Thermo Fisher Scientific DynaChip Software Owner's manual

Brand: Thermo Fisher Scientific

Model: DynaChip Software

Type: Owner's manual

DynaChip™

Software

Manual

Software Version 1.1.x

Rev 002

DynaChip Software v1.1.0 Manual Page 2

-2 -

Contents: Page

Section 1. Software Overview ....................................................................... 4

Loading the software ......................................................................................... 4

First-time installation.......................................................................................... 4

Upgrade installation - Database Upgrading........................................................... 4

Using the software............................................................................................. 5

Software Summary ............................................................................................ 7

Overview – Browse Menu ................................................................................... 9

Making changes: ............................................................................................... 9

Browse Patients:...............................................................................................10

Browse Requestors: ..........................................................................................10

Browse Samples: ..............................................................................................11

Browse Tests: ..................................................................................................12

Browse Runs:...................................................................................................13

To Finalise a Run ..............................................................................................13

To Import data.................................................................................................13

To print a Report ..............................................................................................13

Editing a Run: ..................................................................................................14

Browse Frequencies – Population tables for vPRA ................................................15

Section 2. Workflow .................................................................................... 16

Overview – Wizards Menu .................................................................................16

Test Wizard - overview......................................................................................16

Finalising a Run and generating a worksheet.......................................................18

Assay steps:.....................................................................................................22

Alarms during assay..........................................................................................22

End of Assay ....................................................................................................23

Run Imports.....................................................................................................23

Section 3. Analysing Data............................................................................ 24

Specificity Tab..................................................................................................24

aPRA ...............................................................................................................25

vPRA ...............................................................................................................25

Masked Antigens ..............................................................................................25

Substance Tabs ................................................................................................26

Searching for HLA antigens................................................................................27

Working with spots and cut offs.........................................................................27

Statistics Tabs ..................................................................................................29

Antigen Table...................................................................................................29

Excluding antigens............................................................................................29

Tail analysis Tab...............................................................................................30

Basis of Tail analysis:........................................................................................30

To use Tail analysis: .........................................................................................30

Reports............................................................................................................31

Section 4. Administrative Features ............................................................. 33

Users...............................................................................................................33

Updates ...........................................................................................................33

Settings ...........................................................................................................33

System Registry................................................................................................33

User Registry Overrides.....................................................................................34

Security Settings...............................................................................................34

DynaChipTM Processor .......................................................................................34

Manual control..................................................................................................35

DynaChip Software v1.1.0 Manual Page 3

-3 -

Section 5. Tips and FAQs ............................................................................. 36

Tips:................................................................................................................36

Sorting.............................................................................................................36

Frequently Asked Questions...............................................................................36

Troubleshooting................................................................................................38

DynaChip Software v1.1.0 Manual Page 4

-4 -

Section 1. Software Overview

Loading the software

The DynaChipTM software can be launched from the shortcut which should be installed on the

desktop of the computer. Alternatively, the program is at C:/Program files/Dynal/DDS/DDS.exe

The program will start up with a splash screen that displays which version number is being

used:

First-time installation

If this is the first time the software has been installed, then a new database should have been

created. However, a newly created database does not contain any product information or

antigen frequency data. To apply these, see ‘Updates’ in section 4 of this manual. The update

files can be found on the software installation CD in the folder ‘Updates’. Product updates for

newly released batches and products are supplied on CDs in the relevant kits.

Upgrade installation - Database Upgrading

Part of the new version of the software is that changes have been made to the database

structure. If the software is being run connected to an old database, an error message will

occur:

Selecting ‘Yes’ opens the Database Settings dialogue box:

DynaChip Software v1.1.0 Manual Page 5

-5 -

Ensure that the correct database is selected, and then select the ‘Upgrade’ option. This will

apply the updates to the existing database – no changes will be made to existing data.

Note that once a database has been upgraded, all copies of the software that connect to this

database will also need to be upgraded – different versions cannot share the same database.

Using the software

The screen will open showing the options to Login or Exit – no work can be performed without

a user logged in. Using the settings option under the Administration menu, the database to

connect to can be chosen, if not currently set correctly.

When the user clicks on Login, a dialogue box will open

DynaChip Software v1.1.0 Manual Page 6

-6 -

The correct user name should be chosen from the drop-down menu, or typed into the top box,

and then the password entered. Users can be set up with different privilege levels – either

‘User’ or ‘Supervisor’ or ‘Administrator’. These levels affect the access of the user to advanced

features within the software.

