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How to organize your lab with the electronic lab notebook eCAT

Posted by Rory on September 20th, 2010 @ 10:09 am

Background:  research in the lab

The electronic lab notebook eCAT can be configured in many ways.  One of the most common configurations is for the single lab, typically including a lab head, postdocs, students, support staff and possibly  visitors. In this post I’m going to show you a typical model for how to set up eCAT for a lab.  We’ve made a video that covers the same ground, so if you’d rather watch the video, here it is!

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/tutorials/research/research.flv

Lab information basically falls into two categories. First, there is public, i.e., lab-wide, information, such as protocols, supplies, reagants, etc. This can include research data that everyone should have access to. Second, there is information generated by one person and typically thought of as private, or at least only available to others at the discretion of the author. There is a third kind of information, research data related to activities of a group — I’ll consider that later.

Basic eCAT set up

Data in eCAT can be organised to look like this diagram  from Mike Shipston’s lab:

At the top level there are two folders for the two different kinds of information:  Users contains the “private” information, and Lab Resources contains the “public”, i.e., lab-wide, information.

Within the “Users” folder there is a subfolder for each lab member. The lab member can put whatever they want in there, but there will always be a set of folders named for the projects that person is working on, and within those project folders a set of experiment records for each of the experiments that person has done.

Within the “Lab Resources” folder there are subfolders for each of the different types of resource, such as protocols and molecular tools, and within those further subfolders, for examples constructs and oligos in molecular tools.

Sharing

One of the important aspects of this organization of information is the way sharing is set up.

By default, everyone can see inside the Users folder.

Within that folder, the permissions on the individual lab member’s folders are set so that only approved people can see what is in the folder and its children – the individual themselves, and perhaps the lab-head or other supervisor as well. Records below that, such as Projects and Experiments, are set to inherit permissions from their parent records – so they have the same permissions as the individual lab member’s folder.

The Lab Resources folder  does not come preloaded in eCAT and needs to be created. All subfolders of Lab Resources need to be viewable by everyone. Depending on how you want to run the lab, selected people or anyone in the lab will have permission to add records and edit records. For example, permissions on the the Constructs folder can be set so that anyone can add to it or edit records in it, while permission on  the Oligos folder can be set so that only a few users can add to it or edit records contained in it. Again, lower-level records are set to inherit their permissions from their parent record so that they have the same behaviour as is set at the higher level.

Groups

We’ve seen how eCAT can work with individual users. You can  use Groups to make sharing even simpler. For example, you may want to create a group for the members of the lab working on a specific Project.

You might want all the work for that Project to be placed in one folder, with any member of the group able to add records and edit records in that folder. In that case you’d establish a folder Project X in the Projects folder. And for permissions you would create an eCAT group with all the people working on project X in it, and set the Project X folder to give permission to that group to add and edit. An advantage of having the group is that you don’t have to set permissions for each individual.  When someone joins the lab or leaves you can simply  add them to the group or remove them from the group.

Customizing eCAT

So that’s an example of a structure you can use to get your lab working with eCAT. There are also various ways to customize eCAT so that it better fits your work pattern. One simple way to do that is to customize the Favorites menu on the Dashboard page.

The Dashboard lets you quickly see records you have been working on and the Favorites menu lets you filter the Dashboard. So clicking on “My Projects” shows you just the Projects you can see.

You can customize the Favorites menu by clicking on “Customize menus” in your Preferences. You are taken to a page which shows the classes in the system. For example, if you always work with Lab Protocols and want to be able to quickly see them, you can add them to your Favourites menu.  When you return to the Dashboard My Lab Protocols is now visible, and clicking on the My Lab Protocols link shows you just your protocols. This is just one example of how you can customize eCAT by using Preferences!

So that’s a quick overview of organizing lab research information in eCAT. eCAT is incredibly flexible, so an almost infiite variety of  variations are possible.  Why not sign up for a free trial and explore what set ups makes sense for your lab!

Notifications in the electronic lab notebook eCAT

Posted by Rory on September 6th, 2010 @ 9:03 am

Increasingly electronic lab notebooks are about more than just recording experimental data.   They are tools, platforms, environments — call them what you will — that support collaboration among groups of scientists.  Sometimes those scientists are in the same lab or at least the same building.  Sometimes they are spread out around the world.  Regardless of the number of people involved and their locations, productive collaboration is not possible without effective communication.  So the new breed of ELNs needs to include good mechanisms for communicating.

With this in mind, Version 3.3 of eCAT, which was released in July, has a new notifications system.  It’s designed to be

  • simple
  • easy to use
  • closely integrated with eCAT’s collaborative research capabilities

A simple system

There are two kinds of notifications in eCAT — messages and tasks — and they are exceedingly simple.  They look just like emails, and in fact they are  kind of an  email system which is internal to eCAT.

Easy to use

The notifications tab appears at the top of each eCAT page.  To send a message or a task, you start by clicking on the notifications tab.  Then you choose create task or create message.  If you choose create message the following screen appears:

Then enter who you want to send your message to — one or more members of the group you are working with — fill in the subject, compose your message and press send.  Pretty simple — just like an email.  And a red flag will appear on each recipient’s notifications tab, so they know that there is a new message waiting for them to read.

