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 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 upload images to an electronic lab notebook

Posted by Rory on October 12th, 2010 @ 12:48 pm

The thing you’ll probably want to do  most often with images is insert them into a record you’re working on.    For example, here’s what one  user of the electronic lab notebook eCAT wants to do in eCAT — no doubt representative of lots of users:

“Every day, I take a few pictures, so I want to upload the images directly into my[eCAT] field journal.  I want it to have a paragraph of writing, then a few pictures for that day, then another paragraph, then more pictures, etc.  When I’m finished, I want to be able to print out my field journal with the pictures at the appropriate places, all as one document.”

So how do you get images into eCAT to do that?

1.  Images from the web

To insert an image from the web into an eCAT record, you go to the record, click edit, and then click on the ‘insert image’ icon in the eCAT record editor, which looks like this

The following box will popup:

To find the url of the image on the web, right click on the image, select ‘copy image location’, paste that into the ‘image url’ field in the popup box, and select ‘insert image’.  The image will be inserted into the eCAT record you are editing.

2.  Images from your files

If you want to insert an image from one of your files into an eCAT record, just go to the record you want to insert the image into, click edit, and then click in the location you want to insert the image.  Then click on the following button in the eCAT editor to find the file you want to insert:

The following box will popup:

Next, select an attachment store and a file, and click insert.  A link to the image file will be created at the location in the record you indicated, and when you save the edit you have made, a thumbnail of the image will appear at that location.

3.  Getting images into your files and ready for insertion into eCAT

If you want to insert an image from your files into eCAT, you first want to make sure it’s there in your files in a way that eCAT can see!  Here’s a quick primer on ways of getting images into your files.

Personal and Team Hosted versions

If you’re using a Personal or Team Hosted eCAT it’s  easy to get an image file into a place eCAT can see.  Take a look at this page, http://myecat.axiope.com/help.html?page=DesktopStore_Windows, and when you have your folder set up, just drop the files you want to work with in eCAT into the folder.

Install version

If you’re using an Install version, your IT or the person who runs your eCAT server should have already set up ‘attachment stores’.  These are places where you can put  image files that eCAT can see.

Your image files are now visible to eCAT.  To insert them into an eCAT record just follow the simple steps set out in Section 2 above.

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.

Notifications in the electronic lab notebook eCAT

Posted by Rory on September 6th, 2010 @ 9:03 am

Increasingly electronic lab notebooks are about more than just recording experimental data.   They are tools, platforms, environments — call them what you will — that support collaboration among groups of scientists.  Sometimes those scientists are in the same lab or at least the same building.  Sometimes they are spread out around the world.  Regardless of the number of people involved and their locations, productive collaboration is not possible without effective communication.  So the new breed of ELNs needs to include good mechanisms for communicating.

With this in mind, Version 3.3 of eCAT, which was released in July, has a new notifications system.  It’s designed to be

  • simple
  • easy to use
  • closely integrated with eCAT’s collaborative research capabilities

A simple system

There are two kinds of notifications in eCAT — messages and tasks — and they are exceedingly simple.  They look just like emails, and in fact they are  kind of an  email system which is internal to eCAT.

Easy to use

The notifications tab appears at the top of each eCAT page.  To send a message or a task, you start by clicking on the notifications tab.  Then you choose create task or create message.  If you choose create message the following screen appears:

Then enter who you want to send your message to — one or more members of the group you are working with — fill in the subject, compose your message and press send.  Pretty simple — just like an email.  And a red flag will appear on each recipient’s notifications tab, so they know that there is a new message waiting for them to read.

Enhances research collaboration

So far so simple and easy, but the neatest thing is how notifications in eCAT integrate with the rest of eCAT.  To see how that works let’s look at another screenshot, this time of a task which has been composed and is about to be sent:

You will see that there is a link to the mouse colony experiment, the experiment I want Nigel, Jonathan, and Leigh to comment on.  And actually this is a record like other eCAT records, so you have the full power of eCAT’s editor at your disposal in composing this task.  In addition to making a link to the mouse colony experiment, you could have linked to web pages, inserted images, included more complicated formatting, etc.  So you’re able not just to send isolated messages, but to create messages and tasks which are tightly integrated with the work you and your colleagues are doing. eCAT provides an integrated environment for collaboration and communicating about that collaboration.  That’s useful when, as in this example, you are doing joint research.  It’s also useful for instructors who are using eCAT as a teaching tool.  You can send messages and set tasks for an individual student, a group of students, or the whole class.  And, with tasks, as shown in the above screenshot, you can set priorities and due dates.

