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How to set up a new lab with an electronic lab notebook

Posted by Rory on October 4th, 2010 @ 9:44 am

I recently  came across a great primer on how to set up and run a new lab.  It’s called How to set up a new life science lab without HHMI funding, and it was put together by some people at Dartmouth to welcome new faculty members.  Their recommendations are simple:

  • You’re the best postdoc you’ll have for many years; stay at the bench
  • Grow slowly and selectively
  • Hire a research associate who is a stable person and not too proud to help you be more productive
  • Submit grants early
  • Compartmentalize and plan your time
  • Balance novel and risky experiments with meat and potatoes
  • Attend just one meeting a year

Hmm, I thought, eCAT can help with each of those recommendations.  Here’s how.

Stay at the bench

Spending time at the bench is one thing when your main focus is your own research, quite another when you have all the responsibilities and commitments that come with setting up and running a lab.  To make time for research, you’ll need to be well organized and efficient in carrying out and  documenting your experiments.  And you’ll need to be in close touch with the research  everyone else in the lab is doing — you’re not on your own or supervising one or two people any longer, you’re leading a group.

An electronic lab notebook can help on both accounts.  Larry Gonzalez  at the University of Okhlahoma summarized nicely how eCAT helps both him and his lab get better organized:

“eCAT  helps keep me organized, and it’s very good at increasing my efficiency in documenting my research.  Myself or a research technician or a post doctoral fellow can generate a protocol and store it in eCAT.  We can create the data forms that can be filled out manually and entered during an experiment, and we can link to external files.  And if someone would prefer to use another program like Excel to generate spreadsheets instead of entering data into eCAT they can create a spreadsheet and we can link to that file, and its all kept together and organized well in eCAT.  And then when an experiment is completed we’re able to export the data to an external statistical data program for subsequent analysis.”

Grow slowly and selectively

An important benefit of a good electronic lab notebook is that it is flexible enough to grow as your lab grows.  In the most obvious way, it should be able to accomodate the addition of new lab members by making it easy to set up new accounts for them.  There are also less obvious things a good ELN can help with, like  having the ability to set up groups of users.   In eCAT you can set up an  ‘all users’ group, with permissions set on what records the members of the lab can view, what records they can edit, etc.  So you don’t have to set up a new permissions regime for each new person who comes into the lab; you just add them to the all users group and it happens automatically.

Another aspect of eCAT’s ability to help integrate new lab members easily is that, as Alex Swarbrick of the Garvan Institute in Sydney pointed out,

“Since everyone uses the same interface, it is easier for new people to understand the way the lab works and to pick up on projects.”

Hire a research associate to help you be more productive

Postdocs have to be self sufficient and multi-talented to survive, much less thrive, so working with someone else who helps manage you and your new lab may take some getting used to.  To develop a good relationship with a research associate and get the most out of them involves not only interpersonal skills; you also need to establish an environment where collaboration and communication takes place as naturally and as easily as possible.

Introducing an electronic lab notebook as the place where everyone in the lab documents and shares experimental data, as well as meeting notes, protocols and other information not only makes your life easier, it also makes your research associate’s life easier.  And that’s crucial because given the explosion in demands on your time that come with runnning your own lab, your productivity is now impacted by your research associate’s productivity.  If they are left to chase bits of information scattered around other people’s paper lab notebooks, in random disk drives, and on personal computers, a lot of their time is going to be wasted.

With an electronic lab notebook, your research associate can have access to all group records, and can set up structures for recording and organizing things like lab protocols that make it easy for them, and you, to find information.  Heather McClafferty, research associate to Mike Shipton at The University of Edinburgh’s Centre for Integrative Physiology, said after the lab had adopted eCAT:

“Having everything tied together under one resource, so results, protocols, constructs, where things are physically, having everything together under one system has just been perfect.”

