Where sample management meets electronic lab notebook



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How to set up a freezer sample management system in your lab in less than 10 minutes

Posted by Rory on April 14th, 2011 @ 5:35 pm

A common sound in the lab is the yelling alarm coming from the deep freeze, followed by the miserable face of a hand-frozen graduate who was searching for a plasmid construct.

Every lab has stories about its freezers and what lurks inside them.  Those samples dated 1990 that someone came across just the other day.  Or the aliquots you put on the shelf on Monday that  mysteriously vanished by Thursday.   It’s things like this that drive some lab heads, in desperation, to try out expensive LIMS solutions that usually turn out to be so complicated they gather dust in a corner of the lab.

With this background in mind, we designed CAT 4.0, an electronic lab notebook which now includes sample management, for labs which don’t have huge budgets or sophisticated technical resources, but do need to keep their samples better organized.  To do that we knew we had to keep it simple!

To prove the point, in the rest of this post I’m going to take you through setting eCAT 4.0 up to manage freezer samples. As you’ll see this can be done by anyone with ordinary computer skills — such as  a lab manager, a research technician or a postdoc — in three simple steps.

Step one:  Designate inventory roles

The eCAT administrator first needs to designate one or more members of the lab as Inventory Managers, and all members of the lab who will be using the system as Inventory Users.  Inventory Managers, as described below, have the ability to configure the system, and Inventory Users are able to use it to manage their samples.  To give an eCAT user an Inventory Manager or Inventory User role, just edit the user’s profile as shown below and select the Inventory Manager button.  A popup appears, explaining that Inventory Managers can do everything in the system, i.e. create containers and sample templates and create, move and edit their own and other user’s samples and containers.

To give a user Inventory User rights, simply select the Inventory User button rather than the Inventory Manager button.

Step 2: Create a freezer

The Inventory Manager is now ready to create your first freezer.  To do that go to the Inventory tab, and select Create New Container from the menu on the left, and then Freezer from the drop down list that appears. You are shown the following screen.

Click next at the bottom right (not shown on the above image) and you are taken to the second and final screen in the series  –  just give the freezer a name and a brief description, click finish and your first freezer is ready!

Step 3:  Add a shelf, a rack, and a freezer box

Next add a shelf to the freezer, and a rack to the shelf, using the same two step process you used to create the freezer. Finally, add a box to the rack, again using the same two step process.  There are  a variety of freezer box configurations to choose from. We’ll select a 10×10 freezer box, as shown in the following screenshot.

And after we give it a name and a description, the freezer  box is ready, and Inventory Users can start adding samples to the box! In the tutorial video we’ve made showing how to set up containers those three steps take less than five minutes.  I bet it won’t take you much more than that, even on the first try.

Up and running in less than ten minutes!

So it just takes 5 – 10 minutes to set eCAT up for your lab to begin managing their samples.  And that’s 5 – 10 minutes for someone with normal computer skills, not an IT person.  Of course there are lots of other ways of managing your samples in eCAT 4.0, like creating containers with your own configuration.  As I’ve described in another post, that’s just as simple as creating containers from eCAT’s pre-existing templates.

Freezer sample management made simple!

Posted by Rory on April 4th, 2011 @ 3:28 pm

Flexible sample creation

In my last post I gave some examples to show how useful it is to be able to create and configure sample containers.  In this post I’m going to focus on creating samples – once again focusing on the benefits of flexibility.

Lots of samples to choose from

As with containers, the electronic lab notebook eCAT comes preloaded with lots of preexisting sample types.  Here are a few examples:

A data template for each kind of sample

Each sample has a record template associated with it, so you don’t need to start from scratch each time you enter information about a new sample you are adding to eCAT.  Here is the Anti-PKN antibody template, for example

The above screenshot shows you the fields associated with the aliquots created from the new sample. There’s also a set of fields related to the sample itself.

Create your own sample types!

