Where sample management meets electronic lab notebook

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An easy way to distinguish samples from aliquots

Posted by Rory on April 25th, 2011 @ 7:17 pm

When you aliquot a sample, it’s important to keep an accurate record of information about the sample, as distinct from the aliquots that have been created. It’s equally important to keep track of what happens to the aliquots over time, as they get taken out of and put back into the freezer, actions are performed on them, and they get used up.  To do that you need a convenient way of associating information with both the group of aliquots that came from a single sample, and each individual aliquot. This post explains how to keep track of your samples and aliquots using the simple sample management system in the electronic lab notebook eCAT.

Aliquot information

In the following screenshot, the group of six plasmid aliquots which come from a single sample have been highlighted in green.  We are going to edit information about just one of these aliquots, and have selected the ‘edit aliquot information’ icon at the top left.

When we click on the icon a box pops up, as shown in the screenshot below, and we can enter information about just this aliquot, including its name, container label, concentration and volume.  We can also make notes about this aliquot and generate a barcode label for it.

Sample information

We can also enter information that should be associated with all the aliquots in this group.  To do that, as shown in the next screenshot, we click on the ‘edit sample (set of aliquots) information’.

When we click on that icon, we are taken to the record where all the information about the sample from which the aliquots were made is kept (In the screenshot below you see just a part of that record).    The kind of  information that can be recorded in the record is specific to the particular sample type, plasmid in this case.  When we enter information into one of the fields here, this information will be kept for all the aliquots in this group.  For example if we  select ‘bovine’, when we look at the sample information for all six of the aliquots in the group, they will all show this bovine reference.

So there it is, eCAT helps you record information about individual aliquots, and information about groups of aliquots from the same sample, and it automatically keeps them separate!

How to set up a freezer sample management system in your lab in less than 10 minutes

Posted by Rory on April 14th, 2011 @ 5:35 pm

A common sound in the lab is the yelling alarm coming from the deep freeze, followed by the miserable face of a hand-frozen graduate who was searching for a plasmid construct.

Every lab has stories about its freezers and what lurks inside them.  Those samples dated 1990 that someone came across just the other day.  Or the aliquots you put on the shelf on Monday that  mysteriously vanished by Thursday.   It’s things like this that drive some lab heads, in desperation, to try out expensive LIMS solutions that usually turn out to be so complicated they gather dust in a corner of the lab.

With this background in mind, we designed CAT 4.0, an electronic lab notebook which now includes sample management, for labs which don’t have huge budgets or sophisticated technical resources, but do need to keep their samples better organized.  To do that we knew we had to keep it simple!

To prove the point, in the rest of this post I’m going to take you through setting eCAT 4.0 up to manage freezer samples. As you’ll see this can be done by anyone with ordinary computer skills — such as  a lab manager, a research technician or a postdoc — in three simple steps.

Step one:  Designate inventory roles

The eCAT administrator first needs to designate one or more members of the lab as Inventory Managers, and all members of the lab who will be using the system as Inventory Users.  Inventory Managers, as described below, have the ability to configure the system, and Inventory Users are able to use it to manage their samples.  To give an eCAT user an Inventory Manager or Inventory User role, just edit the user’s profile as shown below and select the Inventory Manager button.  A popup appears, explaining that Inventory Managers can do everything in the system, i.e. create containers and sample templates and create, move and edit their own and other user’s samples and containers.

To give a user Inventory User rights, simply select the Inventory User button rather than the Inventory Manager button.

Step 2: Create a freezer

The Inventory Manager is now ready to create your first freezer.  To do that go to the Inventory tab, and select Create New Container from the menu on the left, and then Freezer from the drop down list that appears. You are shown the following screen.

Click next at the bottom right (not shown on the above image) and you are taken to the second and final screen in the series  –  just give the freezer a name and a brief description, click finish and your first freezer is ready!

Step 3:  Add a shelf, a rack, and a freezer box

Next add a shelf to the freezer, and a rack to the shelf, using the same two step process you used to create the freezer. Finally, add a box to the rack, again using the same two step process.  There are  a variety of freezer box configurations to choose from. We’ll select a 10×10 freezer box, as shown in the following screenshot.

And after we give it a name and a description, the freezer  box is ready, and Inventory Users can start adding samples to the box! In the tutorial video we’ve made showing how to set up containers those three steps take less than five minutes.  I bet it won’t take you much more than that, even on the first try.

Up and running in less than ten minutes!

So it just takes 5 – 10 minutes to set eCAT up for your lab to begin managing their samples.  And that’s 5 – 10 minutes for someone with normal computer skills, not an IT person.  Of course there are lots of other ways of managing your samples in eCAT 4.0, like creating containers with your own configuration.  As I’ve described in another post, that’s just as simple as creating containers from eCAT’s pre-existing templates.

Freezer sample management made simple!

Posted by Rory on April 4th, 2011 @ 3:28 pm

Flexible sample creation

In my last post I gave some examples to show how useful it is to be able to create and configure sample containers.  In this post I’m going to focus on creating samples – once again focusing on the benefits of flexibility.

Lots of samples to choose from

As with containers, the electronic lab notebook eCAT comes preloaded with lots of preexisting sample types.  Here are a few examples:

A data template for each kind of sample

Each sample has a record template associated with it, so you don’t need to start from scratch each time you enter information about a new sample you are adding to eCAT.  Here is the Anti-PKN antibody template, for example

The above screenshot shows you the fields associated with the aliquots created from the new sample. There’s also a set of fields related to the sample itself.

Create your own sample types!

So eCAT comes preloaded with lots of different sample types, each of which has a record template associated with it. This helps you jump into eCAT with a running start.  But you’re not limited to what’s preloaded into eCAT.  Just the opposite in fact.  In designing the new sample management side of eCAT we’ve carried over one of the fundamental design principles that people rave about in the electronic lab notebook side of eCAT, namely flexibility.

You will almost certainly be dealing with types of samples that don’t come preloaded in eCAT, and even for preloaded sample types you may want to record different kinds of information about the samples than is provided for in the existing record templates associated with each sample.  So, In eCAT 4.0 we’ve made it exceedingly easy to create new sample types and edit templates associated with existing sample types!

Creating new sample types

The screen below shows how easy it is to create new sample types

To start  give the new sample template a name and, if you like, upload a new image for the new template.  All sample templates  come with Volume, Barcode, Sample Source and Description fields.  If that’s all the fields you want, just save the template and you’re done!  But you can also add whatever additional fields you want.  To do that just click on the add field button at the bottom right of the screen.

Amending existing sample templates

It’s equally easy to amend existing sample templates.  To do that simply copy an existing template and then use the following page to edit it

You can see that the screen is the same as the screen for creating a new sample template from scratch.  Simply give the new template a name, upload a photo for it if you like, and then add fields.

Next time: setting up sample management in eCAT 4.0

So that’s a quick guide to containers (last week) and samples,  the building blocks of eCAT 4.0, the electronic lab notebook that lets you manage experimental data and sample data together.  Next time I’ll cover how to set eCAT 4.0 up for your lab.