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Quick Overview of eCAT

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What is eCAT?

eCAT is an electronic lab notebook for documenting and sharing experimental data, sample data and other kinds of information. eCAT has been designed to allow users to store, organize and share data of any form in any way you like. That's very important to scientists because no software can understand the work you do. It has to be flexible enough to adapt itself exactly as you want and that's what eCAT does.

Tabs

Across the top of eCAT are a series of tabs

eCAT tab menu

eCAT tab menu

You access things in eCAT and carry out actions through these tabs. Let's start with the dashboard.

The Dashboard

When you first login to eCAT you are taken to the Dashboard. This screen lets you see all your data inside the system and gives you a quick way of creating new data, or importing data from other sources.

Creating a record

To get started, let's create a new Project. To do this, mouse over the "Create New" menu at the top left page of the page, and select the "Project" entry.

The create new menu

The create new menu

You will be taken to the following page:

Editing a project

Editing a project


Projects

You have already created a Project and are now editing it! So what is a Project? Well it's a record. The other things that were in the "Create" menu would also have created records - a Folder record, an Experiment record, an Antibody record, etc.

As you can see Project records look pretty familiar - kind of like a Word Document. Projects have a single field called "Description". You can enter any kind of text here and when you click "Save" at the top you will have finished creating a Project. You are taken to the screen shown here - the created Project.

Viewing a project

Viewing a project


Working with records

Now that you are viewing the actual created record, you will notice that you are no longer in the Dashboard tab at the top of the page, but are instead in the Notebook tab. This is because you are now viewing a record. The menu on the left looks quite different from the Dashboard menu.

The record and children menus

The record and children menus

Most of the entries here should be reasonably familiar to you. You can do the normal things you would expect with a record in a file system - edit it, copy it, move it, delete it, share, etc. Let's instead focus on what happens when you use the menu under the Record menu - the Children menu.

Like the dashboard, the Children menu in a record has a Create New function. Here, however, you will be creating a new record that is a child of the current record. So we are going to create a new record that is a child of this Project. This is like making the Project a 'container' for whatever you are about to create. You can do this with all records - in eCAT all records can have child records.

Experiments

If you use the Create New menu here to create an "Experiment" you are taken back to the editing screen. Saving your record again takes you to the view of the experiment.

An experiment

An experiment

As you can see an experiment is very different from a project. Experiments have many fields, whereas there is just a single field in a Project. Experiments have fields for Method, Objective, Procedure, Results, Discussion, Conclusion and Comments. In other words, experiments have a structure that guides users in how they should complete these experiment records.

Record templates

eCAT comes preloaded with more than 20 templates in addition to Project and Experiment.

Creating your own templates

You can also create your own new record templates. You can create your own templates to describe whatever data you want - an Antibody, an Experiment, an Oligo or even a non-scientific object like a DVD collection if you felt so inclined. You can read more about records and templates here.

Folder Structure

So its easy to create different kinds of records, but where are these records actually being created? If you look at the top of the record, just under the Experiment title, you will see the record path. This is the location inside eCAT where the currently viewed record lives.

The record path

The record path

So Experiment lives inside First Project as we already knew because we created Experiment as a child of First Project. But it seems First Project lives inside something called "jonathan" which in turn lives inside "Users" which lives inside "Record Tree". This is all pretty straightforward.

Just like Windows or OSX, you have a file system in eCAT. This filesystem is made entirely of records. The top, or root, of the filesystem is called "Record Tree". Just like Windows and OSX we then have a Folder (a Folder is another type of record very much like Project but with no description field) called Users. Inside this folder, whenever a new user is added to the system a new home folder is created for that user. For the purposes of this help document we are logged in as jonathan.

The Dashboard, again

So the Dashboard creates records in a user's home folder by default. That's where we created First Project. We then created the Experiment inside First Project. Let's go back to the Dashboard and take a look:

The record path

The dashboard showing the new records

The Dashboard is now showing the two newly created records at the top of the list. That's what the Dashboard does - it takes you back to where you have just been working. You can get a lot of records into eCAT pretty fast, and the Dashboard also lets you filter and search quickly to find what you are looking for. For more information on this page click here.