So eCAT comes preloaded with lots of different sample types, each of which has a record template associated with it. This helps you jump into eCAT with a running start.  But you’re not limited to what’s preloaded into eCAT.  Just the opposite in fact.  In designing the new sample management side of eCAT we’ve carried over one of the fundamental design principles that people rave about in the electronic lab notebook side of eCAT, namely flexibility.

You will almost certainly be dealing with types of samples that don’t come preloaded in eCAT, and even for preloaded sample types you may want to record different kinds of information about the samples than is provided for in the existing record templates associated with each sample.  So, In eCAT 4.0 we’ve made it exceedingly easy to create new sample types and edit templates associated with existing sample types!

Creating new sample types

The screen below shows how easy it is to create new sample types

To start  give the new sample template a name and, if you like, upload a new image for the new template.  All sample templates  come with Volume, Barcode, Sample Source and Description fields.  If that’s all the fields you want, just save the template and you’re done!  But you can also add whatever additional fields you want.  To do that just click on the add field button at the bottom right of the screen.

Amending existing sample templates

It’s equally easy to amend existing sample templates.  To do that simply copy an existing template and then use the following page to edit it

You can see that the screen is the same as the screen for creating a new sample template from scratch.  Simply give the new template a name, upload a photo for it if you like, and then add fields.

Next time: setting up sample management in eCAT 4.0

So that’s a quick guide to containers (last week) and samples,  the building blocks of eCAT 4.0, the electronic lab notebook that lets you manage experimental data and sample data together.  Next time I’ll cover how to set eCAT 4.0 up for your lab.

Flexible sample management: an electronic lab notebook that handles inventory management

Posted by Rory on March 28th, 2011 @ 2:13 pm

In my New Year’s Eve post  I announced the imminent arrival of eCAT version 4.0, which includes sample management. The final pre-release build is now  complete, so I can start a series of posts, with screenshots, covering various aspects of eCAT with inventory, leading up to the April release. Very exciting!  I am going to begin with containers, and next week I’ll talk about samples.

Flexibility — the guiding principle of sample management with eCAT

I can’t think of a better focus to begin with than flexibility.  In version 4.0 we have worked hard to produce a sample management system which gives you lots of templates — so you can just start using eCAT to manage your samples without the need for any configuration — but at the same time is very easy to configure, and hence can be set up to meet the demands of a wide variety of sample management situations and needs.

Container templates

As you’d expect, sample management in eCAT is organized around containers and samples.  It comes preloaded with a range of container templates.

Containers that hold other containers

First, there are containers that can hold other containers, including various sizes and configurations of freezers, racks, and well plates. Here are examples of each of these container types.

Freezer

Vertical 4x4 Box Rack

7x1 vertical well plate rack

Containers that hold samples

There are also containers that hold samples.  Examples include:

Freezerbox 9x9

Pie Shaped Wedge

12x8 Well Plate

Configure your own container templates!

You can also configure your own containers, with eCAT’s easy to use sample template builder that lets everyone in the lab — those with no special computer skills included — easily and quickly build their own sample templates in just two simple steps.

The first step is to select what kind of container you want to create, give it a name and a description.  Here’s an example — creating a new kind of freezer box.

Creating new container type step 1

The second step is to modify the box’s dimensions to reflect the shape you need.

And that’s it; you’ve created a new freezer box!

So there’s an initial taster of sample management in eCAT.  It’s ready for use out of the box, it’s intuitive and easy to learn, and it’s incredibly flexible.  Next week I’ll cover samples.  Dealing with samples in eCAT is just as flexible as dealing with containers — you can use eCAT’s extensive list of pre-existing sample templates, or create your own!

Coming in 2011: an integrated system for managing samples and experimental data

Posted by Rory on December 31st, 2010 @ 11:20 am

Happy New Year!

