Workflows

Create a Plate Set

  1. Click the ‘Projects’ hyperlink on the global navigation pane. Navigate into the project that will contain the plate set. Note that the ‘Plate Set For…’ link now indicates the default working project.

  2. Select the check box near the plate set into which you would like to add a new plate set. Click the tools icon and select add to project…

  1. Fill in the required information and click submit.
Item Notes
Type Choose a descriptive type that can later be used for sorting
Layout Check the Layout viewer to learn about the different layout options

Available layouts are presented in the dropdown appropriate to the plate format/type:

Once complete, the new plate set will be visible in the client window.

Entities

Entities

LIMS*Nucleus defines a hierarchy of 5 entities.

A project contains plate sets, each of which contains plates etc. Projects can only be created by an administrator. Plate Sets can be created by users. Other entities are created automatically as needed. Plates, wells, samples are created at the time of plate set creation.
Plates and wells are created automatically during rearraying operations.

Workflows

Example data sets

LIMS*Nucleus example database contains plate sets, plates, hit list, assay runs and data. The various projects are at different stages of completion to demonstrate the functionality of the application.

Project ID Description Utility
PRJ-1 3 plate sets with 2 96 well plates each; includes data and hit lists visualize data; visualize hit lists; group plate sets;
PRJ-2 1 plate set with 2 384 well plates each; includes data create hit lists
PRJ-3 1 plate set with 1 1536 well plate visualize data
PRJ-10 2 plate sets with 10 96 well plates each add data;create hit lists; subselect plate sets



### Files for import

Provide your own import files or use the supplied data below:

Description File
Accession IDSs for PS-1 ( 2 96 well plates, 4 controls) accs96x2controls4.txt
ELISA data for 2 96 well plates with 4 controls col 12 (LYT-1) sample96controls4lowp2.txt
HTRF data for 5 96 well plates with 8 controls col 12 (LYT-7) sample96controls8low5plates.txt
A new 384 well layout with controls randomly placed controls8scatteredNoEdge384.txt

Statistics for example assay data files

Assay Run File Response mean(neg) stdev(neg) neg + 3SD
AR-1 ar1data.txt raw 0.1155 0.07 0.3255
bkgrnd_sub 0.1146 0.0697 0.3236
norm 0.1807 0.1172 0.5322
norm_pos 0.1971 0.1236 0.568
% enhanced NA 0 NA
AR-2 ar2data.txt raw 0.0945 0.0332 0.1942
bkgrnd_sub 0.0922 0.0357 0.1993
norm 0.1381 0.0601 0.3184
norm_pos 0.1641 0.0703 0.3751
% enhanced NA NA NA
AR-3 ar3data.txt raw 2850 2616.2951 10698.8853
bkgrnd_sub 2849.9978 2616.2935 10698.8781
norm 0.1102 0.1076 0.4331
norm_pos 0.1184 0.1095 0.4469
% enhanced NA NA NA
AR-4 ar4data.txt raw 0.109 0.066 0.3069
bkgrnd_sub 0.1076 0.066 0.3057
norm 0.1513 0.0956 0.438
norm_pos 0.1906 0.1168 0.5411
% enhanced NA NA NA
AR-5 ar5data.txt raw 0.0764 0.0512 0.23
bkgrnd_sub 0.0728 0.0512 0.2265
norm 0.0895 0.0629 0.2783
norm_pos 0.1259 0.0885 0.3914
% enhanced NA NA NA
Features

Features

LIMS*Nucleus falls into the “systems” category of LIMS development. LIMS*Nucleus contains a limited set of features and is designed to be integrated into a larger system.

Goal

Comprehensive but limitted feature set (multi-well plate sample management) with well defined inputs and outputs designed to be incorporated into a larger system.

Implemented features

Create project, plate set, plates, wells with and without samples
Group plate sets into a new plate set
Subset plates from a plate set into a new plate set
Reformat plates from 96 into 384 well plates and 384 into 1536 well plates
Apply assay data to plate sets
Visually or algoritnmlically evaluate assay data
Identify hits as samples surpassing a threshold; create hit lists
Create worklists for liquid handling robots
Rearray hits from a hit list into a new plate set
Apply user generated barcodes to plates
Apply user generated accession IDs to samples

Next>> Canonical workflow

Workflows

File Import Form

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:

File Formats

File Formats

File characteristics

Tab delimitted ASCII text Header required Column names must be all lower case Column name spelling is critical Column order is critical

Data import

Plate order is defined by the plate set. Import plates must be in the same order as the plate set

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plate	well	response
1	1	0.293825508745667
1	2	0.114021462999455
1	3	0.238314598659791
1	4	0.396061216051141
1	5	0.296039032793309
1	6	0.442385430319253

Accession ID import

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plate	well	accs.id
1	1	AMRVK5473H
1	2	KMNCX9294W
1	3	EHRXZ2102Z
1	4	COZHR7852Q
1	5	FJVNR6433Q
1	6	WTCKQ4682U

Barcode ID import

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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

Bulk target import

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project	target 	description	accession
1	muCD71	Mouse transferrin receptor	FHD8SU29
1	huCD71	Human transferrin receptor	JDHSU789
1	cynoCD71	Monkey transferrin receptor	KSIOW8H3
1	BSA	Bovine serum albumin	KEUI87YH
2	Lysozyme	Lysozyme	KDJFG98D
2	GAPDH	Glyceraldehyde Phosphate Dehydrogenase	KFIIOD09
2	ICAM4	ICAM 4 integrin	KL0OIE7U
2	IL21R	IL21 receptor	KOI89IUY
Workflows

Group plate sets

Only plate sets can be grouped. Navigate into the project of interest containing the plate sets to be grouped and highlight the plate sets. Select Utilities/Group from the menu bar:

A dialog will open. Fill in the name and description for the new plate sets. The source plate sets must be of the same format and layout, which will be indicated in the dialog box. Select a plate type and press OK.

Developer

Labsolns Guix channel

View the channels video for details on how to set up a Guix channel.

  • Installation

labsolns can be installed as a Guix channel. To do so, add it to ~/.config/guix/channels.scm:

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(cons* (channel
        (name 'labsolns)
        (url "https://github.com/labsolns/labsolns")
        (branch "master")
        ;; Enable signature verification:
        (introduction
         (make-channel-introduction
          "c82e51a51e9cfb0b1b8ae8f40e5746cbdd308d6b"
          (openpgp-fingerprint
           "E709 94D1 9CB0 FE2B CAC4  9E54 0BF8 F292 4D2B 1944"))))
       %default-channels)

Then run guix pull.

If you receive error messages like “…commit nnnn is not a descendant of nnnnn …” use

guix pull –allow-downgrades.