Compound Ordering & Logistics
COOL
User guide

by John Marelius
Last updated 2002-06-12, covers the COOL module in BeeHive version 1.33.

Overview

Procedure

Registering an assay request without requesting a new sample

Introduction

COOL is a system to manage the logistics of sending compound samples for chemical and biological assays. It provides interfaces for creating orders of compound samples for assays, for organising the samples on plates and for processing the requests and marking them as completed. These are forms (windows) in BeeHive where the user fills out fields. In addition, the database of requests can be searched using the standard BeeHive queries.

The typical work flow will be that

Someone requests an assay (or a set of assays) using one or more compounds.
The compound collection unit prepares the requested samples and send them to the persons in charge of the assays.
The persons who runs the assays process the samples and confirm that the request has been completed.

Note that Cool does not affect how assay result data is being handled.

Each project will be able to define sets of assays that will be performed e.g. for all new compounds. Such sets can be requested in a single operation.

This second generation COOL system is different from the first version in the following respects:

It is integrated in BeeHive, instead of being a stand-alone application.
Samples will be delivered in numbered, barcoded containers (plates and vials).
It uses the new plate database to keep track of plates (and vials).
Information on plates delivered through COOL is automatically imported into ActivityBase.
Plate information is also accessible through BeeHive using standard BeeHive queries.
E-mail notifications are sent to recipients of samples, both when an order is placed and when the samples are dispatched.

Still, the user inteface for placing orders and marking requests as completed are nearly unchanged.

Loading the COOL module

COOL is a module in BeeHive, a component that can be enabled (loaded) or disabled (unloaded) by you as a user. Before you can use the COOL module, you must load it.

Select File->Modules->COOL from the menu bar.
A check mark will appear by the menu item and a new menu 'Cool' appears to the right on the menu bar.

You only need to do this once, the next time you start BeeHive, the COOL module will be loaded at start-up.

Figure n: Use the Modules sub-menu to load COOL the first time you want to use it.

Order samples for assay

Overview

To request samples of compounds to be sent for a particular assay, you need to provide the following information:

Compound IDs. You may also select a particular batch if there is more than one batch of a compound. Alternatively, you may give batch numbers, in which case the compound IDs are looked up for you. You may include any number of compounds in your order.
Assay names. You pick assays from a list of registered assays. Each assay is associated with a recipient, i.e. the person to recieve samples, the form and the amount of solution or dry substance required.
Assays may also be grouped into assay sets which are convenient when a fixed combination of assays are to be run for each compound. You may request any number of assays of your selected compounds in your order.
Additional details (optional). If necessary, you can change the form and amount of sample and the recipient and add comments.
Project. You need to identify the project for which you are making the order.

The COOL request window is organised into these four sections, numbered as above, to make it easy to fill out all the necessary information. It is best to complete the sections in order, because some operations will not be enabled until you have completed the previous sections. You will see this as grey, disabled buttons.

An order in COOL contains all the requests for individual compounds made on one occasion by one user for one project. A new order is created when you press the 'Submit' button in the COOL Order window.

Procedure

The following list gives the details on how to prepare an order.

0. Select 'Order' from the 'COOL' menu.
If you don't see the COOL menu, you need to load the COOL module as described above.

Select compounds in the top panel of the window. You may do this in several ways:
- Type in compound IDs in the column 'Compound ID'. As soon as you have typed a complete compound ID (including the suffix letter, if present), the program will look up all batches of that compound and the batch numbers will be shown as a drop-down list in the 'Batch' column. The most recent batch will be selected by default. To select another batch, double-click the batch number to activate the drop-down list and pick another item from the list. Data on that batch (avaliability, submission date etc.) will be shown.
- Type in batch numbers in the column 'Batch'. As soon as you have typed a complete batch number, the corresponding compound ID will be shown in the compound ID column, and batch details in the columns to the right. Other batches of the same compound will be loaded into the drop-down list.
- Paste compound IDs in the column 'Compound ID'. You may copy from within BeeHive or from any other application. The data you paste by pressing Ctrl-V must have one compound ID at the beginning of each row. After pasting, you may select batches as above.
- Paste compound IDs and batch numbers. If you have a list containing both compound IDs and batch numbers, you can paste that. Make sure the cursor is positioned in the Compound ID column when you press Ctrl-V to paste. The data you paste must have a compound ID at the beginning of each row, a separator (tab, comma, semicolon) and a batch number. You may mix rows containing batch numbers and rows without batch numbers.
- Paste batch numbers in the column 'Batch'. The data you paste by pressing Ctrl-V must have one batch number at the start of each row.

To add a new row as you type, press the down key.

To change a compound ID or batch number, double-click that cell.

To insert a new row after the current row, click the 'Insert' button.

To delete the current row, click the 'Delete' button.

To clear the compound list, click the 'Clear' button.

Note that you can only edit the two leftmost columns 'Compound ID' and 'Batch'.

Click the check-box 'Info' to display a pop-up window with the structure of the compound on the current row, and earlier requests of that compound.

Figure n: Selecting a batch in the compound selection panel of the order window.

Select an assay or a set of assays from the drop-down list 'Assay'.
If you want to add a comment to each request, type it in the 'Comment' field.
Click 'Add requests' to create a request for the selected assay for each of the compounds you selected above. If you have chosen a set of assays, requests will be created for each compound for each assay in the set.
Inspect the requests to verify that all the information is correct.
You can change the sample form, concentration, amount, recipient and comment by double-clicking a cell and editing the value.
- To delete the request on the current row, click 'Delete'.
- To clear all the requests you added, click 'Clear'.
Select the project for which you are making this order from the drop-down list 'Project'.
Click 'Submit'. You will be prompted to confirm submitting the order.
- You cannot submit an order until you have selected a project and added at least one request.
- When the order is submitted, e-mail messages are automatically sent to each person listed as recipient of any of the samples in your order. The messages contain a list of the compounds and assays you ordered.
Figure n: The order window with an order ready to be submitted. Note that different assays may be requested in the same order.

Registering an assay request without requesting a new sample

If samples of the compounds to be assayed are already available to the recipient - that might be yourself - you may still want to register assay requests so that the logistics functionality of the system is maintained, i. e. so that you and other users can see that the compounds have been submitted for the assay. To register such a request that does not need to be dispacthed by Compound Collection, construct the request as usual. Then set the 'Amount' column to zero, to indicate that no new sample is required.

Figure n: Set 'Amount' to zero to register a request without requesting a new sample.

Processing assay requests

As the designated recipient of samples for a particular assay, you will recieve samples in numbered containers. The samples may be delivered on plates of in vials - discuss your preferences with Compound Collection. Samples delivered on a plate may correspond to a single order, or may contain samples from more than one order.

To see the list of assay request for your particular assay

Select 'Run assay' from the Cool menu.
Select your assay from the drop-down list 'Assay'.

Figure n: The 'Run assay' window.
To see more details about individual requests, check the 'Info' check box to open the request information window.
Mark the completed requests with a check mark in the column 'Completed'.
To complete all requests with the same plate ID as the current row, press 'Complete Plate'.
To cancel a request that cannot be completed, place the cursor on that row and press 'Cancel'.
Press 'Save' to save your changes. After saving, the save button will be disabled until you make any further change that needs to be saved.
To undo your changes, press 'Reset'. This will reload the form and discard your changes since you opened the form or since you last saved it.
Press 'Close' when you are finished.

By default, the form shows only requests that have not been completed or cancelled. To show all requests, including completed or cancelled ones, check the box 'Show completed requests'. The box is disabled when there are unsabed changes.

Compound Ordering & Logistics COOL User guide

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