Where sample management meets electronic lab notebook



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Making life easy by using groups in the electronic lab notebook eCAT

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

Where to get started when setting up eCAT for your lab?  Probably the first thing you’ll want to do is to create accounts for all the people who will be using eCAT.    That’s simple, and its covered in the User management section of the User Guide.  What next?

All Users group

It’s good practice to set up a group call ‘All Users’ to which all users belong.   Setting up groups is simple, it’s similar to setting up individual users, and its covered in the Group management section of the User Guide.  Why set up a group for all users?  Because it makes your life as administrator so much easier going forward!  Once you’ve got an All Users group, for each new permission you want to set, instead of setting the permissions for that record for each individual user, you simply set the permissions for the All Users group, and all users automatically have those permissions.   Moreover, because permissions in eCAT cascade downward, once you have set permissions for a parent record, those permissions are automatically inherited by all children, and children of children, etc., of that record.  So you only need to set the permissions for a single record and those permissions will hold for all users for that record and all its descendants.  You don’t have to worry about permissions again for that set of records.

Other groups

After you have set up the All Users group, it would be useful to consider how you are planning to use eCAT.  Are there natural subsets of users within the group of people who will be using eCAT?  For example, is there a subgroup in the lab which deals with inventory?  Is there a subgroup which deals with external collaborations?  Are there several subgroups working on different kinds of projects?  Are there two or more labs sharing eCAT?  In these or other similar situations it may make sense to set up one or more groups which  including the people who will be working together on a particular matter or set of matters.  Once you have set up, say, the Inventory group, then you get the same streamlined permissions benefits for the records that Group is working on as were described above with the All Users group.

Flexibility on permissions is always there!

OK, it’s nice that you can deal with permissions in such an efficient way, but what if you want to change things later on or want to do some fine tuning?  No problem, that’s easy too!  Let’s say you’ve set the default permissions for the Inventory group’s records so that everyone in the Inventory group has view and edit permission on the group’s records, and everybody else in the lab has view only permission, because normally you don’t want people who aren’t members of the Inventory group to mess around with records the group creates.  But then the Inventory group sets up a Project that everyone in the lab will be invited to comment on.  To make that possible, all you need to do is to give the All Users group edit permission for that Project.  The All Users group will already have view permission on the Project, by default, and now it will also have edit permission.  Or, perhaps you only want a subset of users to be able to comment on the Project.  In that case you can take an existing group, if there is an appropriate one, or create a new one, and give that group edit permission on the Project.  Then the members of that group, along with the members of the Inventory group, will be able to comment on the Project, and everyone else will only be able to view it.

So groups in eCAT are pretty useful, can save a lot of time, and don’t interfere in the least with eCAT’s flexibility.  In fact they enhance it!

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 ways to get the most out of templates with the electronic lab notebook eCAT

Posted by Rory on July 29th, 2010 @ 7:00 am

Version 3.3 of eCAT, which was released on July 8, comes pre-loaded with more than 20 templates.  Here are four ways to make good use of them:

  1. Get an idea for how other scientists are using eCAT.
  2. Understand the wide range of information that eCAT can help you to manage,  from experimental data to protocols to freezer samples to meeting notes to CHiP extracts to constructs to records about lab personnel and equipment.
  3. Grab a template for your own use; by clicking the “Copy Template” button at the top of the template, you will create an editable copy of the template in your home folder.
  4. Make a blank version of the template; clicking the “Create New” button at the top of the template will create a blank version of the template with the fields not filled in.