I hope 2011 proves to be a good year for you.  2011 is going to be a very big year for eCAT because in the spring we will be launching version 4.0, which will integrate sample management with eCAT’s existing notebook capabilities.  Here’s a sneak preview.

eCAT 4.0:  a system for managing samples and experimental data together

eCAT 4.0 will have a fully fledged sample management system, including

  • Storage of all sample information, aliquot numbers, dates, web links and images
  • Graphic display of containers with samples
  • Naming containers
  • Assigning roles – who can do what with which categories of samples
  • Setting alerts
  • Generating reports
  • Support for barcoding

And this sample management system will be  integrated with eCAT’s existing notebook capabilities, which include

  • Creating and importing research data
  • Putting structure into research data
  • Controlled sharing of data between individuals and groups
  • A messaging system

What does ‘integration’ mean?

Integration means  the sample management side of eCAT and the notebook side of eCAT operate together as two components of a single application.  It also means you have the ability to generate links between individual  sample records and individual notebook records.  For example, the sample management section of eCAT gives you a visual representation of where each of a set of aliquots is stored on a shelf in a container in a freezer, and the record for each aliquot contains a link to the record of the experiment in which the aliquot was used.

Why is integration a big deal?

Integration of sample data and experimental data brings lots of benefits . . .

  1. Fewer lost and mislabelled samples
  2. Clearer visualization of relationships between samples and experiments
  3. Reduction of experimental error
  4. More effective search
  5. Higher quality analysis
  6. Productivity gains

What’s coming next

In the last part of 2010 the alpha and beta versions of 4.0 were tested by existing eCAT users and labs which are new to eCAT.  Just before Christmas we incorporated their feedback into the final specs for the spring release.  Over the next couple of months I will be providing regular updates on development in the run up to the release.  I will also be blogging about some of the fascinating feedback and suggestions we got from testers, and I’ll go into more detail about what 4.0 is going to look like — including screenshots! — and what you will be able to do with it.

Stay tuned!

How to use experiment templates and other templates in an electronic lab notebook

Posted by Rory on December 15th, 2010 @ 9:56 am

Standard templates

eCAT has two kinds of templates.  First, there are about  50 standard templates (called classes) that come pre-loaded in eCAT.  Here are a couple of examples.  First, an experiment:

The experiment template is pretty straightforward.  It consists of seven text fields — method, objective, procedure, etc.

Here is another example, a freezer box this time.

This one gives you an idea of the range of fields you can have in eCAT, including text but here also string, barcode and reference.  You can also have lots of other kinds of fields, such as number, time, text box, etc.

Example Templates

eCAT also has example templates.  These are standard templates which have been filled in.   Here is part of the filled in experiment template

Some of the fields have been filled in with text, and a table has been created or inserted into one of the fields.

And here is the filled in freezer box template:

As with the experiment template, the fields have been filled in.

Creating your own templates

eCAT makes it easy to create your own templates.  You can do that by modifying an existing template, or by creating one from scratch with eCAT”s template builder — anyone can do it, no need for IT expertise!

Using templates

eCAT also makes it easy to use templates, both those that come preloaded in the system and those you create.  From the dashboard, select ‘Create New’, and then ‘Use Template’, as shown below

You will be taken to the following page which shows the templates in eCAT.

Click ‘Preview’ on the template you want, and the template will appear.  Then click ‘Copy Template’ at the top of the template and a new copy of the template will be created for you to work with.

The 4 most requested features in the electronic lab notebook eCAT

Posted by Rory on December 6th, 2010 @ 9:14 am

Usually I write about what’s in eCAT and what you can do with eCAT.  Today I’m going to highlight things that are not — yet — in eCAT.  Here are the four most requested features.

Export to PDF

More convenient export of records is important for a couple of reasons.  First, you may want to save a copy of a record, or multiple records, in a form that is easy to reproduce and/or show to others.  Second, easier export of records provides a feeling of security that you can always get your data out of eCAT.

