1. Core LIMS Training: Entering Experimental Data

2. Course Topics Creating an Experiment
Entering End Point Data From Experiments
Entering Raw Plate Data From Experiments
Reviewing/Editing Raw Plate Data
Finding Experiments
Creating New Assays and Protocols
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3. Assays, Experiments, and Protocols
Assay Type – One or more assays that are in the same category and generally track the same result types. Must be defined by administrator. (Example, Cytochrome P450 assays or Cell-based assays)
Assay – One or more experiments that are tracking the same set of conditions and result types. Commonly named by the biological target. Can be defined by scientist or administrator. (Example, Cyp2D6, Cyp3A4)
Experiment – Set of samples tested together under the same set of conditions. Defined by scientist. (Example, ‘Plate 1 tested on 3/12/12’)
Protocol – Description of conditions associated to an experiment. May be defined by scientist or administrator.
Plate Map – Description of plate locations of controls and standards associated to an experiment, if relevant. May be defined by scientist or administrator.
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4. Data Setup Prior to Experiment
Sample Lots are registered
- chemist or inventory manager
- usually needed every experiment unless retesting old compounds
Containers are created
-biologist or chemist or inventory manager
-can skip this step if uploading end point data
-may be done during registration
Plate Maps are created
- biologist or inventory manager or administrator
- only needed when plate layout is new
Biologist
creates experiments
Assay types, protocol types, experiment types are configured
- administrator
- only needed when new type of experiment (like different result types)
Assays and Protocols are created
- biologist or administrator
- only needed when new target or procedure
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5. Types of Experimental Data Entry
Experimental data entry can be divided into 2 categories:
Simple Data Entry
Values are uploaded from a data table (or manually typed) and mapped directly into database fields
Experimental data is automatically linked to the molecule and lot; you can also link to the container if desired
Ideal for end point data (where analysis may have been calculated with external software tools)
Complex Data Processing or Curve Fitting
Raw plate data is automatically loaded into the Core LIMS
Intermediate values are calculated from the raw data
Scientist reviews and edits any values before writing to the database
Experimental data is automatically linked to the molecule, lot, and container
Ideal for high-throughput screens which require routine analysis steps
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6. Creating an Experiment
Both types of experiments (simple and complex) by defining a new experiment
You will need to select Create from the appropriate experiment sub-type in the Experiments main menu. Check with your administrator if you are not sure which experiment type is correct.
This assumes that your administrator has pre-defined any assays, protocols, or plate maps you need
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7. Defining Experiment Metadata
You may have corporate naming conventions to follow for naming experiments or you may want to select a name that will help you find a specific experiment in a search
Select a project
Your administrator may configure other fields here for data to enter that applies to the entire experiment (for example, notebook #)
The assay will define which data fields are collected
You don’t need a plate map for simple data entry, but you will need to specify them for curve fitting
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8. Experiment Details Record
To manually type in data for simple data entry
To associate a plate for data processing
To make a template file for simple data entry
To upload a file for simple data entry
Once you have created an Experiment record, you are ready to enter the data
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9. Simple Data Entry Workflow
This is the generic process to enter end point values for an experiment (any calculations on raw data was done with external software tools)
Associate Containers (optional)
File Upload (Excel file)
Validate to Edit Data(optional)
Create Experiment
(associate assay and protocol)
Comments (optional)
Attach Files (optional)
Publish
Manually Type In Samples
Validate to Enter Data
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10. Data File Upload
The easiest way to do a simple data entry is to use the File Upload link and create an Excel file
Select Experiment Result File when prompted for File Type
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11. Data File Upload
Copy and paste the most relevant template into Excel (You can also use the Template Download hyperlink from the Experiment Details page to generate a file)
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12. Creating a File to Upload
Enter the sample and lot identifiers that you want to associate biology data to
Enter any relevant assay data
It is OK to leave cells blank if there is no data
Cells should contain values, not calculated Excel formulas or complex formatting
File should be saved as .txt or .xls (NOT .xlsx)
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13. Uploading the Excel File
Once the Excel file has been created containing all the data that needs to be entered, browse to the file and select the Upload button
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14. Verify the Uploaded Data
To release the data to colleagues, go directly to Publish
Click on Validate if you need to manually edit the data
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15. Validating Data
This step is optional if you need to manually edit the data
The original uploaded file is automatically attached so colleagues can compare it to any edits that were made later
To release the data to colleagues, go to Publish
Type in any desired changes
Deselect any rows that you want to remove
If you make any changes to this page, don’t forget to use the Update Values button to write them back to the database
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16. Entering Data Without an Excel File
This step would only be used if you had a small amount of data that you wanted to enter manually without an Excel file
1) Click on the Samples link to get to this page
3) Use the Add New Samples button to write the data to the database – entered compounds will be visible in the table
4) Go to the validate page to enter the data for each compound
2) Type in the compounds that you want to enter data for
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17. Attaching Documents
You may want to attach documents that are related to an experiment so that they can be easily found when looking at experiment reports
Note: any files uploaded through the File Upload link are attached automatically
You can also attach procedure docs to protocol records
1) Click on the Files Icon to view or add new files (a highlighted icon indicates there are already attached files)
2) Choose a file type
3) Click the submit button
4) Browse to the desired file
5) Select the Project
6) Hit the Upload button
7) Click on the View File link to open a copy of an attached file
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18. Adding Comments
You may want to add comments for your colleagues to see.