Submit grants early

Submitting grants early requires organization.  That’s pretty obvious.  What may be less obvious is that organization becomes a bigger challenge, but can also bring bigger rewards, when you are at the head of a group, even a small one like your first lab.  Your research associate and your students can both be useful resources for preparing for grants:  carrying out preliminary research, finding data from previous projects, and researching and preparing applications.  They will do all this much more effectively with an electronic lab notebook.  With an ELN it is easier to share data and communicate about it, data from previous projects is archived and easily searchable, and when it comes time to prepare the application, (a) people are already working in the same integrated environment, and (b) the data needed to support the application is readily available for inclusion into it.

Compartmentalize and plan your time

The organization theme is obviously relevant here.  But how does an electronic lab notebook help?  First, an online ELN like eCAT is accessible 24/7 from any computer with a web browser.  That means you don’t have to set up a specific time to see what others in the lab have been doing.  No need to make an appointment to go over a student’s paper lab book.  Instead, as Alex Swarbrick says, “I can use eCAT to remind myself of recent experimental results without hassling someone in the lab.”  And Alex, and other eCAT users, are free to arrange their time in the way that suits them, rather than having to fit in with arbitrary schedules, or what’s convenient for others.  The result is more time to spend, and to allocate in the way you find most effective.

Balance novel and risky experiments with meat and potatoes

One of the benefits of a flexible ELN is that it allows you to structure your experiments, and those of others in the lab, in the way that best suits your research.  Mike Shipston at Edinburgh put it this way:

“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 its every easy to put that information together.”

Having a structured record of your lab’s experiments — yours but also everyone elses — means that you are more likely to spot patterns, discrepancies, and problems.  And see the woods from the trees and develop a better sense of what’s risky and what’s meat and potatoes, and why.

Attend just one meeting a year

This is one bit of advice you almost certainly are not going to follow!  The reality is that you’re going to find yourself on the road quite a lot, whether it’s attending a conference or meeting collaborators about a grant proposal or work on a grant in progress.  With an online ELN like eCAT, you can stay in touch with the work that’s going on back in the lab because you can login over the internet and see what people having been doing, in the evening, between meetings, or whenever it suits you.  And with eCAT’s notifications system, you can send and receive messages about people’s research, and even put links to experiments and other records in the messages, which makes it easy to work collaboratively even when you’re on the other side of the world.  So if don’t follow this last bit of advice, and end up attending meetings regularly, with eCAT you will still be able to keep up with other aspects of your lab’s research.

How to teach biology, chemistry or physics with the electronic lab notebook eCAT

Posted by Rory on September 27th, 2010 @ 11:53 am

People often associate electronic lab notebooks with research.  That’s not surprising since that’s mostly what they’re used for!  But there is also  growing interest in using electronic lab notebooks as teaching tools, in both  universities and secondary schools.  For example, Dave Lunt at the University of Hull has an excellent presentation on using ELNs for student research monitoring.  In this post I’m going to go through setting up eCAT for teaching a class in science subjects like biology, chemistry and physics.  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/teaching/teaching.flv

The scenario

To make it practical, let’s use a real  scenario.  Say you’re teaching Biology 101.  You’ve got 20 students enrolled in the autumn semester.  As part of the course the students will be doing some exercises and also carrying out some experiments.  Some of these will involve group work, and some will be individual work, for assessment.  You want to use the electronic lab notebook as an environment where students can document experiments and carry out exercises, and you can see their work and comment on it.  You want some of the students’ work to be private — only you and each student have access to it.  And you want some of the work to be accessible more widely so that groups of students can work together.

Setting up eCAT

You can use either of the group versions of eCAT — Team Hosted, which Axiope hosts on our servers, or Install, which is installed on your server.  To get started you login as admin.

