error and Alert Troubleshooting489
- QC Errors-Sequencing and Fragment Analysis489
- QC Errors-Sequencing490
- QC Errors-Fragment Analysis490
- QC Errors-Spectral Calibration (Manual)492
- QC Errors-Sequencing or Fragment Analysis Install Run494
- Cloud Analysis Troubleshooting495
- Consumables Troubleshooting495
- Home Screen and General Instrument Software Troubleshooting496
- Install Run Troubleshooting498
- Instrument Troubleshooting499
- Library Troubleshooting500
- Maintenance Wizard Troubleshooting501
- Plate Troubleshooting501
- Plate File Troubleshooting501
- Plate Manager Software Troubleshooting502
- Remote Monitoring Software Troubleshooting505
- RFID Troubleshooting507
- Run Troubleshooting507
- Plate Alert Troubleshooting507
- Plate Alert Troubleshooting (Automated Barcode Workflow)509
- Run History Troubleshooting511
- Run Queue Troubleshooting511
- SAE Troubleshooting511
- Sample and Data Troubleshooting512
- Sequencing and Fragment Applications513
- Sequencing Applications517
- Fragment Analysis Applications519
- Settings Screen Troubleshooting519
- Sign in Troubleshooting520
- Software Troubleshooting521
- Spatial Calibration Troubleshooting522
- Spectral Calibration Troubleshooting523
- Thermo Fisher ™ Connect Troubleshooting524
- Voice Command Troubleshooting525
APPENDIX B Run Modules and Dye Sets526
- Run Modules, Read Lengths, Size Ranges, and Run Times526
- Dye Sets530
APPENDIX C Instrument Specifications531
- Instrument Dimensions and Clearance531
- Operating Specifications533
- Environmental Requirements533
- Electrical Requirements534
- Wired and Wireless Network Options and Requirements535
- Network and Firewall Requirements536
- Power and Communication Connections537
APPENDIX D Catalog Numbers539
- Plates Bases Retainers and Septa539
- Instrument Consumables540
- Sequencing Analysis Reagents and Consumables540
- Fragment Analysis Reagents541
APPENDIX E Radio Frequency Identification (RFID) Technology542
- RFID Precautions for Use542
- Locations of RFID Read/Write Units543
- RFID Function543
- RFID Specifications544
- RFID Troubleshooting545
- Symbols on this Instrument546
APPENDIX F Safety547
- Standard Safety Symbols547
- Location of Safety Labels547
- Control and Connection Symbols549
- Conformity Symbols550
- Safety Information for Instruments Not Manufactured by Thermo Fisher Scientific550
- Instrument Safety550
- General550
- Physical Injury551
- Electrical Safety552
- Cleaning and Decontamination553
- Instrument Component and Accessory Disposal553
- Laser Safety554
- Safety and Electromagnetic Compatibility (EMC) Standards554
- Safety Standards555
- EMC Standards555
- Environmental Design Standards556
- Radio Compliance Standards556
- Chemical Safety558
- Biological Hazard Safety559
APPENDIX G Documentation and Support560
- Related Documentation560
- Customer and Technical Support561
- Limited Product Warranty561
- Index562

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