PDF import

Scientists make extensive use of PDFs, so it’s not surprising that the ability to import PDFs into eCAT is a frequently requested feature.

Import as a database

eCAT’s ability to import spreadsheets as spreadsheets is very popular.  But it would also be useful lto be able to import data from a spreadsheet in tabular form, i.e. using a CSV importer.

Image annotation

A large percentage of researchers in biology and medicine make extensive use of images in their research.  The ability to annotate those images is essential to them, so they need this feature in an electronic lab notebook.

A short post this time but hopefully a useful one.  Thanks for the feedback!  All four of these features will be in the spring 2011 release.

What sharing features would users like in the Personal version of the electronic lab notebook eCAT?

Posted by Rory on November 29th, 2010 @ 6:22 pm

Data sharing for scientists

Over on the Electronic lab notebook blog I have recently been posting about data sharing, asking What kind of data sharing do scientists want?, and then What kind of application would permit controlled data sharing among scientists? So what about data sharing in eCAT?  The Team Hosted and Install versions of eCAT support sharing, and also have full support for creation and administration of groups.

Sharing data in the Personal version of eCAT

The Personal version of eCAT, however, does not currently support sharing.  The Personal version is used by individuals to record and structure their data.  People obviously find that useful in itself, but presumably the ability to share data with others would make the Personal version of eCAT even more useful.  To test that assumption, we recently asked a number of regular users of the Personal version whether they thought the ability to share data in eCAT would be useful.  The answer?  A resounding yes!  100% of the users responding to the survey said sharing would be useful!  The following examples give you a flavor of how people think they might use sharing:

“I think that document sharing is an excellent idea. There are three of us in our lab group that are using the Personal edition of eCAT.  We use Google documents already so a transition would not be too hard.”

“I have a technician that I would like to have start using an electronic lab notebook, but I need to be sure that she’s entering data correctly, documenting correctly, etc.  If we could share documents, then we could easily do that.”

We also asked what kinds of features the users thought would be useful in a Personal version of eCAT that supported sharing.  Three features were discussed, and reactions to all three were mixed.

Chat

A couple of people said that chat would not be necessary because plenty of chat applications were already available.  But one of these went on to say:

“If the chats were auditable and traceable like signed documents they might be useful for intra lab communications between the PI and us. “

And one person was very enthusiastic about the possibility of better collaboration emerging from the introduction of chat.  He said:

“I would love to see something like a persistent chat/discussion for each project/experiment etc. Something that allowed for an ongoing discussion for each record. If you created something like this the option of an email notification of updates would be great. Sort of a very basic version of Google Wave connected to each record. If more than one user sharing the record is online at the same time there could perhaps be some form of on screen notification that the chat/discussion was updated.”

Journal or diary view of the research record

This same user suggested the addition of a diary or journal view of a user’s activity:

“I think that a lot of researchers are used to the standard lab notebook. You have all your notes in a chronological order. Instead of just being able to sort the records in different ways, and then view them one by one, I would very much like to be able to simply select a sorting and then view them all in a single series. This could simply be one record after another with perhaps the date clearly marked at the top. Sometimes it’s just easier to follow how your ideas evolved over time in this way.”

This journal or diary view is something that keeps coming up in discussions with users.

For example, Kim Martin at Edinburgh University has developed the idea of a journal view or ‘journalling’ in an electronic lab notebook as a way of being able to look back at the process of her work during a particular period of time.   To do this she wants to be able to very easily create a snapshot of everything she was doing on a particular day.

Kim’s concept is that the electronic lab notebook would, through automatic linking, support the creation with a single click of a’ journal view’ of research and related activity undertaken on any given day.  One of Kim’s key objectives is to gain insights on the process of research which may have been undertaken some time ago, as a mnemomic device.

Profile-based search

Again, this idea got a mixed reception.  Some said they had tried it in other applications and not found it useful.  Others said that since it was already available in other applications, it would not be useful to replicate it in a sharing version of eCAT.  And others said it would be useful, but that it might make more sense to integrate eCAT with other applications, e.g. OpenWetWare and Mendeley, that already provide profile-based search.