Both versions of eCAT come preloaded with a Projects folder and a Users folder. You’ll be using both of these folders.  Here a a few screenshots of eCAT illustrating some of the actions described below:

  1. To get started, click on the admin tab and then Users, and set up user accounts for the students who will be taking the class this semester/term.  When you do this each user will automatically get a home folder with their name; these will appear under the Users section of the record tree.
  2. When each user logs in, they can create whatever they want in their home folder and only they (and you the admin) can see it.
  3. Staying in the admin section, click on Groups.
  4. Create an All Users group, and add every user to this group.
  5. Create four working groups (we’ll call them Group A, Group B, Group C and Group D) with five students each; these are the groups that will be working together on experiments.
  6. Now go back to the record tree and, under Projects, create a new folder for Group A. To do this, click on “Create New” and then select “Create as Owner” after selecting the Folder class type. Call this folder, “Group A Materials”.
  7. Click on advanced Sharing, and give Group A view, edit, append and download permissions.
  8. Then create a child record under the Group A Materials folder – an Experiment.  But this time click on “Create as Parent”. Then also create a Document record in the same way.
  9. Do the same to create Materials folders and Experiment and Document records for Groups B, C and D.
  10. Now go back to the Record Tree, click  the Projects folder, and create a child folder called ‘Course materials’.
  11. Use this folder to place materials you want  people to look at.  For example, you may want to create a set of instructions for using eCAT during the course.  You can do this by creating a new document in this Course Materials folder.  You also can import pre-existing documents, spreadsheets and images, for example you could import an ‘Initial Materials’ document. Give all groups view permission for this folder so that they can see all the course work.

Using eCAT

It’s that simple!   eCATis now  set up and ready to go.  How you use it is of course up to you.  But here are some simple examples of the kinds of things you can do with the set up you now have in place.

  1. Document experiments.  Each individual student and each group can use the Experiment record that has been set up for the group to document their first experiment.  As shown below, the Experiment record already is divided into fields for Method, Procedure, Objective, Results, Discussion, Conclusion and Comments.  For the Group records, you may want to set up some standard procedures (see below for more on this) to ensure that things are well organized and recorded.  For example, you could have a rule that each time a member of a group makes an entry in a Group record they should place their initials by the entry.
  2. Comment on experiments.  As admin, you have edit permission on all the records that have been created.  So, you can comment on the experiments  the groups and the individuals carry out.  Just do this in the Comments field, and it will be clear that the comment has been made by you.
  3. Create new records.  You, individual students and groups can create new records, as needed, as the semester proceeds. You/they can create new experiment and document records.  You/they can also create other kinds of records from the more than 20 preexisting templates that eCAT comes with.  And both you and they can also create records of your own design using eCAT’s class creator function.
  4. Communicate.  You and the students can use eCAT to communicate about Biology 101.  You can send messages about assignments, deadlines, etc., and you can also create tasks.  In both cases these can be addressed to individuals or to groups, and in both cases you can include links to eCAT records, so for example you could send a message to Group A about a particular experiment they are working on with a note that you have made a comment on it, and you can link to the experiment in the message.

Instructing the class on how to use eCAT

At the start of the course you’ll want to introduce eCAT to the class.  There are various ways to do that, and you’ll probably want to use some combination of:

  1. Having everyone view the Getting started with eCAT video, on their own and/or as a class so that there is an opportunity for questions and discussion.
  2. Preparing some specific instructions covering how you have set eCAT up, how you plan to use it and standard procedures to follow, and making these available, e.g. in a powerpoint presentation (which can be attached to an eCAT record) or a document placed in eCAT.
  3. A demo of eCAT.

Getting eCAT ready for reuse next semester

Your eCAT  licenses are reusable.  So if you have 25 licenses, and a class of 20 – 25 students, you can keep reusing the licenses each time you have a new group of students.  So, when the semester is finished, you simply delete from the User list the students who have just finished the course, freeing up the licenses for the students in next semester’s course or another course.

Try for yourself

Now you’ve seen how it works; why not try eCAT yourself?  You can sign up for a 30 day free trial here.

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!


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.

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.

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?