Barcode IDs are imported by plate number. The files page provides details on the file format, with a 10 plate sample file available. Navigate into the project of interest and highlight the plate set of interest. From the menu select Utilities/Import Barcodes:

The import barcode form will appear - select file. A truncated sample of file contents will appear belwo the ‘Submit’ button for confirmation:

The example barcode import file looks like:

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plate 	barcode.id
1	LN000001
2	LN000002
3	LN000003
4	LN000004
5	LN000005
6	LN000006
7	LN000007
8	LN000008
9	LN000009
10	LN000010

Once imported, barcode ids will appear in the plate table:

Example barcode ID import file:

Email already exists.
Wallet/Customer ID not generated.

Contact info@labsolns.com for assistance.

Multiple workflows use a file import form show below. Text provides instructions as well as an example of what the contents of the file should look like. Import files are always tab delimitted plain text. Column order, spelling and capitalization are critical:

Post file selection trucated contents of the import file are displayed for confirmation prior to submission. If file contents are determined to be incompatible with requirements for a particlar import e.g. wrong number of rows/columns, incorrect header, a warning will be issued:

LIMS*Nucleus makes use of the following definitions:

Sample: Item of interest being tracked by LIMS*Nucleus, i.e. the item in wells. Examples would be compounds, antibodies, bacterial clones, DNA fragments, siRNAs.

Target: the item with which the sample interacts, usually coated on the bottomn of the microwell plate e.g. the antigen for an antibody or the enzyme (target) of a compound.

When creating layouts there are three attributes that need to be defined:

LIMS*Nucleus support 5 sample types:

LIMS*Nucleus has twenty pre-defined layouts installed at the time of system installation. Custom sample layouts can be defined and imported by administrators. A sample layout import file that defines four control wells at the bottom of column 7 looks like:

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well	type
1	1
2	1
3	1
4	1
5	1
...
51	1
52	1
53	2
54	2
55	3
56	4
57	1
58	1
...

92	1
93	1
94	1
95	1
96	1

When viewed in the layout viewer, the above file would provide the following sample layout:

For every sample layout imported, an additional 5 layouts are created that define sample and target replication. These layouts are discussed in detail on the replication page.

Here is a sample layout import file that defines 8 controls in a 384 well plate, randomly scattered, excluding edge wells

When reformatted into 1536, the layout will look like:

Composed of plates Specific to a project All plates within a plate set must be of the same format (e.g. 96 well) Plate sets can be merged together (different plate types OK) When created, all plates in a plate set will be of the same plate type

A variety of installation/configuration scripts for both the client and the PostgreSQL database server are provided as links on this web site or packaged with the LIMS*Nucleus client. Various scripts are described below. Scripts without hyperlinks are included in the install package.

Supplied Scripts

Sample: Item in a well. Could be antibody, small molecule, virus, antisense oligo, expression construct, etc.
Target: Material coated on or in an assay plate. Substance of interest that will interact with samples.
Rearray: Select random samples (hits) across a plate and place them in a new plate.
Reformat: Combine plates of one format into a higher density plate e.g. collapse four 96 well plates into a 384 well plate
Group: Combine two or more plate sets into one plate set; combine a subset of plates from a plate set into a new plate set
Format: Number of wells in a plate e.g. 96, 384, 1536.
Hit: A sample that surpasses and assay threshold.
Source: Plates from which samples are drawn.
Destination: Plates into which samples are deposited.
Plate set order The assigned order of plates within a plate set. Order is visible in the client.
Required data Data required for LIMS*Nucleus to function e.g. plate layouts, assay types, well types
Example data Fake data that can be used to test LIMS*Nucleus functionality

Tutorial 1 covers in detail steps that are glossed over in this tutorial. Tutorial 3 covers creation of the target layout.

Looking at available sample 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. (see tutorial 2 )

4S2T: Each sample tested in duplicate on 2 targets. Note that target replicates are in the same column.

Following tutorial 1 I will rearray the 10 plates of PS-6 into a new plate set applying the 4S2T sample layout. Ten 96 well plates in quadruplicate will requires ten 384 well plates, one 96 well plate in all 4 quadrants of a 384 well plate:

I will use the target layout created in tutorial 3 as the target layout, providing me with duplicate assay results for each sample.

Use the data file plates384x10_4S2T.txt which contains demonstration data for ten 384 well plates. The data has been generated such that replicates are one above the other in the same column 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. Note that plate set, hit list, and assay run ids may differ from what is shown if you worked through all the tutorials:

Select the file you downloaded:

Provide requested information and import data:

View the assay run and hit list under PS-12

Navigate into HL-9 and view hit availability. Note that the hit list has 306 hits. PS-6 is the master plate that provides the hits. The discrepancy is discussed below.

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, 306 hits will be identified. The hit list could have been created here, but was already auto-generated on import.

View the new plateset PS-13. Note the associated worklist because this plate set was created by a rearray action.

Note that the hit list contains 306 hits but the parental plate set PS-6 only contains 276 of the samples designated as clones. Seven of our samples have scored as hits on both target 1 and 2. This can be seen in the exported worklist below. For example sample SPL-2829 scored on both targets, but will be rearrayed only once. To characterize which samples score on which target, you must export the results and analyze outside LIMS*Nucleus.

Processed data can be exported for further analysis. While viewing an assay run, use the ‘View all data’ to generate a table that can be exported to Excel:

Results are exported into whatever application you have associated with .csv files:

Note that due to the use of defined targets, the target annotation appears in the worksheet. For targets both the name and accession are available. Sample accessions were not imported and so don’t appear. Compare to an analysis where the default target annotation is used, such as PRJ-1, AR-1. The generic target label “Target1” is used, without any associated accession:

Purpose

Ease your organization into Urbit by using the Urbit ID system to validate users. Use the Landscape viewer to distribute software - in this case a simple hyperlink to an internally developed web app. No hoon coding required. The web app must be modified to accept white listed Urbit IDs.