Generally, data observations should be entered in free text fields of the experiment record (for example, a Notes field) and comments should be used for capturing your interpretations of the data.
Comments are only accessible from the Experiment Details record and are not pulled directly into reports (although comments may be linked to automated alerts)
Records that have comments will be highlighted in another color
Click on the Experiment links to return to the main Experiment record
Previous comments are listed in chronological order in a table
Type in your text and hit the Enter button to add your comment
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19. Publishing Data
During the data entry process, data is saved to the database, but it is not available to non-biologists for viewing until it is published
Only unpublished data is open for editing
Data that is manipulated may be versioned so that changes are transparent to users (raw data files are also attached for later comparison)
Published data can be unpublished by administrators and later republished – this will remove the data from view by other scientists while biologists make corrections
Depending on your corporate rules, publishing data may be linked to automated alerts, moving compounds into new workflow queues, or other events
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20. How Do I Publish an Experiment?
From any of the data entry pages, click on the Publish link
Once it is selected, you will be taken directly to the published record (there will be no intermediate pages for you to interact with)
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21. What Does a Published Record Look Like?
After a record has been published, the Actions to enter data will be replaced with Reports
Colleagues will use the View Report link to get the detailed Experiment Report
There is also a publish status flag
The system automatically records the user, date and time that the record is published
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22. Hands-On Practice
Create a new experiment record using any assay in your system
Use the Data File Upload link to get the column headers and copy them to an Excel file
Add test compound id’s and some dummy data to create an Excel file for uploading
Upload the Excel file to Core
Validate the data (make some edits or remove a row)
Attach a document to the experiment
Add a comment to the experiment
Publish the experiment
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23. Complex Data Processing Data Entry Workflow
This is the generic process to enter raw plate data for an experiment and calculate the end point values within the Core system
Create Experiment
Associate Containers
Drop raw plate files into file loader
Validate Controls
Comments (optional)
Attach Files (optional)
Validate Candidates (raw or intermediate data)
Publish
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24. Creating a Data Processing Experiment
Just like the Simple Data Entry example, start with creating a new experiment
Data Processing Experiments will need to associate a plate map (for locations of standards of controls – NOT contents)
If you are using a non-standard plate setup that is not listed, you can define your own (See the Samples & Containers training slides)
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25. Associating a Container
Instead of telling the system which compounds will be tested directly, for Data Processing Experiments you tell system which plate(s) to test
The plate already has the details of which compounds are in each well
See the Samples & Containers training slides to learn how to create a plate
Select Containers to enter the information
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26. Associating a Container
If you don’t remember the plate name, you can find it using Search Containers
Type or scan in the plate name(s) and hit the Add Containers button
It does not matter what order you type in the plates
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27. Entering Raw Plate Data
Unlike the Simple Data Entry, do NOT use the Data File Upload link to upload files
Instead, drop the raw data files into a specific folder on your corporate servers (your administrator can provide the exact file path for your corporate folder)
Once copied into the folder, a File Daemon will automatically associate and upload the file to the correct experiment based on the file name (make sure the File Daemon is turned on!)
After a file is successfully loaded, it will disappear from the server folder and it will be visible in the Core experiment page you created
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28. Requirements for the Raw Data Files
Files should come directly from instruments and should not be manually processed by users
All wells should have a reading (even if a blank well)
Only one plate per file (i.e. if an experiment contains multiple plates there will be a file for each plate)
Do not re-use the same plate barcode identifier for multiple experiments (See the Samples & Containers training slides to see how to quickly copy a plate)
The name of the file must start with the plate barcode identifier
The name of the file may contain other information to help you identify a file (such as a date), but it should separated from the plate barcode by an underscore
File should be saved in tab delimited text format (.txt)
Example file names:
MT3.txt
MT4_ txt
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29. How Can I Tell My File Is Uploaded?
The raw data file you dropped into the server folder is automatically attached during the upload process and the icon will be colored – click on the Files Icon to view it
(Tip: if you don’t have access to your drop folder, you can upload the raw file through here manually)
The Intermediate Data link will be added to the hyperlink when there is raw data uploaded that needs to be processed
Click on the Validate link to view the uploaded data and start processing it
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30. Data Review You can accept/reject data at all levels:
Remove a raw data point
Remove a calculated intermediate value (%Inh, etc.)