NB – The first time the software is used, ‘Administrator’ will be the only available option, and a

password will need to be set. Passwords are case sensitive.

To create new Users, login as an Administrator-level user. Only these users can access the

Browse Users screen, where users can be added, disabled or deleted.

DynaChip Software v1.1.0 Manual Page 7

-7 -

Software Summary

The DynaChipTM Software is based around an SQL Server database. The database stores results

from individual Tests – each Test relates to one DynaChipTM, and these are the basic units of

the database.

Each Test must be linked to a Sample. Several Tests can be linked to the same sample – e.g. if

a repeat test is required, or a titration. Samples can also be linked to a Patient, although this is

not strictly necessary. Several Samples can be linked to a Patient – i.e. samples taken over a

period of time.

Each Test must have a Product associated – at the time of writing, there is only one Product

released, but it may be possible in the future to choose between, for example, Screening,

Specificity or Single antigen Products.

At the time of creation, each Test automatically includes the details of the User logged on.

Each Test can also have a Requestor – e.g. name of the Doctor or Clinician or Department

requesting the test be carried out.

Tests must be placed in a Run, and the Run must be finalised to be performed on the

DynaChipTM Processor. The Test location in the plate and the User who finalised the Run are

also recorded.

Once a Run has been performed, the raw data is added to the Test by importing. The User who

imports the data is recorded.

The data is then viewable through the software. Statistical tests are carried out to determine a

list of possible specificities, and the final reviewed specificity is recorded.

Specificities and data can be printed out or saved as PDF files for record-keeping.

DynaChip Software v1.1.0 Manual Page 8

-8 -

Workflow:

The software is also designed to enable use of macros, written in JScript or VBScript. The use

of these macros would permit transfer of data between LIMS systems or Microsoft Excel and

the DynaChipTM software. For more detail on parameters needed to write these macros, please

contact your local sales representative or Technical Services (eurotech@invitrogen.com).

DynaChip Software v1.1.0 Manual Page 9

-9 -

Overview – Browse Menu

All the layers of data stored in the database can be accessed from the Browse Menu.

The first five items in the ‘Browse’ menu open up a date-filtered view of the stored data, with

the Filter Options tab at the top left of the view. To see an alternative subset of the data in the

database, open the Filter Options tab by moving the mouse over it, and enter the details to

filter with. To see all data in the database, use the ‘Clear’ button.

Making changes: All Users can edit data. To ensure database integrity, Tests cannot be

deleted once created, and for other types of records, only un-associated data can be deleted.

The final item – ‘Browse Frequencies’ – opens a view of data which is only editable by

Administrator-level users.

In all views, changes made are not implemented until the record is saved – by clicking the icon

of the disk with a blue arrow.

To discard changes, click instead the icon with a red cross.

DynaChip Software v1.1.0 Manual Page 10

-10 -

Browse Patients: Opens a list of Patients. Details of Patients can be seen, and the list can

be filtered based on any of these details by using the ‘Filter Options’ tab in the upper left of the

window. Any Patient record can be opened by selecting the Edit icon, or by double-clicking the

record.

Opening a Patient record shows three tabs:

Patient Details allows editing of details, and addition of any comments.

Sensitising Events allows entering of patient genotype and any data about sensitising events.

Patient Samples allows viewing and opening of any samples associated with that Patient.

Note: Not all samples will have a Patient associated, as there is no requirement.

Browse Requestors: Opens a list of Requestors. Opening a Requestor record allows

viewing of details associated with that Requestor.

DynaChip Software v1.1.0 Manual Page 11

-11 -

Browse Samples: Opens a list of Samples. Details of Samples can be seen, and the list can

be filtered based on any of these details by using the ‘Filter Options’ tab in the upper left of the

window. Any Sample record can be opened by selecting the Edit icon, or by double-clicking the

record.

Opening a Sample record shows two tabs:

Sample Details allows editing of details and addition of any comments. In addition, an

existing Patient can be associated to the Sample.

Test Details allows viewing and opening of any Tests associated with that Sample. In addition,

a new Test can be requested on the Sample.

DynaChip Software v1.1.0 Manual Page 12

-12 -

Browse Tests: Opens a list of Tests. Details of Tests can be seen, and the list can be filtered

based on any of these details by using the ‘Filter Options’ tab in the upper left of the window.

Any Test record can be opened by selecting the Edit icon, or by double-clicking the record. This

view has many columns (more than viewable at once on most screens), the order of which can

be changed by dragging using the mouse.