Comments on these views and further suggestions are welcome!

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How to evaluate the electronic lab notebook eCAT in 6 easy steps

Posted by Rory on November 22nd, 2010 @ 11:08 am

Over on the Electronic lab notebook blog I’ve just written a general post on how to evaluate software, with a particular focus on electronic lab notebooks.  In this post I’m going to guide you through the process of evaluating eCAT.

Step 1:  Poke around the Axiope website

Spend some time on the Axiope website.  You can learn a lot from the website about both eCAT and Axiope.  We try to be as transparent as possible — the website explains how much eCAT costs,  that there is a  free Personal version, and what the differences between the Personal version and the two group versions — Install and Team Hosted — are.  The website goes through what eCAT does — with videos and text that focus on the practicalities of setting up and using the software.  In addition, you can get a perspective on how other people are using it, and what they like about it, from the Who uses eCAT section.  From all  this you should be able to get a decent feel for whether eCAT looks as if it will be able to solve your problem.

Step 2:  Decide which version of eCAT to try

There are three versions of eCAT.  The free Personal version is for individual use. It’s for individual scientists who want a better way of recording and organizing research data, and value the ability to put structure into the record they keep of their research.  The other two versions, Install and Team Hosted, are for labs.   The Install version is installed on your computers behind your firewall, and it has a big advantage — your files can be ‘mapped’ to eCAT so that eCAT can see them and and there is no need to upload files.  The Team Hosted version is hosted by Axiope.  You still get administratrive control, but you don’t have to worry about computers or backup, we take care of that.  It’s useful for labs that don’t have a computer system available to install eCAT on or aren’t confident about their IT support.

Step 3:  Sign up for a trial

Once you’ve decided which version you want, you can sign up for your free Personal account and/or for a free trial of the Team Hosted or Install versions.  Some people sign up for a Personal account and get a free trial of one of the group versions.   Signing up for a Personal account or a Team Hosted trial is very straightforward — after you register Axiope sends your login details, and you can login and get started.  The Install version works a bit differently.  After you register you are taken to instructions for downloading and installing eCAT.  But again, once eCAT has been installed, you are ready to begin testing.

Step 4:  Set up testing accounts

With both the Team Hosted and Install versions, at an early stage you will want to login as the admin user and use the administrative privileges the admin user has to set up accounts for others in your group who will be testing eCAT.  That’s descibed here for Install.  For Team Hosted, logged in as the admin user, you will need to set up attachment stores for the other user accounts you set up.   You need to first create the user’s account, then save their information, and then go back into the user and edit it again to create the attachment store.   Each user will need to set up a store folder to access their files with the attachment store that has been set up for them.  The instructions for that are here.  There is also a video on how to organize your lab with eCAT, which might be worth watching before you get started setting up user accounts.

Step 5:  Try it out!

If you are a Personal user, you will have skipped Step 4, and you can just  login and get your teeth into eCAT.  Individual testers of the Team Hosted and Install versions can do the same once the person acting as admin has set up their accounts.  There is also a Getting Started video that many people find useful.

As you put eCAT through its paces there are a couple of things to remember.  First, you need to keep the problem you are hoping eCAT will solve in the back of your mind and ask yourself periodically how good eCAT is at solving the problem.  But at the same time it’s a good idea to keep something of an open mind, because using  eCAT may put the problem in a  different perspective, or even bring you to the realization that you have a  different problem than you thought you did at the outset and/or that eCAT is really useful even though it only partially solves your original problem.

Second, how good is Axiope at explaining how to use eCAT?  Are the how to videos and video interviews with users informative?  How about the brief videos inside eCAT explaining how to do certain things and perform certain tasks?  And how about the User Guide? Is it easy to navigate?  To the point?

