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How to organize your lab with the electronic lab notebook eCAT

Posted by Rory on September 20th, 2010 @ 10:09 am

Background:  research in the lab

The electronic lab notebook eCAT can be configured in many ways.  One of the most common configurations is for the single lab, typically including a lab head, postdocs, students, support staff and possibly  visitors. In this post I’m going to show you a typical model for how to set up eCAT for a lab.  We’ve made a video that covers the same ground, so if you’d rather watch the video, here it is!

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/tutorials/research/research.flv

Lab information basically falls into two categories. First, there is public, i.e., lab-wide, information, such as protocols, supplies, reagants, etc. This can include research data that everyone should have access to. Second, there is information generated by one person and typically thought of as private, or at least only available to others at the discretion of the author. There is a third kind of information, research data related to activities of a group — I’ll consider that later.

Basic eCAT set up

Data in eCAT can be organised to look like this diagram  from Mike Shipston’s lab:

At the top level there are two folders for the two different kinds of information:  Users contains the “private” information, and Lab Resources contains the “public”, i.e., lab-wide, information.

Within the “Users” folder there is a subfolder for each lab member. The lab member can put whatever they want in there, but there will always be a set of folders named for the projects that person is working on, and within those project folders a set of experiment records for each of the experiments that person has done.

Within the “Lab Resources” folder there are subfolders for each of the different types of resource, such as protocols and molecular tools, and within those further subfolders, for examples constructs and oligos in molecular tools.

Sharing

One of the important aspects of this organization of information is the way sharing is set up.

By default, everyone can see inside the Users folder.

Within that folder, the permissions on the individual lab member’s folders are set so that only approved people can see what is in the folder and its children – the individual themselves, and perhaps the lab-head or other supervisor as well. Records below that, such as Projects and Experiments, are set to inherit permissions from their parent records – so they have the same permissions as the individual lab member’s folder.

The Lab Resources folder  does not come preloaded in eCAT and needs to be created. All subfolders of Lab Resources need to be viewable by everyone. Depending on how you want to run the lab, selected people or anyone in the lab will have permission to add records and edit records. For example, permissions on the the Constructs folder can be set so that anyone can add to it or edit records in it, while permission on  the Oligos folder can be set so that only a few users can add to it or edit records contained in it. Again, lower-level records are set to inherit their permissions from their parent record so that they have the same behaviour as is set at the higher level.

Groups

We’ve seen how eCAT can work with individual users. You can  use Groups to make sharing even simpler. For example, you may want to create a group for the members of the lab working on a specific Project.

You might want all the work for that Project to be placed in one folder, with any member of the group able to add records and edit records in that folder. In that case you’d establish a folder Project X in the Projects folder. And for permissions you would create an eCAT group with all the people working on project X in it, and set the Project X folder to give permission to that group to add and edit. An advantage of having the group is that you don’t have to set permissions for each individual.  When someone joins the lab or leaves you can simply  add them to the group or remove them from the group.

Customizing eCAT

So that’s an example of a structure you can use to get your lab working with eCAT. There are also various ways to customize eCAT so that it better fits your work pattern. One simple way to do that is to customize the Favorites menu on the Dashboard page.

The Dashboard lets you quickly see records you have been working on and the Favorites menu lets you filter the Dashboard. So clicking on “My Projects” shows you just the Projects you can see.

You can customize the Favorites menu by clicking on “Customize menus” in your Preferences. You are taken to a page which shows the classes in the system. For example, if you always work with Lab Protocols and want to be able to quickly see them, you can add them to your Favourites menu.  When you return to the Dashboard My Lab Protocols is now visible, and clicking on the My Lab Protocols link shows you just your protocols. This is just one example of how you can customize eCAT by using Preferences!

So that’s a quick overview of organizing lab research information in eCAT. eCAT is incredibly flexible, so an almost infiite variety of  variations are possible.  Why not sign up for a free trial and explore what set ups makes sense for your lab!

User preferences in the electronic lab notebook eCAT — it’s configurable!

Posted by Rory on August 30th, 2010 @ 7:00 am

eCAT was designed to be a very flexible system, so that you can set it up in a way that suits your research and your working practices.  The underlying system is flexible, and we’ve made it even more flexible by giving each user the ability to opt for different settings, by using the Preferences tab.  We recommend that you take a look at preferences, because they let you do some pretty useful things.

For starters, you’ll probably  want to organize your folders in a way that you’re familiar with in other systems, and suits your work patterns, your mental picture of your work, etc.  By default, when you create new records eCAT puts them in your User folder, and that may suit you just fine.  But there are two other options, to put new folders in the Projects folder or the Root folder.   If you want to use one of those folders instead of the User folder, just go to the Preferences tab and, under the Dashboard preference,  select Projects Folder, as shown in the image below.

Another preference a lot of users find useful is selecting a default class when creating a new record.  There are lots of different kinds of classes in eCAT, which is really useful if you are a group doing a range of different kinds of research.  But what if you are an individual, and 90% of the time you are working with just a single record class?  Say Experiment.  If that’s the case, then you  can select Experiment as shown below, and when you want to create a new record it will automatically be an Experiment record!   You can of course change the preference back if you later decide you want to create a record of a different class.

So there are two examples of using Preferences to tailor eCAT to suit the way you work.  There are plenty of others — why not check them out!


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!

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.

Getting started with the electronic lab notebook eCAT — it’s easy!

Posted by Rory on August 5th, 2010 @ 7:00 am

What’s the best way to get started with eCAT?

The two simplest things to do are (a) import some of your existing data, and (b) create new data in eCAT.  You can do both of these from eCAT’s dashboard, which looks like this:

To import existing data —  a word document, a spreadsheet, or an image — click ‘Import’ and choose what you would like to import, say a word document.  You will be given the option of browsing documents  stored on your computer, so just choose the document you want to select, and then click ‘import’.  The document you have selected is created in your personal space.  To view it simply click on the record with the name of the document and the document will appear, with the correct formatting, just as in the original word document.  You can then continue editing the document in eCAT.

Importing existing data is also covered in the following video

Importing documents, spreadsheets and images

Another way to get started is to create new data in eCAT.  That’s just as easy as importing data!  Again you start at the dashboard, and this time click ‘Create New’.  You will be given a list of types of record that come pre-loaded in eCAT, such as experiment, project, antibody, etc.  Just choose one — for example freezer — and a blank version of the record will appear

You can now begin to edit the record!

For more ideas on how to get started with eCAT, please take a look at the Getting started with eCAT video.

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 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!

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?