Tests have a status flag:

Unlisted – Test exists, and is currently editable, but is not currently attached to a Run. This

can be done using an ‘Edit Run’ screen.

Listed – Test is attached to a Run, but is still currently editable

Finalised – Test is attached to a Run which has been finalised, and is therefore not editable.

However, results have not yet been returned from the DynaChip Processor.

Analysed – Test has been carried out, and results are available for review. To view results

open the Test and choose the Results tab.

DynaChip Software v1.1.0 Manual Page 13

-13 -

Browse Runs: Opens a list of Runs. Opening a Run shows the Tests to be carried out/that

have been carried out in that Run. This is the main screen used to access data and print

reports. Depending on the stage in the workflow, each Run has a particular status, with

coloured icons to indicate status:

To Finalise a Run for processing on the DynaChip Processor, select the Finalise icon:

This exports a file to the DynaChip Processor, and can only be carried out on a computer

connected (either directly or via the network) to a DynaChip Processor. When a Run is finalised,

no editing can take place of any Tests or other details associated with the Run.

At this point, a worksheet is generated to assist work in the lab. This can be printed or saved.

To Import data from a Run that has been carried out, select the Import icon:

This will open a dialogue box of the location where data is stored by the DynaChip Processor.

The most recently carried out Run will always be stored in the highest-numbered folder. Data is

automatically associated to the correct Run.

If an error occurs during import, there will be a dialogue box asking if you wish to accept the

import. Always select ‘No’, and then contact Technical Services.

To print a Report, first select the Run, then select the icon . This icon will only be

available when an Imported Run is selected. See the Report section of this manual for more

information.

DynaChip Software v1.1.0 Manual Page 14

-14 -

Editing a Run: The name of a Run (which is still editable) can be changed by opening the

Run and choosing the ‘Run Details’ tab. The Tests on the Run can be changed by opening the

Run and choosing the ‘Run Tests’ tab.

In this Edit Run window, there is a graphical representation of the 96 wells available for

carrying out Tests in a single Run. Wells with a Test are highlighted in green, while wells

without a Test that will be wasted if no Test is added have a purple outline.

To remove a Test from the Run, first select the Test. Then select the Delete icon:

To add a currently Unlisted Test, select an empty position. Then select the Add icon:

This will open a window with a filtered view of all currently Unlisted Tests. To create a new

Unlisted Test, either use the Test Wizard, or use the New Test icon while viewing a Sample.

To add all currently Unlisted Tests to the Run, select the Bulk add tests icon: This will fill

the whole plate if there are that many currently Unlisted Tests. If this requires more strips than

currently available from the kit, use the tickboxes above the strips to remove strips until the

number of strips to be used matches the number of strips available.

Note – Never deselect strips from the middle of the Run, only from the end. The instrument will

process all wells between the first and the last on the layout as shown on this screen.

To save changes made, the Save icon must be selected – if the window is closed without

saving, changes will be lost.

DynaChip Software v1.1.0 Manual Page 15

-15 -

Browse Frequencies – Population tables for vPRA

The other item in this menu is ‘Browse Frequencies’. The Frequencies screen shows the

population data used to generate virtual PRA (vPRA) values based on the results of the test.

There are 5 available populations, of which 4 are initially blank. Administrator-level Users can

enter data into these populations, to represent the local distribution of HLA alleles. To do this,

open the table up to the allele level, and select the allele to be edited. Once edited, data can be

saved and reloaded.

The screen also allows vPRA values to be generated for a user-defined antibody specificity, for

each of the populations entered. The user can type, or paste, the antibody specificity into the

box at the top of the page. The PRA will be calculated in the blue rows above the Class I

section and the Class II section of the table.

DynaChip Software v1.1.0 Manual Page 16

-16 -

Section 2. Workflow

Overview – Wizards Menu

The Wizards menu always contains the Test Wizard – a simple interface that allows creation of

Tests and Runs, using either existing data in the database or creating new records of Patients,

Samples and Requestors. The menu can also include any Macros that have been written into

the software, but the default installation does not include any.

Test Wizard - overview

Launch the Test Wizard from the Wizards menu:

The Test Wizard will open up in a new floating window. Each line in the window represents a

Test. All columns are resizable, and the order can be changed by dragging.

The Run tickbox in the first column controls whether the newly-generated Test is immediately

added to a Run, or just created as an Unlisted Test (for use when adding Tests to an existing

Run).

