Where sample management meets electronic lab notebook



Current Articles | RSS Feed

Permissions and sharing in the electronic lab notebook eCAT III: Setting up a project for multiple members of the group

Posted by Rory on August 23rd, 2010 @ 7:00 am

In the previous post and the one before that I covered the basics of the eCAT permissions system and explained how simple permissions work for individual eCAT users.  In this post I’m going to explain how you can set up a Project that multiple members of the lab can work on.  Again we will follow Sarah.  Only this time Sarah is not setting up an experiment  for herself, she is setting up a Project that will be worked on by some and possibly all other members of the lab.

To facilitate this, she sets the scene by not creating a new record directly from the Dashboard.  As we discoverd last time, when she does that the record goes directly into her personal user folder.  Instead she clicks on the Records tab and then on the Projects folder.  Then she clicks Create new, and selects Project.  And this time the project she creates (we’ll call it Group project) appears under the Projects folder.

To set the permissions for Group project, Sarah clicks on Sharing in the menu on the left.  This time she wants to access the full sharing settings, so when the Simple sharing screen appears

Sarah clicks on the ‘here’ link in the text at the top and accesses the full sharing screen for Group project:

This time by default Sarah has a full set of permissions for this record, and no other user — or group of users — has any permissions.  Sarah can then set whatever permissions she wants for each invidividual user.  Perhaps everone in the group will be given view permission, so they can all follow the progress of the project, and active participants will be given edit permission, but only Sarah, as the person managing the project, will have delete and sharing permission.

Since child records inherit the permissions of their parent, all the records that are created in this Project, e.g. experiments, antibodies, protocols, etc., will automatically have the same permissions as the ones Sarah set on the original Group project record.  That keeps things from getting confused.  But if Sarah — and only Sarah because in this case she has only given herself permission to set sharing permission — decides that it’s useful for any particular record that is created under Group Project to have a different set of permissions, then she can reset the permissions for that particular record.

So that’s it!  A quick overview of how to get started creating records in eCAT for your own use and for use by a group, and how to set permissions for those records.

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.”

Using the electronic lab notebook eCAT as a replacement for a paper lab notebook

Posted by Rory on July 26th, 2010 @ 7:00 am

Wikipedia defines electronic lab notebook as “a software program designed to replace paper lab notebooks“.  So how can you use eCAT to replace something that looks like this?

Let’s look at this question first from the individual’s point of view and then from the lab’s point of view.  Here’s what Andreas Johansson of Lund University in Sweden says:

“I use eCAT for everything in the laboratory when I need to make a note of anything.  I use it for my experiments and my protocols.  But I also use it for things I didn’t use it for before I had an electronic lab notebook.  I use it for digital photos, so protein gels, screenshots of my HPC runs, screenshots of the small things I see during my experiment.  Before I would have just made a small note about it, now I have a photo of it.  And I also add time stamps during an experiment so I can easily see at what point I did a certain thing.

The main result is very very large quality improvements.  It also 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.

And here’s what Alex Swarbrick at the Garvan Institute in Sydney, Australia says about his lab’s use of eCAT:

Everyone uses it as an electronic notebook, so they can compile the diverse collections of data that we generate as biologists, such as images and spreadsheets. We use to it to take minutes of meetings. We also use it to manage our common stocks of antibodies, plasmids and so on. Finally, 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.”

Of the many benefits of using eCAT as an electronic lab notebook noted by Andreas and Alex, three are worth highlighting:

  1. eCAT serves as  a ‘paper lab notebook plus’ because you can use it to record not only garden variety experimental data but also things like images and spreadsheets which can’t conveniently be entered into a paper lab notebook.
  2. eCAT allows you to manage other kinds of information such as notes from meetings, protocols and inventory, as well as experimental data, in a single, integrated environment.
  3. Unlike a paper lab notebook, which by definition is a tool for individuals, eCAT is a group tool that allows controlled  sharing of data.

4 things postdocs and graduate students like about the electronic lab notebook eCAT

Posted by Rory on July 22nd, 2010 @ 7:00 am

Last time some PIs told us what they like about eCAT.  This time its the turn of postdocs and graduate students.

  1. The thing I like best about eCAT is it’s very simple to use.  I looked at some other electronic lab notebooks and they were complicated or overly designed.  eCAT has a very simple interface.  It’s very flexible so I can just go in and immediately start writing my lab notebook the way I used to with a paper lab notebook.  It’s simple, I don’t have to spend any time figuring it out.” (Matt Nicotra, University of Pittsburgh).
  2. “It also 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)
  3. “Members of our labs are starting to realize the power of allowing them to more natively integrate electronic sources of data (documents, images, web links, etc.), which was not something readily accomplished with a paper notebook.” (Morten Jensen, University of North Carolina, Chapel Hill, and Hoang Pham, Lawrence Berkeley Labs)
  4. “The great thing that we saw in eCAT was a system that could be suited to varying needs as they change over time. It had a nice architecture in place that could be well suited to our needs right now, but also one that was flexible enough to handle all kinds of different data needs as they emerge in the future.” (Trevor Covert, Washington State University)

Why not see for yourself?  Sign up for a  free trial of the Team Hosted or Install versions of eCAT, or get your own free Personal account!

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