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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.

Permissions and sharing in the electronic lab notebook eCAT II: simple permissions for individual eCAT users

Posted by Rory on August 19th, 2010 @ 7:00 am

As noted in the last post, the underlying principle of eCAT’s permissions system is that all records inherit the permissions their parent record has, unless the permissions on the record are reset.  With that in mind, let’s see what happens when a new user creates their first record in eCAT from the eCAT dashboard. You can do that in one of three ways:  by creating a new record, by importing a document, spreadsheet or image, or by creating a record from one of eCAT”s preexisting templates.  In all three cases, the new record will by default be created in your personal ‘user’ folder.  For example, when a new user called Sarah creates her first record, Experiment 1, it is automatically saved in her sarah folder, as shown below.

Like all records, the Experiment 1 record inherits its permissions by default from its parent record, which is the sarah folder. Like all user folders, by default’ sarah’ has all six permissions available in eCAT.  As noted in the previous post, these are:  view, append, edit,  delete, download, and sharing.   So, Experiment 1 has these permissions too, and Sarah can view the Experiment 1 record, edit it, delete it, etc.  Sarah doesn’t need to do anything to make this possible, it just happens automatically in eCAT.

But Sarah has more control that that — she can also change the permissions on Experiment 1 (and of course on other records she creates).  To do that she clicks on ‘sharing’ in the menu at the left of the screen and the following page appears:

By clicking the boxes in Step 1 she can give other eCAT users the ability to view Experiment 1, to edit it, to delete it or to set permissions for it.  And, using Step 2, she can decide which users have these permissions.  Its completely flexible, and well suited to actual lab practices.  For example, Sarah might decide to give view only permission to most members of the lab, and edit permission to another lab member she is working with on Experiment 1 and to the PI, so that the PI can make comments in Experiment 1.  And Sarah has this flexibility for all the records she creates.  If she does nothing they remain private.  But if she wants she can share a record, again in whatever way she wants.

In the next post I’m going to cover sharing and permissions for groups, and give an example of how a lab testing eCAT can set up a Project that multiple members of the lab can work on.

Permissions and sharing in the electronic lab notebook eCAT: the basics

Posted by Rory on August 16th, 2010 @ 7:00 am

If your group is trying out eCAT, one of the first things you”ll want to do is work out an appropriate permissions policy for the members of the group who will be using eCAT.  And once you’ve got the policy in place, you’ll want to let everyone in the group know how permissions work.

The first thing to note is that eCAT is very flexible about permissions — you can set up just about any kind of sharing you want.  Permissions automatically flow down from parent to child records, so once the permissions have been set on a record there is no need to reset them for child records, unless you want to have different permissions on a particular child record, in which case you can vary the permissions for that record.

So what kinds of permissions are available in eCAT?  As this screenshot from the advanced sharing feature shows, there are seven:  from parent, view, append, edit,  delete, download, and sharing.

If the ‘from parent’ box is checked the permissions for that record are the same as for the record’s parent.   And as noted above  that is the default position.   If  the from parent box is not checked, then permissions for the record are determined by the boxes that are checked. Each user only has permission to do something — view the record, edit it, etc., if that box is checked.  The first five of the permissions are pretty obvious, and the last, ‘sharing’ determines who can set permissions on that record.  So in the example shown above Bob’s and Ian’s permissions for that record are taken from the record’s parent, and Mike has permission to view the record and append things to it, but not to edit it, delete it, download things to it, or set permissions for it.

That covers the basics.  In the next post I’m going to explain how sharing and permissions work for individual eCAT users, and in the post after that I’ll give an example of how you can set up a simple sharing system for an eCAT trial.

Preparing for patent filing with an electronic lab notebook

Posted by Rory on August 12th, 2010 @ 7:00 am

One of the questions that often comes up when people are considering adopting an electronic lab notebook is whether ELNs generally and the particular ELN being considered can be used to record research which may be used in a patent filing.  Often people get caught up in a theoretical conundrum about this question, but thankfully an increasing amount of practical guidance is available on the web from knowledgeble sources, i.e. practicing IP attorneys and legal scholars.  In this post I am going to highlight two recent examples.

The first is a recent blog post byJohn Boger.  He makes the following recommendations for groups  using an ELN to record research for use in patent filings:

“(1) institute a written policy for electronic record-keeping that is distributed to all involved employees; (2) establish a firm schedule for creating permanent back-up copies of all electronic lab notebooks.  All electronic signatures should be completed prior to the back-up process.  “Write-once” media should be used for the back-up; (3) number all discs (in progress and back-up) in consecutive order with permanent labels that note the disc number, start and end date; (4) validate the computer system used to ensure that it is operating properly and is free of viruses or other malicious applications; (5) all daily entries should be dated or time-stamped via a separate server.  Consistent use of electronic signature is a must with encryption software; (6) any commercial software package or bundle purchased should use “write once, read many times” technology; and (7) access to the computer and/or computer system should be restricted with screen and keyboard locks and password protection in place.”

The second is a webast by Professor Lisa Dolak at the Syracuse University School of Law titled, Establishing First to Invent and Electronic Lab Notebooks.  Professor Dolak echoes John Boger in making the point that in the case of both paper lab notebooks and ELNs, to prove admissibility, credibility and corroboration of evidence submitted in support of patent claims courts will scrutinize what SOPs have been put in place, for example relating to signing records, and whether those SOPs were followed in practice.

The point that strikes me about the perspectives brought to bear by both Professor Dolak and John Boger is their focus not on the ELN, but rather on the SOPs that need to be put in place to support a patent filing.  For many small labs, considering the adoption of an ELN should therefore be the beginning, not the end, of the process of thinking about putting in place a robust patent preparation strategy.

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.”