Where sample management meets electronic lab notebook



Current Articles | RSS Feed

Exporting data from an electronic lab notebook

Posted by Rory on March 15th, 2012 @ 6:08 pm

The importance of export

Most electronic notebooks are locked down, and are built on the principle that things should be kept within the system and not shared outside it.  But that doesn’t fit with the real requirements of researchers, who need to be able to control  access to and sharing of their data.  For example, you might want to export some data to share with a collaborator who isn’t using the same electronic notebook as you, or you might want to export all your data when you are moving on to another lab.  So, as I have argued elsewhere, http://elnblog.axiope.com/?p=1037, it’s important to be able to export data from an electronic lab notebook.

eCAT’s new data export capability

We’ve just released a new version of eCAT (4.0.11) which, for the first time, supports export (other than exporting the XML, which is already possible.  With the new version it’s possible to export from both the Notebook and the Inventory (i.e. sample management) sides of eCAT.

eCAT Notebook records are now exportable to ODF (Open Document Format = the format for Open Office).  We have chosen that format for two reasons.   The first is that eCAT is platform-agnostic; it runs on Windows, OS X and Linux, and so does ODF.  The second is that ODF supports retention of links and embedded images, so after export the formatting will be retained.

It’s also possible to export eCAT Inventory records to CSV.  We have chosen to start with CSV because in our experience scientists like to see sample data in spreadsheets.

We see this initial  export capability as a modest but important starting point for making data from eCAT ‘portable’. We plan a series of future releases with additional kinds of export capabilities.

The following brief video shows you how the new export function works.

http://www.axiope.com/electronic-lab-notebook/video/export/export.flv

Electronic notebook for a PhD student

Posted by Rory on February 15th, 2012 @ 10:33 am

The goal:  a paperless PhD

Mark Hughes, a first year PhD student at Edinburgh University whose research focuses on better understanding of neuronal networks, had a novel idea:  to do a ‘paperless’ PhD.  The reason was simple: “The potential exists to do almost everything electronically so why complicate matters with paper?”

The right lab

Luckily for Mark, one of his supervisors, Professor Mike Shipston, head of the Centre for Integrative Physiology at the University of Edinburgh, was already using the eCAT electronic lab notebook.  Mike introduced eCAT to Mark and suggested that Mark use it from the outset of his PhD.

Issues to consider

Mark was concerned about three issues in particular:

  1. Experimental design
  2. Where to store his data
  3. Backing up the data

How Mark uses eCAT

Mark uses eCAT “as a  place to articulate thoughts (e.g. experimental design, planning a supervisor meeting) and as a place to summarise (and sometimes store) findings and important data.”  So it solves the first of his two issues.  The eCAT he uses is installed on computers in the Shipston lab, which takes care of data backup, so his third problem is also solved.  If Mark used the free Personal version of eCAT, a cloud service hosted by Axiope, his data would be backed up nightly by Axiope, so again this issue would be taken care of.

How eCAT helps Mark

Mark says that eCAT helps him in three ways:

  1. It serves as a daily reminder of scientific theory . . . why am I doing this experiment?!
  2. It’s also an electronic repository for his thought processes.
  3. He can store data in eCAT or link data to it.

You can view Mark’s presentation, “eCAT for a 1st year PhD student“, here.

 

How to drag and drop files into an electronic lab notebook

Posted by Rory on December 16th, 2011 @ 10:33 am

Drag and drop.  It’s often the easiest way to work with files.  You can do it with Dropbox.  You can do it with Google Docs. And now you can do it with an electronic lab notebook!

Today Axiope is releasing version 4.08 of eCAT.  With version 4.08 you get the convenience of drag and drop, and the full functionality of a simple to use electronic lab notebook.

To see drag and drop in eCAT 4.08 in action, watch this video

http://www.axiope.com/electronic-lab-notebook/video/import-overview/import-overview.mp4

What if the scientists in Naturally Obsessed had used iPads?