Prepare Linux

The following is a modification of the hello app found on developers.urbit.org. I am starting with a new instance of Debian 11 on AWS. Note that some of the commands below will need to be modified with your AWS credentials, configuration. This video walks through the process.

Update, install some utilities and create a swap space:

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sudo apt-get update
sudo apt-get install git

sudo fallocate -l 2G /swapfile
sudo chmod 600 /swapfile
sudo mkswap /swapfile
sudo swapon /swapfile

edit fstab:

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sudo nano /etc/fstab

add the following line:

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/swapfile swap swap defaults 0 0

Prepare new desk contents

Clone the required desks and merge them into your project desk OR git clone the limsn project and apply modifications. Note that this process slightly differs from developers.urbit.org which is out of date:

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projects$ git clone https://github.com/urbit/urbit urbit-git
projects$ git clone https://github.com/tloncorp/landscape

projects$ mkdir urblimsn

cp -rfL /home/mbc/projects/urbit-git/pkg/base-dev/* /home/mbc/projects/urblimsn
cp -rfL /home/mbc/projects/landscape/desk-dev/* /home/mbc/projects/urblimsn

projects/urblimsn$ echo "[%zuse 415]" > sys.kelvin
projects/urblimsn$ echo "~zod" > desk.ship

projects/urblimsn$ nano desk.docket-0

Modify the contents of desk.docket-0 to suit your needs:

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:~  title+'LIMS*Nucleus'
    info+'A link to LIMS*Nucleus Web App.'
    color+0x81.88c9
    image+'https://github.com/mbcladwell/limsn/raw/main/limsn/pub/img/las-walpha-small.png'
    base+'limsn'
    glob-ames+[~zod 0v0]
    version+[0 0 1]
    website+'https://github.com/mbcladwell/urblimsn'
    license+'MIT'
==

The merged desks, auxilliary files and glob can be cloned, see below.

Prepare fake zod

Start up a fake zod, create and mount a new desk, delete the desk and git clone its replacement:

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curl -L https://urbit.org/install/linux-x86_64/latest | tar xzk --transform='s/.*/urbit/g' && ./urbit
./urbit -F zod
~zod:dojo>|new-desk %limsn
~zod:dojo>|mount %limsn

Ctrl-d   (to kill zod)

cd into zod and delete the new desk. git clone its replacement. The cloned directory contains the merged dev desks, desk.ship etc. as well as a glob:

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cd ./zod
zod$ rm -rf ./limsn
zod$ git clone https://github.com/mbcladwell/urblimsn.git limsn
cd ..

Get the glob out of the desk or the desk will not compile:

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$ mv ./zod/limsn/glob .

On local machine transfer glob to local machine:

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scp -r -i labsolns.pem admin@ec2-3-145-214-48.us-east-2.compute.amazonaws.com:./glob . 

On zod:

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~zod:dojo>|commit %limsn
~zod:dojo>|install our %limsn

Assuming fake zod is on your local machine you can point your browser to localhost:8080 and see landscape with a new LIMS*Nucleus tile with spinner indicating “loading”. For AWS I use my temporary IP: http://3.142.185.219:8080.

To complete the install you must upload the glob. First modify index.html to suit your needs:

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<!DOCTYPE html>
<html>
  <head>
     <meta charset="UTF-8" />
    <script src="https://unpkg.com/@urbit/http-api"></script>
     <script src="/session.js"></script>
  </head>
  <body>
  </body>
  <script>
     location.replace('http://3.145.214.48:3000/urbit?name=' + window.ship);
  </script>
</html>

The javascript helper scripts are discussed in the http api guide. Note the ‘window.ship’ variable which provides the ship name (‘zod’ in this example) for appending to your web app’s urbit controller. In LIMS*Nucleus, urbit ids must be white listed in the ‘person’ table:

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lndb=> select * from person;
 id |  lnuser  |      passwd      |       salt       |       email       | usergroup 
----+----------+------------------+------------------+-------------------+-----------
  1 | ln_admin | 1d52114553ae31b3 | a39b69e5fd79854b | info@labsolns.com | admin
  2 | ln_user  | ca6468f6ff4a82e6 | e999f4c34635f943 |                   | user
  3 | demo     | 97f8647f1067346d | 55ecb01c50cb1ae1 |                   | user
  7 | zod      | 1f4973fea4b98a05 | 616c7e5555c1df62 |                   | admin
  8 | nus      | 9a58637cbeab8afc | 8e4d24fcb45af66c |                   | user
(5 rows)

lndb=> 

Note the the urbit ID password hashes are a hash of the salt only as the password is blank. Urbit users come to the app prevalidated.

To upload the glob navigate to localhost:8080/docket/upload, select the limsn desk, press browse and select the glob directory and press the “glob!” button. Returning to zod you should now see:

Click on the LIMS*Nucleus tile and you will be redirected to the web app and logged in.

To allow zod to distribute this link, at the dojo:

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~zod:dojo>:treaty|publish %limsn

Now if I create a fake ~nus on the same instance of AWS but broadcast on port 8081, I can query ~zod on 8080 for software offered. We can piggyback on the Urbit desk distribution mechanism to distribute software - though in this example we are simply distributing a hyperlink allowing redirection:

Contact info@labsolns.com if you need help with installation/configuration/customization/troubleshooting.

URL: labsolns.com
email: info@labsolns.com

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