Getting around in eCAT

Lets go back to the Experiment again. You can do that by clicking on the name of the record in the dashboard. Click on Experiment. Remember we created it in First Project in the home folder of a user called Jonathan. Here again you can see its path.

The tree/menu toggle

The tree/menu toggle

Now click on the TREE button above the menu.

The record tree

The record tree

The record tree is displayed. This shows you the hierarchy of records in a way that should be familiar to any Windows or OSX user - it's just like the list of Folders you see in Windows Explorer or Finder. You can use the record tree to navigate around records instead of using the Dashboard or drilling down from parent to child. If you wish to keep displaying the tree (instead of the menu) check the "Keep Open" checkbox at the foot of the tree page. For more information on the record tree, read this topic.

You have learned a lot already! You can now create and edit records of different types and find them on the dashboard, and you have an understanding of how eCAT stores these records in a tree structure. But there is a lot more to eCAT than that!

Managing sample data

You can do a lot more than just work with notebook entries - eCAT provides a complete sample management solution as well, and fully integrates that with your notebook. To get started with samples, go to the Inventory tab.

Before you can create samples, you need to first create a container. To start creating a container, click "Create New Container" in the main menu. You are taken to the following screen.

Creating a sample container

Creating a sample container

Here you can see all the container types in the system. There are many different types, but we are going to create a container that samples can go in (you can also create containers that contain other containers), so will create a Freezer Box for this example, so we will select "Freezer Box 8x8". The screen updates as follows:

Selecting a sample container

Selecting a sample container

Click next, and give your Freezer Box a name and a description. Click Finish and you have created a container.

Creating samples from here is easy. Just click on a location in the tray (note how the selected location is highlighted in red) and then click the create button (the most left button) as shown below.

Creating new samples

Creating new samples

The list of available sample templates is shown. Samples are very similar to records in eCAT in that they are defined by a template. The list of sample templates shown here is the list of sample types that comes preloaded in eCAT but just as with records its easy to create your own sample types in eCAT. See here for an a description of how to do that.

The sample templates

The sample templates

Select the Cell-Line Sample, and your sample is created in the location you specified.

One difference between samples and records is that samples can be aliquotted. This creates a set of samples that share a common piece of sample information based on the sample template, but that also have a set of values unique to each aliquot. You edit this aliquot and sample information in different ways.

Editing sample information

To edit this information, you click the following icon when you have a single sample or aliquot selected.

Editing sample data

Editing sample data

You are then taken to the editing screen. Editing sample information in eCAT is very similar to editing notebook records. Take a look at this topic for more data on editing.

Remember that if you have multiple aliquots of this sample, then all of the aliquots share this sample information that you are currently editing, so any changes will be reflected in all the aliquots.

Editing data for a single aliquot

The second type of information, aliqout information, is unique to each aliquot. You can edit that information by selecting an aliquot and clicking the button shown below.

The aliquot button

The aliquot button

The following dialog is shown:

Editing aliquot data

Editing single aliquot data

So you have easily created a container, stored a sample in it, and explored how eCAT stores sample information for aliquots and samples. You can do a lot more with samples including viewing sample reports, printing and barcoding, checkin and checkout of samples, setting alerts and working with samples on the Workbench.

What else can I do in eCAT?

You can work with your files in eCAT, either by importing them from your local computer or by linking to them from file stores inside eCAT. You can import most office documents like Word and Excel and many image types, even special scientific images such as Zeiss LSM or Biorad confocal.

As well as helping you manage your data eCAT also lets you share it and communicate with other eCAT users. There is an internal messaging and task manager system which you can read about here and here. You can also use the sharing systems inside eCAT to share your records with other users and groups, allowing them to collaborate with you on your projects.

There is also an easy to use and powerful search system which lets you find and display records in a variety of ways and a complete preferences feature which lets you setup eCAT the way you want it.

Don't forget that as well as this User Guide there are also videos which cover the things you can do and explain how to use eCAT. Click here for those.