Posted by Rory on October 4th, 2011 @ 12:40 pm

 

Professor Mike Shipston using eCAT on the iPad in his lab

 

Imagining Naturally Obsessed in the age of the iPad

About a year ago I wrote a post speculating about how the research dynamics in the Shapiro lab might have differed if the scientists in the film Naturally Obsessed: The Making of a Scientist had used an electronic lab notebook.  The award winning film chronicles the experiences of three PhD candidates in the laboratory of molecular biologist Lawrence Shapiro at Columbia University Medical Center.   Here’s the plot, as summarized on the Memorial Sloan-Kettering Cancer Center website

“In the film, shot mostly in Dr. Shapiro’s lab, the students are trying to beat worldwide competition in identifying the molecular workings of the protein AMPK, which controls whether fat is burned to produce energy or is stored as fat. The three scientists struggle with various personal challenges: Robert Townley has a history of rebellious behavior; Kilpatrick Carroll questions whether he should leave academia for industry; and Gabrielle Cubberley wrestles with self-doubt about succeeding in such a competitive environment. At the end of the film, Townley achieves success in his project and publishes the results, with Dr. Shapiro as the only other co-author, in the journal Science.”

I concluded that the use of an electronic lab notebook would have changed – for the better – the relationships between the lab head and graduate students, among the students, and between individuals and their own research.

A year has passed since that post but it seems more like a generation because of the advent of the iPad.  It occured to me that it would be fun to take another look at the Shapiro lab, and speculate about how the research dynamics in the lab would have further evolved if the lab members had accesss to iPads.  To bring home the possibilities that have emerged with the iPad, I’ve used a couple of photos of the iPad in action in a lab environment, not the Shapiro lab, but the lab of Professor Mike Shipston, Director of the Centre for Integrative Physiology at the University of Edinburgh.  Using Mike’s lab as an example brings the story down from the cloulds of speculation into the concrete world of the here and now, because the members of Mike’s lab are already using an electronic lab notebook – eCAT – and eCAT is now available on the iPad.

Reimagining the way you relate to your research

Some quotes from the film give a flavor of the research experience of the Shapiro lab members:

“Two and a half years of doing experiments and having them not work.”

“We did an experiment a year ago, the crystals were too disordered.  We went back to the drawing board.”

“You learn so much from failure, nothing from success.”

With the eCAT electronic lab notebook on an iPad, you have an electronic version of your lab book.  That’s pretty amazing.  Like your lab book, you can take it with you everywhere in the lab — at your workbench, to meetings, etc.  And eCAT has a sample management system built in, so you can also use your iPad when you’re checking samples in or out of the freezer.  But unlike your paper lab book, eCAT is electronic, so you can  make links between experiments and protocols or meeting notes, and between experiments and the samples used in the experiments.  And searching for information is much easier, and can be carried out in a fine grained way that’s impossible in a paper notebook, e.g.  you could search for all the experiments that have a methods field containing the word Elisa.

So it seems clear that if Rob, Kil and Gabrielle had been using eCAT on the iPad, their experience would have been markedly improved.  Yes, there would have been plenty of failed experiments, but they would have spotted the errors and problems much quicker, and hence made better and earlier use of their failures.  And they would have had a better handle on the crystals and how they related to the experiments the crystals were used in, again accelerating the learning process.

Mike with eCAT on the iPad at the freezer

Sharing your research with colleagues

There was plenty of one to one interaction between the Shapiro lab mambers  – Kil sums it up when he says, “It’s not just my data that enriches the experience, Rob has been sitting across from me, working here, and has done many experiments that I never would have thought to do, and they’ve turned out to be really useful.”

The possibilities for sharing and digesting information would be greatly enhanced just by using an electronic lab notebook — Kil and Rob could have shared their experimental writeups online, anytime, anywhere, not just when they were together in the lab, looking at someone’s lab notebook.  With eCAT on the iPad, the potential for sharing and collaboration takes another leap forward.  With iPads you can ‘compare notes’ and quickly find past experiments and, e.g. the protocols that were used in those experiments, anywhere in the lab, at the workbench or the freezer, or outside the lab, over lunch.   And the iPad is inherently ‘shareable’ in a way that a pc or mac, or a lab notebook, is not; Kil would be able to say to Rob, ‘here, let’s try this,’ on Rob’s iPad if he wanted to illustrate an idea.

Improving lab dynamics

eCAT on the iPad makes possible better communication and sharing not only on a one to one basis, but also across the lab.  In the absence of an electronic lab notebook, the Shapiro lab appeared to operate through a series of one to one relationships, between the PI, Larry, and each student, and between individual students.  An electronic lab notebook  provides a convenient environment where the lab, as a group, can share research and ideas about their research.   eCAT on the iPad enables this sharing to take place in an instant and immediate fashion.  For example, in a lab meeting you can show the other members of the lab the results of your current experiment, and if you have made a link in the experiment record to the protocol used in the experiment, when the PI asks about the protocol, instantly bring it up for discussion.  Then, if you are tasked with taking notes about the meeting, when the meeting moves on you can switch to the document you’ve created for the meeting note, and then share that with everyone as soon as the meeting has ended.

