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How to teach biology, chemistry or physics with the electronic lab notebook eCAT

Posted by Rory on September 27th, 2010 @ 11:53 am

People often associate electronic lab notebooks with research.  That’s not surprising since that’s mostly what they’re used for!  But there is also  growing interest in using electronic lab notebooks as teaching tools, in both  universities and secondary schools.  For example, Dave Lunt at the University of Hull has an excellent presentation on using ELNs for student research monitoring.  In this post I’m going to go through setting up eCAT for teaching a class in science subjects like biology, chemistry and physics.  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/teaching/teaching.flv

The scenario

To make it practical, let’s use a real  scenario.  Say you’re teaching Biology 101.  You’ve got 20 students enrolled in the autumn semester.  As part of the course the students will be doing some exercises and also carrying out some experiments.  Some of these will involve group work, and some will be individual work, for assessment.  You want to use the electronic lab notebook as an environment where students can document experiments and carry out exercises, and you can see their work and comment on it.  You want some of the students’ work to be private — only you and each student have access to it.  And you want some of the work to be accessible more widely so that groups of students can work together.

Setting up eCAT

You can use either of the group versions of eCAT — Team Hosted, which Axiope hosts on our servers, or Install, which is installed on your server.  To get started you login as admin.

Both versions of eCAT come preloaded with a Projects folder and a Users folder. You’ll be using both of these folders.  Here a a few screenshots of eCAT illustrating some of the actions described below:

  1. To get started, click on the admin tab and then Users, and set up user accounts for the students who will be taking the class this semester/term.  When you do this each user will automatically get a home folder with their name; these will appear under the Users section of the record tree.
  2. When each user logs in, they can create whatever they want in their home folder and only they (and you the admin) can see it.
  3. Staying in the admin section, click on Groups.
  4. Create an All Users group, and add every user to this group.
  5. Create four working groups (we’ll call them Group A, Group B, Group C and Group D) with five students each; these are the groups that will be working together on experiments.
  6. Now go back to the record tree and, under Projects, create a new folder for Group A. To do this, click on “Create New” and then select “Create as Owner” after selecting the Folder class type. Call this folder, “Group A Materials”.
  7. Click on advanced Sharing, and give Group A view, edit, append and download permissions.
  8. Then create a child record under the Group A Materials folder – an Experiment.  But this time click on “Create as Parent”. Then also create a Document record in the same way.
  9. Do the same to create Materials folders and Experiment and Document records for Groups B, C and D.
  10. Now go back to the Record Tree, click  the Projects folder, and create a child folder called ‘Course materials’.
  11. Use this folder to place materials you want  people to look at.  For example, you may want to create a set of instructions for using eCAT during the course.  You can do this by creating a new document in this Course Materials folder.  You also can import pre-existing documents, spreadsheets and images, for example you could import an ‘Initial Materials’ document. Give all groups view permission for this folder so that they can see all the course work.

Using eCAT

It’s that simple!   eCATis now  set up and ready to go.  How you use it is of course up to you.  But here are some simple examples of the kinds of things you can do with the set up you now have in place.

  1. Document experiments.  Each individual student and each group can use the Experiment record that has been set up for the group to document their first experiment.  As shown below, the Experiment record already is divided into fields for Method, Procedure, Objective, Results, Discussion, Conclusion and Comments.  For the Group records, you may want to set up some standard procedures (see below for more on this) to ensure that things are well organized and recorded.  For example, you could have a rule that each time a member of a group makes an entry in a Group record they should place their initials by the entry.
  2. Comment on experiments.  As admin, you have edit permission on all the records that have been created.  So, you can comment on the experiments  the groups and the individuals carry out.  Just do this in the Comments field, and it will be clear that the comment has been made by you.
  3. Create new records.  You, individual students and groups can create new records, as needed, as the semester proceeds. You/they can create new experiment and document records.  You/they can also create other kinds of records from the more than 20 preexisting templates that eCAT comes with.  And both you and they can also create records of your own design using eCAT’s class creator function.
  4. Communicate.  You and the students can use eCAT to communicate about Biology 101.  You can send messages about assignments, deadlines, etc., and you can also create tasks.  In both cases these can be addressed to individuals or to groups, and in both cases you can include links to eCAT records, so for example you could send a message to Group A about a particular experiment they are working on with a note that you have made a comment on it, and you can link to the experiment in the message.

Instructing the class on how to use eCAT

At the start of the course you’ll want to introduce eCAT to the class.  There are various ways to do that, and you’ll probably want to use some combination of:

  1. Having everyone view the Getting started with eCAT video, on their own and/or as a class so that there is an opportunity for questions and discussion.
  2. Preparing some specific instructions covering how you have set eCAT up, how you plan to use it and standard procedures to follow, and making these available, e.g. in a powerpoint presentation (which can be attached to an eCAT record) or a document placed in eCAT.
  3. A demo of eCAT.

Getting eCAT ready for reuse next semester

Your eCAT  licenses are reusable.  So if you have 25 licenses, and a class of 20 – 25 students, you can keep reusing the licenses each time you have a new group of students.  So, when the semester is finished, you simply delete from the User list the students who have just finished the course, freeing up the licenses for the students in next semester’s course or another course.

Try for yourself

Now you’ve seen how it works; why not try eCAT yourself?  You can sign up for a 30 day free trial here.

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.

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.

Free electronic lab notebooks: Evernote and eCAT compared

Posted by Rory on September 2nd, 2010 @ 9:19 am

The Personal version of  eCAT is primarily used by postdocs and graduate students who want an electronic lab notebook  tailored to lab work.  In this post I am going to try to unpick the details of what that means — what kinds of things can you do in eCAT that you can’t do in general purpose free ‘ELNs’ (which when you scratch the surface are usually note taking devices of one sort or another)?  As a way of getting at the answers I’ll compare the Personal version of eCAT with the most popular note-taking software, Evernote, which is  used by lots of scientists.

First, some  things the free versions of eCAT and Evernote have in common:

  1. They’re both online and accessible anywhere, anytime.
  2. They’re both used by scientists to record and manage data from their research.
  3. They’re both simple to use.

But here are four things eCAT has that Evernote doesn’t have, and which help make eCAT a great tool for lab scientists:

  1. eCAT “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).
  2. eCAT comes preloaded with templates specifically designed for capturing and recording different kinds of scientific research.  There is a generic experiment template, and there is also an  antibody template, a freezer box template, a protocol template, a construct template, etc.
  3. eCAT makes it dead simple to build records of your own design, so you can create structures that allow you to  to effectively capture the kind of research you are doing.
  4. eCAT lets you add files to records.  So for example you can attach a spreadsheet with numerical data relating to an experiment, and confocal images of data which is analyzed in the experiment, to the experiment record.

Those capabilities are pretty useful.  That’s why more and more postdocs and graduate students, like Matt Nicotra at the University of Pittsburgh, are turning to eCAT as an ideal tool for  organizing and managing their experimental data.  Watch Matt talking about how he uses eCAT in this video.

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