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Core LIMS Training: Entering Experimental Data

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Presentation on theme: "Core LIMS Training: Entering Experimental Data"— Presentation transcript:

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 5/28/2018 Confidential

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. 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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) 5/28/2018 Confidential

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) 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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) 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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) 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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) 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

37 Completing the Experiment
Attach any other documents Add any comments Publish the experiment so colleagues can view it 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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 5/28/2018 Confidential

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) 5/28/2018 Confidential

42 Creating a New Assay cont.
Assign an Assay Name Decide what types of samples can be tested in this assay 5/28/2018 Confidential

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) 5/28/2018 Confidential

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) 5/28/2018 Confidential


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