Enhances research collaboration

So far so simple and easy, but the neatest thing is how notifications in eCAT integrate with the rest of eCAT.  To see how that works let’s look at another screenshot, this time of a task which has been composed and is about to be sent:

You will see that there is a link to the mouse colony experiment, the experiment I want Nigel, Jonathan, and Leigh to comment on.  And actually this is a record like other eCAT records, so you have the full power of eCAT’s editor at your disposal in composing this task.  In addition to making a link to the mouse colony experiment, you could have linked to web pages, inserted images, included more complicated formatting, etc.  So you’re able not just to send isolated messages, but to create messages and tasks which are tightly integrated with the work you and your colleagues are doing. eCAT provides an integrated environment for collaboration and communicating about that collaboration.  That’s useful when, as in this example, you are doing joint research.  It’s also useful for instructors who are using eCAT as a teaching tool.  You can send messages and set tasks for an individual student, a group of students, or the whole class.  And, with tasks, as shown in the above screenshot, you can set priorities and due dates.

So there’s an introduction to eCAT’s notifications system, and how it can help you and your group enhance your collaboration through better communication.

Adding structure to your research with databases in the electronic lab notebook eCAT

Posted by Rory on August 2nd, 2010 @ 7:00 am

In the last post I talked about various ways of making use of templates in eCAT.  In this post I’d like to touch on a way in which you can add another layer of structure to research data in eCAT — databases.

eCAT makes it easy to construct databases — this happens automatically when you add links between records.  eCAT comes preloaded with three example databases.  Let’s take a brief look at two of them to get an idea of the kinds of databases you might want to create in eCAT.

The first example

shows how a series of records can be linked togethe rin eCAT  to manage inventory.  Each of the items in green represents a different class of record in eCAT.  Boxes (Freezer, Shipping) contain bidirectional links to the items stored in them, in this case Antibodies. Freezer Boxes also are linked to their storage container, in this case Freezer. The Shipping Box class is not contained in a Freezer, but does have a link to an external Internet URL – the tracking website for the courier company. This database comes with built-in documentation in records of class Documentation Page, which contain links to all the different classes used in the database.

In the second example

the Experiment records contain links to Lab Protocols, Mutagenic Oligos, etc. Other classes are generally not linked, but Project records are connected in a parent-daughter manner to Experiments.  So, Professor Mike Shipston lab at Ednburgh University is able to record its experimental data in a single integrated environment, with multiple links to other data the lab deals with such as protocols, constructs and oligos.

Databases for managing inventory and integrating your experiments in the broader context of your lab’s research are just two of the virtually infinite ways in which you can organize your data in eCAT.  Its this kind of flexibility that leads to comments like the following from Mike Shipston:

“The great thing about the eCAT electronic lab notebook is, its incredibly flexible in terms of how you can set it up.”

Using the electronic lab notebook eCAT as a replacement for a paper lab notebook

Posted by Rory on July 26th, 2010 @ 7:00 am

Wikipedia defines electronic lab notebook as “a software program designed to replace paper lab notebooks“.  So how can you use eCAT to replace something that looks like this?

Let’s look at this question first from the individual’s point of view and then from the lab’s point of view.  Here’s what Andreas Johansson of Lund University in Sweden says:

“I use eCAT for everything in the laboratory when I need to make a note of anything.  I use it for my experiments and my protocols.  But I also use it for things I didn’t use it for before I had an electronic lab notebook.  I use it for digital photos, so protein gels, screenshots of my HPC runs, screenshots of the small things I see during my experiment.  Before I would have just made a small note about it, now I have a photo of it.  And I also add time stamps during an experiment so I can easily see at what point I did a certain thing.

The main result is very very large quality improvements.  It also brings structure to your experiments automatically.  Since you are working with project folders you have your own experiments, and you also add protocols, and you add the data and you add whatever electronic stuff you get during the experiments to that folder.  So everything gets sorted by date and time.

And here’s what Alex Swarbrick at the Garvan Institute in Sydney, Australia says about his lab’s use of eCAT:

Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, perhaps the most important feature for us is the ability to link records, reagents and experiments. This allows us, for example, to connect an experimental mouse with the tube containing its tissues in the freezer, to the 6 different experiments (conducted over a year) that analysed those tissues in different ways. Managing this kind of ‘metadata’ is absolutely essential to our work, and very difficult to do without tools like eCAT.”

Of the many benefits of using eCAT as an electronic lab notebook noted by Andreas and Alex, three are worth highlighting:

  1. eCAT serves as  a ‘paper lab notebook plus’ because you can use it to record not only garden variety experimental data but also things like images and spreadsheets which can’t conveniently be entered into a paper lab notebook.
  2. eCAT allows you to manage other kinds of information such as notes from meetings, protocols and inventory, as well as experimental data, in a single, integrated environment.
  3. Unlike a paper lab notebook, which by definition is a tool for individuals, eCAT is a group tool that allows controlled  sharing of data.

4 Things PIs like about the electronic lab notebook eCAT

Posted by Rory on July 19th, 2010 @ 7:00 am

Today I thought I’d let some PIs who are using eCAT in their labs speak for themselves about eCAT.  Here are four things they like about it:

  1. “The great thing about eCAT is, it’s incredibly flexible in terms of how you can set it up. For example each member of the lab has their own folders and puts their own experiments within that, but it’s every easy to put that information together.” (Mike Shipston, Edinburgh University)
  2. “Perhaps the most important feature for us is the ability to link records, reagents and experiments. This allows us, for example, to connect an experimental mouse with the tube containing its tissues in the freezer, to the 6 different experiments (conducted over a year) that analysed those tissues in different ways. Managing this kind of ‘metadata’ is absolutely essential to our work, and very difficult to do without tools like eCAT.” (Alex Swarbrick, Garvan Institute)
  3. “With eCAT we were able to organize all our projects and materials, and create an integrated and searchable database of our work.” (Michael Shtutman, Ordway Institute)
  4. “Because it’s accessible over the internet eCAT is easy to view, from my office or my lab, or at home.” (Larry Gonzalez, University of Oklahoma)

Why not sign up for a free trial and find out how eCAT can help you keep your lab and your research data organized?