Remove a control data point
Remove a final end point calculation for a sample (IC50, etc.)
Remove a plate
Leave an experiment unpublished
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31. Validating the Data
To drill down to details about which compounds are in each well, go to the Container Details page and click on individual wells
The heat map is colored to give a quick visual indicator of activity:
Brighter blue=Least activity
Brighter green = Most activity
Black = Well removed
Click on Validate Candidates to analyze data for compounds and Validate Controls to check data from the assay controls
The plate as a whole can be accepted or rejected (click Accept button to save changes)
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32. Plate Map For This Example
Each column is diluted serially by a factor of 2 from the previous column
Column 1 is the highest concentration and Column 11 is the lowest concentration
Positive Control
Negative Control
Row A and B are duplicate copies of compound 1
Row C and D are duplicate copies of compound 2
Row E and F are duplicate copies of compound 3
Row G and H are duplicate copies of compound 4
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33. Validate the Controls
Click on Candidates hyperlink to Validate sample data
The number before the colon is the well number
The number after the colon is the raw data
Select any outliers that should be removed and click Update Container to recalculate the statistics
Removed wells will be displayed in black
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34. Validate the Candidates
Deselect a checkbox to remove a specific compound from the Experiment Report
Click on the raw data link to accept/reject individual raw data points (not recommended for <3 data points)
Click on the intermediate data link to manipulate Dose Response curves or accept/reject calculated intermediate data points
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35. Validating Raw Data
Note: Since it is not recommended to reject individual points for duplicates, this feature is not always supported for all duplicate assays.
This example is just for training purposes only.
You will see the changes reflected in the averaged statistics on the right
If you want to remove a single point (for example, it is known that well was empty), check the relevant box and hit the Update button to recalculate the changes
The rejected well will now be colored black in the heat map
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36. Validating Intermediate Data
Deselect a checkbox to knock out a point on the IC50 curve
Note: Here you are accepting/rejecting the calculated intermediate data (%Inh, %Activity, etc); if you want to accept/reject raw data use the View Raw Data hyperlinks
Add any desired constraints to lock the curves
Don’t forget to hit the Recalculate button to update any changes
Knocked out intermediates will show in red on this plot and not be visible on heat map;
Knocked out raw data points will not show on this curve plot, but will be black on the heat map
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37. Completing the Experiment
Attach any other documents
Add any comments
Publish the experiment so colleagues can view it
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38. Final Experiment Report
Use hyperlinks to look up the structure, lot, or plate information
The Rejected report would show any compounds (not raw or intermediate data points) that were removed
From the Experiment Details page, click View Report to get to this page
This is a Smart Table report:
Use the scroll bars at the bottom to view data off to the right or hide columns you don’t need
Use the filters to focus on interesting rows
The IC50 curves and underlying data can be viewed by clicking on the intermediate hyperlinks
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39. Hands-On Practice Create a new experiment record
Associate the experiment to a plate (preferably one built during Samples & Containers training)
Create a dummy data file and name it after your plate
Drop the file in the appropriate location
Validate the controls
Validate the intermediate data
Attach a document to the experiment
Add a comment to the experiment
Publish the experiment
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40. Finding an Experiment
If you know the barcode, type it in the Quick Find box
If you created it, look in My Experiments on your My Account page
If Experiment is recent, check the Recent (2 Weeks) report
If Experiment is still active and unpublished, check the Unpublished report
Use the Experiment Query page to query by name, date, assay, author or other filters
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41. Creating a New Assay
In most cases, routine assays will already be in your system for selection in experiments (use the List All sub-menu if you need to check if it is there or not)
To add an experiment with a new assay, you need to create the new assay prior to creating the experiment
Navigate to the Create sub-menu under the appropriate assay sub-type under the Assays main menu (if you need a new assay type you will need to ask your administrator to create it and add it to your menu)
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42. Creating a New Assay cont.
Assign an Assay Name
Decide what types of samples can be tested in this assay
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43. Creating a New Protocol
Just like assays, routine protocols will already be in your system for selection in experiments (use the List All sub-menu if you need to check if it is there or not)
To add an experiment with a new protocol, you need to create the new protocol prior to creating the experiment
Navigate to the Create sub-menu under the appropriate protocol sub-type under the Protocols main menu (if you need a new protocol type you will need to ask your administrator to create it and add it to your menu)
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44. Creating a New Protocol cont.
Your administrator can configure any data fields for the protocol type to make data easier to search
It is a good idea to attach any SOP’s, literature references, or other generic protocol documents to the resulting Protocol Details record so colleagues can view them (experiment-specific documents should be attached to the Experiment Details page)
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