The Test ID box will automatically generate a Test ID based on the date. This can be edited to

a more meaningful ID if required, but note that Test IDs must be unique within the database.

The boxes with a red exclamation mark are required fields – Product and Sample. Products can

be chosen from a drop-down list, on which there will usually only be one choice. The default

layout only requires that Product is set for the first Test, and will be automatically used for

subsequent Tests.

DynaChip Software v1.1.0 Manual Page 17

-17 -

The boxes with a blue question mark are optional fields, where existing data can be used, or

new records can be created.

If using/creating a Sample associated with a Patient, select or create the Patient first. To find

existing data, typing the first few characters will open a list of the matching records in the

database for selection. In the example shown here, typing ‘p’ in the Patient ID box shows three

records. Double-click to select the matching record.

If existing details are selected correctly, the icon will show a red tick mark:

If creating a new record, type in the new details, and the icon will show a yellow star: to

indicate that new data has been entered. In this screen, the new records that can be created by

typing in new details are: Sample, Patient and Requestor.

If a Patient has been chosen, clicking in the Sample ID box will open a list of all samples (if

any) associated with the Patient for selection.

Select the chosen Sample, or enter new details. If new Sample details are entered at this stage,

they will be associated with the chosen Patient.

The most basic (and fastest) use of the Test Wizard is simply to select Product, and then simply

enter Sample IDs. The barcode reader can be used to scan samples if barcode labelling is used

in the lab.

Once a Test has been entered correctly, press ‘Add Test’ to create the next Test. Alternatively,

press the down arrow on the keyboard. The disk icon is used to show whether a Test has been

created yet – this only takes place when ‘Next’ is selected.

To remove a line, select each field containing data and press the delete key on the keyboard.

The other icon used in this window is the re-use option and is available for several

columns. If enabled, when a new line is created, the same data from the previous line is used.

Once all data has been entered or selected, click ‘Next’. If any tests were selected for, using the

tick-box in the first column, these will be added to a new Run (the Run is given an

DynaChip Software v1.1.0 Manual Page 18

-18 -

automatically generated sequential name, which can be altered). If no tests were selected, the

next window will appear blank; new data and Tests entered will be saved into the database for

later use in an ‘Edit Run’ screen, either with ‘Bulk Add Tests’, or ‘Add Test’.

Finalising a Run and generating a worksheet

The next stage for a Run is to finalise the list of Tests and make the data available to the

DynaChipTM Processor for experimental work to be carried out. This action is carried out by

selecting the Finalise icon in the Browse Run screen. A worksheet is generated, which can

be printed or saved and may be used to ensure the User has the correct samples/Tests in the

correct order.

Finalising a Run will only proceed on a computer linked to a DynaChipTM Processor, as the data

needs to transfer to the Processor module. A remote link can be set up from the DynaChipTM

Processor tab of the Settings screen (only accessible by Administrator level users).

Once finalised, the coloured icon in the System ID column for the Run will be yellow. The Run

cannot now be edited, but it is possible to open the Run to view the Tests listed.

At this point in the workflow, the assay should be carried out on the DynaChip Processor,

before importing the data back into the database.

DynaChip Software v1.1.0 Manual Page 19

-19 -

Performing a Run using the DynaChipTM Processor

Once the Run details have been finalised, the Run assay can be carried out using the

DynaChipTM Processor.

First, ensure that the Processor is powered on, and that the lid is closed.

To launch the processor, select ‘Launch Processor’ from the main menu of the software.

This opens the DynaChipTM Processor software module, and initialises the instrument.

[If the Processor is not powered on, a dialogue box will open and give the options ‘Abort, Retry

or Ignore’. Selecting ‘Ignore’ allows the DynaChipTM Processor module to open, but only to

access archived images by selecting the ‘Archive’ button].

DynaChip Software v1.1.0 Manual Page 20

-20 -

To carry out the Run, choose ‘New Test’. This opens a screen with a drop-down menu.

Select the Run you wish to perform. The name of the Run will start with the date it was

Finalised, and then show the Run ID

Click ‘Next’.

Page is loading ...

Thermo Fisher Scientific DynaChip Software Owner's manual

Brand: Thermo Fisher Scientific

Model: DynaChip Software

Type: Owner's manual

Download PDF

report

Thermo Fisher Scientific DynaChip Software Owner's manual

Thermo Fisher Scientific DynaChip Software Owner's manual

Related papers

Other documents