Where sample management meets electronic lab notebook

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Adding structure to your research with databases in the electronic lab notebook eCAT

Posted by Rory on August 2nd, 2010 @ 7:00 am

In the last post I talked about various ways of making use of templates in eCAT.  In this post I’d like to touch on a way in which you can add another layer of structure to research data in eCAT — databases.

eCAT makes it easy to construct databases — this happens automatically when you add links between records.  eCAT comes preloaded with three example databases.  Let’s take a brief look at two of them to get an idea of the kinds of databases you might want to create in eCAT.

The first example

shows how a series of records can be linked togethe rin eCAT  to manage inventory.  Each of the items in green represents a different class of record in eCAT.  Boxes (Freezer, Shipping) contain bidirectional links to the items stored in them, in this case Antibodies. Freezer Boxes also are linked to their storage container, in this case Freezer. The Shipping Box class is not contained in a Freezer, but does have a link to an external Internet URL – the tracking website for the courier company. This database comes with built-in documentation in records of class Documentation Page, which contain links to all the different classes used in the database.

In the second example

the Experiment records contain links to Lab Protocols, Mutagenic Oligos, etc. Other classes are generally not linked, but Project records are connected in a parent-daughter manner to Experiments.  So, Professor Mike Shipston lab at Ednburgh University is able to record its experimental data in a single integrated environment, with multiple links to other data the lab deals with such as protocols, constructs and oligos.

Databases for managing inventory and integrating your experiments in the broader context of your lab’s research are just two of the virtually infinite ways in which you can organize your data in eCAT.  Its this kind of flexibility that leads to comments like the following from Mike Shipston:

“The great thing about the eCAT electronic lab notebook is, its incredibly flexible in terms of how you can set it up.”

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.