Step 6:  When in doubt, ask

As you go through the testing, there are bound to be some things you don’t understand and for which there does not appear to be a ready explanation in the User Guide, the website, or the videos embedded in eCAT.  When this happens, don’t hesitate to ask  us by sending an email to support@axiope.com   And judge us by our response.  How long does it take us to respond?  Is our answer responsive to your question?  Is it honest?  Helpful?

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How to record experiments in lab and science notebooks

Posted by Rory on November 8th, 2010 @ 8:08 pm

In the beginning there was paper

Traditionally, science experiments have been recorded with paper lab notebooks.  There are hundreds of guides on the web, like this one, with advice on how to prepare and keep a paper lab notebook.  Most scientists in pharmaceutical and biotech companies, however, have switched to electronic lab notebooks, and scientists in universities are gradually beginning to adopt electronic lab notebooks as well.

Science Buddies

When we brought out the first version of the eCAT electronic lab notebook in 2009, we wanted students in schools to be able to have access to an electronic lab notebook so that they, too, would be able to benefit from the convenience and increased efficiency that electronic lab notebooks bring.   To do that we established a cooperative relationship with Science Buddies.  Science Buddies is a nonprofit organization that provides “free science fair ideas, answers and tools for serious students”.

eCAT for K1 – K12 students

We wrote a brief overview of how to use eCAT to document an experiment, which appears on the Science Buddies website.  We also set up a dedicated instance of eCAT for K1 – K12 students to use in documenting their experiments, and we made that available through Science Buddies.  You can sign up for an account here.  You get the same functionality as with the normal Personal version of eCAT, and like the normal Personal version, the Science Buddies version of eCAT is free.

eCAT for teaching

We have also received a lot of interest in eCAT from K1 – K12  science teachers.  So, we recently put together a video on using eCAT to teach science classes like biology and chemistry.

To give you an idea of what an experiment looks like in eCAT, here’s an example

How to install and run lab software in a university environment

Posted by Rory on November 1st, 2010 @ 10:15 am

Managed IT environments

If you’re working in a university the odds are you’re in a ‘managed’ IT environment.  In other words, the computer your university supplies you with is controlled by an administrator.  That matters if you want todownload web-based  software for you or your lab to test.  It matters because you may not be able to download a test version of the software without assistance from your administrator, and once you  have downloaded the software, you may not be able to let other members of the lab access the software without administrative privileges, which you probably do not have.  This post looks at how to work within these constraints and find ways for you and other members of the lab to access software you want to test.

Servers

If you want to just test the software yourself, then you can download it onto your own computer — no need to deal with the managed computer system of your group or institution.  But if the software is going to be used by others, and you want them to be able to test it as well, you need to install the trial version of the software on a machine they can all access as a group.  To enable that you install one copy of the software on a single’ server’ machine and then use web browsers to connect to the software.

A server is normally a machine in your lab  dedicated to running services – always turned on and always connected to the lab network. The machine needs to be connected to the lab network and to allow connections to be made to it across your lab network. If you wish to be able to access the software remotely, then the server also needs to allow connections externally, which may require some configuration of your firewall. If you don’t know what the firewall allows, you may need to speak to your IT people.

Administrative privileges

Because web-based software systems are server applications that must be running 24/7,they require administrative priviliges for both the user installing the software and the user running the software. If you do not have administrative permission on your lab’s server, you will need to speak to IT to get the software installed and to run the software. Note that if you shut down the software you will need administrative privileges to start it again.

What to remember

So the key things to remember if you are testing software that various members of a group need to access as a group are:

  1. The software needs to be installed on a server.
  2. Administrative privileges are needed for both the person installing the software and the person running the software.
  3. It’s probably a good idea to speak with your IT people before you get started.

Installing eCAT

These points apply to eCAT, and are explained step by step during the eCAT trial install process.   There  is a more detailed explanation with additional background in the Support section of the Axiope website.