Tab delimitted ASCII text
Header required
Column names must be all lower case
Column name spelling is critical
Column order is critical
Plate order is defined by the plate set.
Import plates must be in the same order as the plate set
1 | plate well response |
1 | plate well accs.id |
1 | plate barcode.id |
1 | project target description accession |
Select the plate set that will receive the data
From the tools icon under import select “Assay Data”
Once imported, the data can be viewed using a scatter plot, which is visible when viewing assay runs, i.e. click on the assay run hyperlink.
Read the reformat overview
Confirm and select target layout if applicable. Note that the destination layout is selected for you, LYT-4. The destination layout is predetermined by the source layout and the level of sample and target replication (see below):
The new plate set, PS-8, is available in the plate set list:
Drill down to see that there are five 384 well plates. The original plate set contained 10 96 well plates in LYT-1 that were reformatted in duplicate using LYT-4. Use the global menu to select plate layouts and drill down into LYT-1 to identify the potential destination layouts for LYT-1. LYT-4 is one option for duplicate samples, with the target being the same across the plate (4T - same target in all 4 quadrants).
This requires ten 384 well plates with the duplicate samples side-by-side using the replication pattern 2S4T:
To confirm the samples are in this format, drill down to wells/samples and sort the samples by clicking on the “Sample” column header. Confirm that the two replicates of each sample are in neighboring wells e.g. A01, A02, and C01, C02 etc.
Please read terms of the license.
Obtain a registration key so you can modify the configuration parameter ‘maxnumplates’.
Use R-Shiny to prototype algorithms and visualizations and extend LIMS*Nucleus. Below is a list of assay runs from Project 1. The assay run hyperlink transfers you to a Shiny dashboard that allows you to manipulate and visualize your data and generate a hit list.
| ID | Name | Description |
|---|---|---|
| AR-1 | assay_run1 | PS-1 LYT-1;96;4in12 |
| AR-2 | assay_run2 | PS-2 LYT-1;96;4in12 |
| AR-3 | assay_run3 | PS-3 LYT-1;96;4in12 |
Target layouts define the pattern of targets coated on assay plates. The available patterns are described on the replication page. Observe the patterns under the “Target Pattern” column and note that singlicates, duplicates, and quadruplicates are the only allowed options. Duplicates are always in the same column, while sample duplicates are in the same row. Before setting up a layout pattern, targets must be imported as described on the targets page. Alternatively you can use the built in generic targets Target1, Target2 etc. Note that assigning targets is not required and is available only to allow merging with target information held in other systems.
To set up a layout, navigate into the project of interest and select the menu item Utilities/Targets/Create Target Layout. Provide a name and description, and select the level of replication desired. The dropdowns will be enabled as needed:
Once the layout is saved, it is available for use during reformatting or plate set creation. Note that the layout will only appear as an option when appropriate selections have been made e.g. replication is singlicates:
General navigation
Create a plate set
Reformat 96 well plates into 384 well plates
Associate assay data with a plate set
Identify hits using an assay threshold
Generate liquid handling robot work lists
Rearray hits into a new plate set
Group two plate sets into a single plate set
Regroup plates within a plate set into a new plate set (split)
Import accession IDs
Browser cookie management can sometimes go awry. Clear the cookies associated with the LIMS*Nucleus (LN) URL and go back to the login page to reset the session id cookie.
Firefox: web/developer/web console while the LN URL is in the address bar. Select the storage tab. On the left under cookes right click on the LN URL and choose delete all. Login to LN. You should see a new cookie ‘sid’ appear.
Chrome: more tools/ developer tools select the LN URL and right click ‘clear’. Login to LN. You should see a new cookie ‘sid’ appear.
ERROR: In procedure setlocale:
In procedure setlocale: Invalid argument
1 | $ export LC_ALL="C" |
ERROR: In procedure open-file:
In procedure open-file: No such file or directory: “/tmp/limsn/tmp/cache/route.cache”
1 | $ mkdir -p /tmp/limsn/tmp/cache |
LIMS*Nucleus does not yet use secure network transfer protocol. If your browser tries to redirect you to an ‘https://‘ URL, manually remove the s to change back to ‘http://‘
Tutorial 1 covers in detail steps that are glossed over in this tutorial.
Looking at available layouts there are 2 that offer replication - 2S4T and 4S2T:
2S4T: Entire plate coated with the same target, samples in duplicate. Note that sample replicates are in the same row.
4S2T: Each sample tested in duplicate on 2 targets. Note that target replicates are in the same column. (see tutorial 3 )
Following tutorial 1 I will rearray the 10 plates of PS-6 into a new plate set applying the 2S4T layout. 10 96 well plates in duplicate will requires 5 384 well plates:
Submit and confirm on the next screen. Note that selections made in the sample replication dropdown limit the options available under target layout - in this case only the default is available. View the target layout for a discussion on optional target layouts, which are only used for data annotation.
