Where sample management meets electronic lab notebook



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4 ways to get the most out of templates with the electronic lab notebook eCAT

Posted by Rory on July 29th, 2010 @ 7:00 am

Version 3.3 of eCAT, which was released on July 8, comes pre-loaded with more than 20 templates.  Here are four ways to make good use of them:

  1. Get an idea for how other scientists are using eCAT.
  2. Understand the wide range of information that eCAT can help you to manage,  from experimental data to protocols to freezer samples to meeting notes to CHiP extracts to constructs to records about lab personnel and equipment.
  3. Grab a template for your own use; by clicking the “Copy Template” button at the top of the template, you will create an editable copy of the template in your home folder.
  4. Make a blank version of the template; clicking the “Create New” button at the top of the template will create a blank version of the template with the fields not filled in.

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 postdocs and graduate students like about the electronic lab notebook eCAT

Posted by Rory on July 22nd, 2010 @ 7:00 am

Last time some PIs told us what they like about eCAT.  This time its the turn of postdocs and graduate students.

  1. The thing I like best about eCAT is it’s very simple to use.  I looked at some other electronic lab notebooks and they were complicated or overly designed.  eCAT has a very simple interface.  It’s very flexible so I can just go in and immediately start writing my lab notebook the way I used to with a paper lab notebook.  It’s simple, I don’t have to spend any time figuring it out.” (Matt Nicotra, University of Pittsburgh).
  2. “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.  It’s much more structure, automatically. (Andreas Johansson, Lund University)
  3. “Members of our labs are starting to realize the power of allowing them to more natively integrate electronic sources of data (documents, images, web links, etc.), which was not something readily accomplished with a paper notebook.” (Morten Jensen, University of North Carolina, Chapel Hill, and Hoang Pham, Lawrence Berkeley Labs)
  4. “The great thing that we saw in eCAT was a system that could be suited to varying needs as they change over time. It had a nice architecture in place that could be well suited to our needs right now, but also one that was flexible enough to handle all kinds of different data needs as they emerge in the future.” (Trevor Covert, Washington State University)

Why not see for yourself?  Sign up for a  free trial of the Team Hosted or Install versions of eCAT, or get your own free Personal account!

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?

7 Things you can do in the electronic lab notebook eCAT (but not Google Docs!)

Posted by Rory on July 15th, 2010 @ 7:00 am

In the last post I looked at how the interface of eCAT version 3.3 is  modelled on the familiar interface of Google Docs.  This time we’ll take a look at things labs can do in eCAT to document experiments and structure and share research data.  Things you can’t do with Google Docs.   It’s a long list but here are some of the main ones:

  • Create templates like the following one with the structure that suits your research rather than the structure imposed by a spreadsheet, a word document or a wiki page

  • Use links between records to create databases like the following one that capture your workflow and relationships like those between an experiment and the samples used in the experiment

  • Utilize the structures you put into your research records to (a) set up uniform methods of entering data, improving its quality and consistency, and (b) conduct fine-grained search — e.g. on all the records with Procedure field containing ‘ELISA’ — so that eCAT becomes a  repository which can be used by newcomers to the lab and others who did not work on a particular piece of research
  • Set up groups of users and variable permissions on a record by record basis, e.g. give the PI view and edit permission on the records in a particular Project or, on a postdocs’s experiment, give view only permissions to a PhD student who has been assigned to observe the experiment, and keep some records entirely private
  • View a full audit trail of all actions undertaken in eCAT
  • Sign and authorize experiments
  • Send messages and set tasks, which can be associated with particular records, so that eCAT becomes a tool for communication as well as collaboration

In sum,with eCAT you get the all the advantages of an online collaborative tool like Google Docs and the ability for everyone in the lab to bring their labbooks online.  So you can manage your research data along with general lab information in a single, integrated collaborative environment.

Familiar interfaces: Why the electronic lab notebook eCAT and Google Docs have similar dashboards

Posted by Rory on July 12th, 2010 @ 7:00 am

When we brought out  version 3.3 of eCAT last week we made the interface

look a lot like the Google Docs interface

Why?  We’re following the advice of our eCAT users! One eCAT user, Andreas Johansson at Lund University in Sweden,  made the point that:

If something is hard to get started with and easy to use a lot of people will just have a look at and never get around to starting the first experiment. The main reason I chose eCAT is because it’s really easy to get started with and use.

We want you to take advantage of  the extra functionality  eCAT offers without having to spend time finding your way around an unfamiliar system.  We know that a lot of labs are using Google Docs as a document sharing and group editing tool, so we thought it was the obvious model to look to when we decided to redesign eCAT’s interface.

The first thing you’ll want to do in eCAT  is either create a new record or import/upload an existing one.  In both Google Docs and eCAT you can do this at the top left.  Then across the top of the page in both Google Docs and eCAT there is a set of tabs giving you access to other things you can do.  And finally, they both give you a list of your recent records in the main body of the page — just like your email inbox.

Another feature  that people find useful in Google Docs is the template page

So, we’ve made a new template page in eCAT that, once again, is modeled on its Google Docs counterpart

So if you use Google Docs, you should find eCAT easy to get started with and use.

10 reasons to try an electronic lab notebook — eCAT version 3.3!

Posted by Rory on July 6th, 2010 @ 3:59 pm

We’re launching a new version of the electronic lab notebook eCAT today.  Why is version 3.3 special?

First, the new features:

  1. a familiar dashboard modelled on Google Docs
  2. the ability to import spreadsheets, images and documents with a couple of clicks
  3. an extensive set of useful templates — experiments, antibodies, CHiP extracts, protocols and many more
  4. a notifications system
  5. a complete series of brief  ‘how to’ videos, embedded on each page of the application, describing the actions you can do on that page.

Second, enhanced support for people interested in learning about electronic lab notebooks and testing eCAT:

  1. The electronic lab notebook blog, covering everything you want to know about electronic lab notebooks
  2. A series of tutorial videos — such as eCAT for PIsGoogle Docs and eCAT, Wikis and eCAT, Patent protection with eCAT, etc.  —  available on our website
  3. An automatic installer that makes it a breeze to set up an eCAT trial
  4. This eCAT blog,  discussing how to get the most out of eCAT and answering questions from users

Third, a growing number of forward looking PIs are adopting eCAT because it combines ease of use, flexibility and the ability to add structure to their research data and enhance collaboration in the lab.  Here’s what Professor Mike Shipston, Director of the Centre for Integrative Physiology at the University of Edinburgh, has to say:

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/user/shipston/shipston.flv