Where sample management meets electronic lab notebook



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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 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.

Tips on screen grabbing scientific images for an electronic lab notebook

Posted by Rory on October 25th, 2010 @ 10:09 am

Most of the images you’ll want to attach to an electronic lab notebook like eCAT  you’ll already have as an image.  Sometimes, however, you’ll want an image of something you can see on your screen, but which isn’t actually an image. A common of example of this is a chart shown in Excel or OpenOffice. It looks like an image, but you can’t export it from Excel as an image. What to do?

There are a variety of things you can do to turn something you see on the screen into an image for upload to an electronic lab notebook like eCAT:

An image on a web page

Right-click on the image (Ctrl-click on Mac), and select “Save image as”.

An image in another application that can export images

Lots of applications that deal with images of one form or another can export them as a standard format such as PNG, JPG or TIFF. Once exported, the image can then be uploaded to eCAT. TIFF is often preferable for scientific images as it can include metadata.

Spreadsheets

Excel does not allow export of charts as images. However, you can add a capability to your copy of Excel which will allow you to export a chart as an image. This is fully described on this web page.

OpenOffice Calc does not allow export of charts as images. However, you can copy the chart and paste it into OpenOffice Draw, which does allow export as an image. Select the chart so it has green handles, copy and paste into Draw, then in Draw while still selected do File | Export.

An arbitrary area of your screen

Sometimes you’d like an image of part of your screen – for example a portion of an image, or a portion of a web page. Different operating systems provide different functionality and applications for this – here are some options:

  • Windows/Vista. Use the PrintScreen button on your keyboard (usually towards the top and right and labelled PrtScr). This will put an image in the Clipboard of what is on your screen. You can then paste this into another program.Or you can use the popular free IrfanView application, downloadable from here . Options | Capture/Screenshot lets you capture the whole screen or a specific window, and then edit it. To select a portion of the image, just click in the window and drag your mouse. Then use Edit | Crop selection to reduce the image to the portion you selected, and finish by saving the image.
  • MacOS. Use the Grab utility, which is located in Applications>Utilities. With the Capture menu, you can choose to capture a specific area of the screen, a specific window, or the whole screen (use Timed Screen). When you save the file, it will be saved as a TIFF image.
  • Linux. Most Linux variants include a screen grab utility, usually under the Applications menu, which will save the screen or a window as an image. To cut out a specific portion of the screen image, the GIMP image editor can be used. Select Tools | Transform Tools | Crop, drag the mouse over the region you want to keep, and press Enter. The image will be cropped and you can save it.

Further ideas on screen grabbing are here .

Once you’ve grabbed your screenshots, you can insert them into a record in eCAT or import them from the dashboard or as a child record.

How to import images from the dashboard and as a child record in an electronic lab notebook

Posted by Rory on October 18th, 2010 @ 10:18 am

Last week I looked at how to insert images into a record in the electronic lab notebook  eCAT.  This week I’ll look at two other ways of importing images into eCAT, from the dashboard and from the record page.

Importing images from the dashboard

To start, just click on the Import menu item and then on Image

You will be taken to the import page, which looks like this:

The import page

You can choose to import images from your local computer by uploading them to the server, or you can import from an attachment store that your administrator has defined for you.

Importing from your local computer

To import from a local file, click “Choose File” or “Browse” (the exact text depends on your browser) and then select the file you want to upload. eCAT supports a variety of image types. The standard common images types are all fully supported – JPEG, BMP, PNG, GIF etc. We also support a range of specific scientific types such as TIFF, Zeiss LSM, Zeiss ZVI, Delatvision, Biorad (.pic) and Metamorph (.stk).

Importing from the local computer

If you wish to remove a file you have selected for upload, then click the red cross beside the file name.

Importing from an attachment store

To import from an attachment store, click the “Import files from attachment stores” button. Then click in a text box that says “Click here to select an attachment”. The following screen will appear.Importing from an attachment store

Select a file to import from the attachment store, and then click “Insert” to add it to list of files to import. You can import more than one file from attachment stores at once by clicking the [+] button to the right of the text box saying “Click here to select an attachment”.

When you have image files selected from either the local computer or an attachment store, click “Import” to import the files. Some image types support a preview and allow selection of the size of thumbnail images you will see in your imported records. If the image type you are importing works this way then you will see a screen similar to the following:

Previewing an imported image

When you have finished selecting the image sizes, click “Save” to save your settings. You will be taken to the target record if you are importing more than one image, or to the record that you have imported if you have imported a single image.

Importing images as children of a record

When you are viewing a record, you can click the “Import” option in the Children section of the main menu on the left hand side.

This will import the image as a child record of the record currently being viewed.

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.