Naturally Obsessesed and Nicely Enabled

The Shapiro lab depicted in Naturally Obsessed and Mike Shipston’s lab are engaged in the same pursuit of scientific knowledge and understanding, and use the same (painstaking) experimental method of trial and error.  But thanks to its use of eCAT on the iPad, the Shipston lab is improving the dynamics of the research process for individual members of the lab and for the lab as a whole in ways that the Shapiro lab, back in 2004 – 2007, could barely have imagined. Fundamentally, the Shipston lab is enhancing and accelerating the ability to learn from trial and error, by making it possible to carry out higher quality experiments and complete them more quickly.  That’s pretty exciting!

Mike with eCAT on the iPad in his office

 

How to make your iPad your lab notebook

Posted by Rory on September 9th, 2011 @ 10:30 am

Your iPad can now be your lab notebook!

Have you ever wanted to make your iPad your lab notebook?  That’s now possible, with the free version of eCAT.  Let’s see how.

Sharing your experiments

Say you’re at the weekly lab meeting, and want to show the other  lab members the experiment you’ve been working on.  You tap on the experiment in the list of records under your dashboard . . .

and the experiment appears.

Your PI asks about about the protocol used in the experiment.  So you just tap on the link to bring up the protocol record . . .

And the protocal appears!

Taking notes

The meeting moves on to a discussion of how to operate the new microscope your lab has just acquired.  You create a new document and start taking notes.

Back at your computer

After the meeting, back at your computer, you find that your new document has been added to the list of records on your dashboard.

That’s because eCAT runs on any web browser, so you can access it, on you iPad, your iPhone or your pc or mac, anywhere, anytime.

To learn more, watch the following video

http://www.axiope.com/electronic-lab-notebook/video/eCATiPadNotebook.m4v

 

How to manage freezer samples using your iPad or iPhone

Posted by Rory on August 17th, 2011 @ 8:55 pm

The iPad: now available for managing freezer samples!

Do you have an iPad or iPhone?  If you do you’re probably already using them in the lab — for example for  reading, and for taking notes when you’re away from your computer.  Perhaps you’ve also thought about using your iPad or iPhone to take notes about or find freezer samples. For example when you’re at the freezer and your computer is back at your workstation.  That would save having to take notes about the samples and then enter the notes again in your computer.

Well, that’s no longer a dream; it’s now eminently possible!  In fact it’s easy!  We’ve just optimized the sample management system in our eCAT electronic lab notebook for the iPad/iPhone.  Here’s how it works.

At the freezer

You’re at the freezer, and you’re going to check in some aliquots you’ve made from a new sample.  You first tap on the freezer you want,

Then select the locations in the box where you want to store the aliquots.

Then select the type of sample you want to enter from the pop up list — cell line in this case —

and the three aliquots appear in the freezer box locations you’ve selected:

While you’re at the freezer, you decide to take some notes about the aliquots you’ve just put in the freezer.  For example, you decide to add an expiry date in the record associated with the aliquots:

Back at your computer

Later, back at your computer, you find that all the information you entered in your iPad is already in eCAT!   When you were at the freezer you made a link between the aliquot record and the record of the experiment where you’ll be using the aliquots.  So, when you’re writing up the experiment you will always to able to see at a click information about the aliquots — where they are stored, what’s happened to them, etc., by just clicking on the link to the aliquot record at the bottom of the experiment record.

 

So there it is: with eCAT on the iPad it’s easy to manage freezer samples, and use them in your experiments. To learn more, watch this video:

http://www.axiope.com/electronic-lab-notebook/video/eCATiPadInventory.m4v

 

 

 

 

 

eCAT 4.0, the electronic lab notebook with sample management, is here!

Posted by Rory on May 20th, 2011 @ 3:18 pm

With the launch of version 4.0 eCAT, the flexible electronic lab notebook, now includes a full sample management capability! 

Beta testers gave 4.0 a big thumbs up.  Sample management is the remaining feature they wanted to make eCAT a killer app.  PIs tell us eCAT 4.0 is saving their lab members a huge amount of time, and that it has become an essential part of the lab fabric.

