Where sample management meets electronic lab notebook



Current Articles | RSS Feed

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.