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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!

The eCAT electronic lab notebook: a time saving technology for labs

Posted by Rory on September 14th, 2010 @ 8:51 pm

Last week eCAT was featured in an article called Time Saving Technology in the Nexxus News Autumn 2010 edition. The other companies featured in the article were:

  1. Actual Analytics, whose technology takes video footage of animals used in scientific research and automatically identifies specific behaviors.  This ensures that data about the animals is captured in an objective fashion, improving the quality of the data on which decisions are made, and significantly reducing the time involved.
  2. Lab901, whose ScreenTape provides a fast solution for automated electrophoresis of DNA, RNA and proteins.

Actual Analytics is about more efficient data capture, and Lab901 is about automated, hence faster, data processing.  The time saving element of each of these solutions is pretty obvious, more or less self evident.  Lab901, for example, says that “On multiple protein and antibody analysis, SDS-PAGE and full analysis can be completed within minutes instead of hours.”  The ROI is readily quantifiable there.  But what about eCAT?  Why did the folks at Nexxus(the Scottish life sciences networking group) decide to include an electronic lab notebook in the company of these two time saving technologies for labs?  I asked Kate Fink, and here’s what she said:

“One of the most consistent things we hear from people and small science businesses is how incredibly busy they are.  Something that saves them time can be a huge benefit . . . so I thought the article could be useful to them . . .  Turns out what tied the [three companies] together to form a cohesive article was their ability to improve efficiency.”

ROI on electronic lab notebooks

It’s a lot harder to quantify the efficiency gains which result when a lab adopts an electronic lab notebook than with the Actual Analytics and Lab901 examples.  Yes, some vendors have done studies concluding that in pharma labs which have adopted an ELN scientists produce and analyze the same amount of data in 80% of the time.   But without being involved in the study it’s hard to know how accurate these conclusions are, and in any event this kind of analysis is not that relevant to PIs in academia, who just don’t think about their labs or their students in these terms.

Decision making in academic labs

So what’s different about academic labs? Here’s a hypothesis:  it has to do with the decision making process.  In pharma labs, although the scientists may be consulted about the possible adoption of an electronic lab notebook, at the end of the day the decision is made by managers and supervisors, not scientists.  Once the decision has been made, training and mentoring will be provided to make the adoption process as painless as possible, but the scientists have no choice but to learn how to use the new system.

In most academic labs, it doesn’t work that way.  Many academic labs are really collections of individual researchers.  In these cases the decision whether or not to adopt an ELN is likely to be truly democratic and collective.  In other cases the PI exercises greater control and there is more of an orientation towards common research.  Even in these cases, however, it’s highly unlikely that the PI will make a unilateral decision about adopting an ELN.  It may be a managed decision, but there will still be strong collective input.

Joshua Shaevitz at Princeton makes the point that “the whole lab has to seriously embrace the new use of technology or the system will fail. Before implementing our wiki system, I setup a mock wiki ELN on my laptop and presented it during lab meeting to show everyone the benefits firsthand. I especially wanted to convince them that the new system would not generate extra work, but would instead make their lives easier.”

Academic labs:  ROI on the process of adoption

This means that for academic labs a key consideration in thinking about ELNs has tobe the the ROI on the process of adoption.  It’s fine to think about the productivity gains — for both individuals and the lab — that will come after the ELN has been adopted.  But these are a pipe dream unless adoption takes place in the first place.  And PIs know that adoption is not going to be easy.  A scientist in a regenerative medicine lab pointed out a typical attitude when he said:

“What amazes me is how little lumpiness there has to be in the use of something for everyone not to want to use it.”

With that attitude to adopting new tools so prevalent in academic labs, PIs know that it will be highly unproductive to attempt to coax, much less coerce, lab members into adopting an electronic lab notebook unless it not only is easy to use but also is easy to learn to use.

Electronic lab notebooks: easier than you think!

Electronic lab notebooks are often perceived to be hard to use, difficult, non-intuitive, and/or things which are only used in commercial settings.  That perception is itself a barrier, but it’s not necessarily a difficult barrier to overcome — with appropriate supporting evidence! — and hence need not be a big drag on the adoption process.  The comment made by Professor Mike Shipston at Edinburgh University (a PI) that

“It was a major surprise; transferring to an electronic lab notebook is actually very easy.”

captures both the typical perception that ELNs are difficult and the reality that adoption of  (in this case) eCAT was very easy.  Andreas Johansson at Lund University (a graduate student), makes the additional point that being easy to get started with eCAT makes it easier to encourage adoption among the lab as a whole:

“The main reason I chose eCAT is because it’s really easy to get started with and use.  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.  eCAT is easy to use; it also means I can ask my colleagues to use it as well.”

Electronic lab notebooks:  a time saving device whose time has come?

I have to say that even I was surprised recently when a new eCAT user, starting from scratch with no prior training or coaching, and completely on his own, created and filled out more than 40 new records, many of which he designed himself, in less than two days, involving only a few hours of work!  When word gets around about experiences like that, perceptions are bound to change, and that means a lower barrier to adoption and a higher ROI on the adoption process.  That’s good news if you’re a PI who is considering adopting a PI for your lab — time saved during the adoption process and time saved once adoption has taken place.

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?

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