In the webinar launching eCAT 4.0, Kevin Cauchi from the College of Literature, Science and the Arts at the University of Michigan said,

“One of the things about eCAT that stands out is it’s affordable, unlike 99% of the systems we looked at.  Also, it’s web based, and it’s very flexible.  Other solutions make you modify the way you work; eCAT let’s you work the way you already work, just in an electronic format. “

You can watch the launch webinar, which includes an introduction to sample management in eCAT, a panel discussion with Kevin Cauchi, Nigel Binns from the University of Edinburgh, Matt Nicotra from the University of Pittsburgh and Nick Gregory of Brady Corp, the leading supplier of labels to labs, and a Q&A with viewers, at http://www.axiope.com/electronic-lab-notebook/blog/product/?p=238.

How to use Google calendar to share information in a lab

Posted by Rory on May 10th, 2011 @ 5:43 pm

Google Calendar in the lab

Lot’s of people  in biomedical labs use Google Calendar. Because multiple calendars can be created and shown in the same view, and each can be shared, either read-only or with full edit control, and with specified people or with everyone in a group via the ‘public calendars’ function, Google Calendar has also become popular with labs for sharing scheduling information around the lab.

Google Calendar in an electronic lab notebook

Google Calendar already integrates with other Google applications, in particular gmail.  But until now it hasn’t been possible to conveniently sync Google Calendar with core lab activities like documenting research and managing samples.  We thought that was a shame, and to put things right we’ve integrated Google Calendar into the latest version of our electronic lab notebook eCAT, which will be launched tomorrow!   Here’s a screenshot showing you what a Google Calendar in eCAT looks like — i.e. just the same as it looks on its own!

 

We’ve made a brief video showing you how to embed a Google Calendar in eCAT. After the launch of eCAT 4.0 on May 11 you can watch the video here.   In this post I’d like to highlight how to use a Google Calendar in conjunction with other features of eCAT to help collaboration and communication with other lab members.

Making the most of Google Calendar in eCAT

With eCAT 4.0 it’s possible for labs to  integrate Google Calendar’s scheduling capability with the rest of their work, including documenting their research and managing samples.  This is a case of 1 + 1 = 3:  eCAT + Google Calendar allows for a step jump in collaboration and communication in the lab.  Here’s how.

As the video explains, when you integrate Google Calendar into eCAT you keep the full range of sharing options you have with Google Calendar — the Calendar can be completely open, or shared with just some members of the lab, and one person, several people or everyone can have edit permission.  And of course you can have more than one calendar in eCAT, so one can be for things that everyone needs to know about, and another one, for example, might be for a group within the lab that’s working together on a particular project.

When you think about it, this fits like hand in glove with eCAT’s own sharing capabilities.

Sharing records

First,  eCAT lets you keep some records private, share other records with selected members of the lab, and have some records be public amongst all lab members.  And like Google Calendar you can set view, edit or edit and view permission on an individual user basis.   There’s more about sharing in eCAT here.

Sending messages

Second, eCAT’s notifications system (explained in more detail here) allows you to send messages and set tasks for others in the group, and include links to other eCAT records in the message.  So for example you can send a message to your PI saying that a particular experiment is ready for their review and including a link to the experiment so that all they have to do is click on the link to be taken to the experiment.  Assuming they have edit permission, they can then comment directly in the experiment.

Setting alerts

Third, the new sample management side of eCAT that’s been added in version 4.0 allows you to set alerts on samples when the sample expires, when the volume reaches a certain level, etc.  Again, these can be shared with other specified members of the lab (For more on alerts, after May 11 you can watch the following video).

eCAT + Google Calendar = a complete collaboration and communication environment!

So with eCAT 4.0 + Google Calendar you have a shared environment for managing samples and documenting research, and an easy way for communicating about your research which includes scheduling, messaging and alerts on samples. We think that’s pretty exciting!

 

What is sample management?

Posted by Rory on May 4th, 2011 @ 12:02 pm

 

Three conceptions of sample managment

Sample management seems like a pretty simple concept — managing your samples for goodness sake!  But in the context of a lab things get a bit more complicated.  I’ve commented below on the three different conceptions of sample management, the perspectives and objectives they imply, and the kinds of tools available for managing samples in each of them.