Click submit to create the new plate set PS-10. Select and assaociate data with the plate set. Use the data file plates384x5_2S4T.txt which contains demonstration data for 5 384 well plates. The data has been generated such that replicates are side by side in the same row and are +/-10% of each other. In the graph below replicates for one plate are color coded and appear at the same X value:
Looking at the response trellised by plate and colored by sample type:
Associate the data with the plate set:
Select the file:
Fill in the required information. Note that I am auto-selecting hits (all samples with a response greater than 3 standard deviations fromt the mean of the negative controls) which activates the hit list name and description text boxes. I did not choose to select the Top N hits so the box where I would enter N remains disabled.
Click import and after a few seconds you are taken to the ‘Plates for PS-10’ page where you can scroll down and see the new assay run and hit list:
Click on the AR-7 link to see a plot of the data. Note that the associated hit list HL-8 has 155 hits.
Responses are plotted in decreasing order with controls color coded. Not that if you select normalized response with a hit threshold set to mean(background)+/-3SD, 155 hits will be identified. The hit list could have been created here, but was already auto-generated on import.
Looking at the hit list view you can see that PS-6, 96 well plates contain all 155 hits that can be rearrayed into two 96 well plates.
Once rearrying is complete, creating PS-11, that plate set is annotated with a worklist indicating that it was generated by a rearray activity. The worklist can be used to physically rearray the samples into the new plate set PS-11.
Tutorial 3 prepares a target layout for the Tutorial 4 discussion on target replication.
LIMS*Nucleus is a client/server application requiring a PostgreSQL database server and an Artanis web server. For use in production, installation on data center or cloud servers is most appropriate. However if you are a Windows user, you may wish to evaluate LIMS*Nucleus on your personal laptop. For that purpose installation on Windows Subsystem for Linux 2 directions are provided below. Note that the easiest way to evaluate LIMS*Nucleus is to work with the instance running on Amazon Web Services. A video is available that describes installation of the client on Windows.
WSL2 on Windows 11 has been tested. Use the windows search tool to find cmd. Open a command prompt in administrative mode:
Install the Debian version of linux.
1 | C:\Windows\System32> wsl --install -d Debian |
You will need to reboot. Upon reboot you will set up your personal user. Use the name “admin” which is the user name hardcoded in the Postgresql installation scripts. If you wish to use a different name, the scripts will need to be modified. Once Linux is installed, install required Linux utilities:
1 | $ sudo apt update |
Launch Linux:
Dowload and run the install script:
1 | $ sudo wget https://labsolns.com/limsn/evaluate/install-limsn-pack.sh |
When prompted indicate IP: 127.0.0.1
Number of plates per plateset: 100 is reasonable
Do you want to set up a local database? “y”
1 | $ start-limsn.sh |
1 | $sudo nano /etc/resolv.conf |
Resolve.conf should look like:
1 | # This file was automatically generated by WSL. To stop automatic generation of this file, add the following entry to /> |
Sometimes Linux is started and you do not have permission to create directories. To take ownership of your home directory execute sudo chown -R $USER .
Test and make sure you can mkdir.
Most likely the script did not have permission to create directories (see above) so the following must be executed manually:
1 | $sudo mkdir -p ./.config/limsn |
Error: artanis/db.scm:162:6: Throw to key artanis-err' with args (500 #<procedure create-new-DB-conn ()> “Database connect failed: “ “could not connect to server: Connection refused\n\tIs the server running on host "127.0.0.1" and accepting\n\tTCP/IP connections on port 5432?\n”)’.
If you restart the terminal, you will need to restart the database server:
1 | $ sudo pg_ctlcluster 13 main restart |
Check that the database is available:
1 | $ psql -U ln_admin -h 127.0.0.1 lndb |
Configure the database manually:
1 | $ sudo sed -i 's/host[ ]*all[ ]*all[ ]*127.0.0.1\/32[ ]*md5/host all all 127.0.0.1\/32 trust/' /etc/postgresql/13/main/pg_hba.conf |
ERROR: no code for module (dbi dbi)
1 | printenv | grep GUI |
You should see GUILE related environment variables e.g. GUILE_LOAD_PATH; if not try:
1 | $ sudo ./bin/init-limsn-pack.sh |
or manually modify .bashrc loaded environment variables:
1 | echo export LC_ALL=\"C\" >> $HOME/.bashrc |
Terminal resart will be necessary.
1 | find ./gnu/store -wholename '*artanis.conf' |
You can delete the Linux instance to recover space, clean up, or start over:
1 | $sudo wsl --unregister Debian |