Samples management as part of a LIMS

Strangely wikipedia does not have a separate entry on sample management.  Instead sample management is covered under section 2.1.1 of the LIMS entry!  There it says, “the core function of LIMS has traditionally been management of samples.”  The entry goes on to point out, however, that over the past 20 years  the focus (or at least the focus of people who look at sample management from a LIMS perspective!) has shifted from managing samples to managing information.  For clinical research and other kinds of research in heavily regulated environments samples have been reduced to a subsidiary role; they are just one of many kinds of  ‘information’ whose history needs to be recorded and tracked, and to the extent possible integrated with other kinds of information about relevant things taking place in the lab.  In these regulated environments the key drivers are accountability and reproducibility:  everything needs to be tracked, recorded, analyzed and prepared for subsequent review and attack.

Sample management as sample tracking

A second perspective puts the focus back on the samples themselves.  Perhaps partly as a corrective to the relegation of samples  in heavily regulated environments to just another form of information, ‘sample tracking’ has developed as a distinct activity in its own right.  A prime example is biobanking. A biobank is defined by Wikipedia as a cryogenic storage facility used to archive biological samples for use in research and experiments.  In biobanking the focus is firmly back on the samples themselves, and as such it is important to track everything that happens to them:  their provenance, when they enter the bank, what happens to them after that, etc. Samples are used in research and experiments, but the focus of the management is on the samples themselves, not the research or experiments or, as when LIMS are involved, the entire information history of the research environment.  Biobanking applications, both generic systems and bespoke systems created or commissioned by biobanks, have developed to carrying out the tracking functions needed by the biobanks.

Putting sample management back into the experimental process

‘Originally’, or back before LIMS and then biobanks anyway, samples were created and collected primarily to be used in experiments and research.  As can be seen from the brief look into LIMS and biobanking above, somewhat ironically one consequence of the scaling up of research that is both cause and consequence of increased regulation and mass collection and storage (biobanking) is that sample management has become divorced from research and experimentation.  Most labs in universities and government research institutions, which operate in a relatively unregulated environment and manage their own samples, view sample management and documenting research as distinct activities.  In line with this, they use different tools to manage samples — typically spreadsheets — and to document experiments — typically lab notebooks.

Since samples are at the heart of a wide range of biomedical experiments, this separation does not make a great deal of sense.   It is likely to persist, however, until affordable and easy to use tools become available that enable labs to manage samples and document experiments in an integrated environment.  That is exactly what we have tried to do with version 4.0 of the electronic lab notebook eCAT, which will be launched on May 11.  eCAT 4.0 has full sample management capabilities including support for barcoding, and these are integrated with the existing notebook functionality so that it is easy to make links and references between samples and the experiments they are used in.

An easy way to distinguish samples from aliquots

Posted by Rory on April 25th, 2011 @ 7:17 pm

When you aliquot a sample, it’s important to keep an accurate record of information about the sample, as distinct from the aliquots that have been created. It’s equally important to keep track of what happens to the aliquots over time, as they get taken out of and put back into the freezer, actions are performed on them, and they get used up.  To do that you need a convenient way of associating information with both the group of aliquots that came from a single sample, and each individual aliquot. This post explains how to keep track of your samples and aliquots using the simple sample management system in the electronic lab notebook eCAT.

Aliquot information

In the following screenshot, the group of six plasmid aliquots which come from a single sample have been highlighted in green.  We are going to edit information about just one of these aliquots, and have selected the ‘edit aliquot information’ icon at the top left.

When we click on the icon a box pops up, as shown in the screenshot below, and we can enter information about just this aliquot, including its name, container label, concentration and volume.  We can also make notes about this aliquot and generate a barcode label for it.

Sample information

We can also enter information that should be associated with all the aliquots in this group.  To do that, as shown in the next screenshot, we click on the ‘edit sample (set of aliquots) information’.

When we click on that icon, we are taken to the record where all the information about the sample from which the aliquots were made is kept (In the screenshot below you see just a part of that record).    The kind of  information that can be recorded in the record is specific to the particular sample type, plasmid in this case.  When we enter information into one of the fields here, this information will be kept for all the aliquots in this group.  For example if we  select ‘bovine’, when we look at the sample information for all six of the aliquots in the group, they will all show this bovine reference.

So there it is, eCAT helps you record information about individual aliquots, and information about groups of aliquots from the same sample, and it automatically keeps them separate!