So there’s an introduction to eCAT’s notifications system, and how it can help you and your group enhance your collaboration through better communication.

Free electronic lab notebooks: Evernote and eCAT compared

Posted by Rory on September 2nd, 2010 @ 9:19 am

The Personal version of  eCAT is primarily used by postdocs and graduate students who want an electronic lab notebook  tailored to lab work.  In this post I am going to try to unpick the details of what that means — what kinds of things can you do in eCAT that you can’t do in general purpose free ‘ELNs’ (which when you scratch the surface are usually note taking devices of one sort or another)?  As a way of getting at the answers I’ll compare the Personal version of eCAT with the most popular note-taking software, Evernote, which is  used by lots of scientists.

First, some  things the free versions of eCAT and Evernote have in common:

  1. They’re both online and accessible anywhere, anytime.
  2. They’re both used by scientists to record and manage data from their research.
  3. They’re both simple to use.

But here are four things eCAT has that Evernote doesn’t have, and which help make eCAT a great tool for lab scientists:

  1. eCAT “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).
  2. eCAT comes preloaded with templates specifically designed for capturing and recording different kinds of scientific research.  There is a generic experiment template, and there is also an  antibody template, a freezer box template, a protocol template, a construct template, etc.
  3. eCAT makes it dead simple to build records of your own design, so you can create structures that allow you to  to effectively capture the kind of research you are doing.
  4. eCAT lets you add files to records.  So for example you can attach a spreadsheet with numerical data relating to an experiment, and confocal images of data which is analyzed in the experiment, to the experiment record.

Those capabilities are pretty useful.  That’s why more and more postdocs and graduate students, like Matt Nicotra at the University of Pittsburgh, are turning to eCAT as an ideal tool for  organizing and managing their experimental data.  Watch Matt talking about how he uses eCAT in this video.

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/user/matt/matt.flv

Permissions and sharing in the electronic lab notebook eCAT III: Setting up a project for multiple members of the group

Posted by Rory on August 23rd, 2010 @ 7:00 am

In the previous post and the one before that I covered the basics of the eCAT permissions system and explained how simple permissions work for individual eCAT users.  In this post I’m going to explain how you can set up a Project that multiple members of the lab can work on.  Again we will follow Sarah.  Only this time Sarah is not setting up an experiment  for herself, she is setting up a Project that will be worked on by some and possibly all other members of the lab.

To facilitate this, she sets the scene by not creating a new record directly from the Dashboard.  As we discoverd last time, when she does that the record goes directly into her personal user folder.  Instead she clicks on the Records tab and then on the Projects folder.  Then she clicks Create new, and selects Project.  And this time the project she creates (we’ll call it Group project) appears under the Projects folder.

To set the permissions for Group project, Sarah clicks on Sharing in the menu on the left.  This time she wants to access the full sharing settings, so when the Simple sharing screen appears

Sarah clicks on the ‘here’ link in the text at the top and accesses the full sharing screen for Group project:

This time by default Sarah has a full set of permissions for this record, and no other user — or group of users — has any permissions.  Sarah can then set whatever permissions she wants for each invidividual user.  Perhaps everone in the group will be given view permission, so they can all follow the progress of the project, and active participants will be given edit permission, but only Sarah, as the person managing the project, will have delete and sharing permission.

Since child records inherit the permissions of their parent, all the records that are created in this Project, e.g. experiments, antibodies, protocols, etc., will automatically have the same permissions as the ones Sarah set on the original Group project record.  That keeps things from getting confused.  But if Sarah — and only Sarah because in this case she has only given herself permission to set sharing permission — decides that it’s useful for any particular record that is created under Group Project to have a different set of permissions, then she can reset the permissions for that particular record.

So that’s it!  A quick overview of how to get started creating records in eCAT for your own use and for use by a group, and how to set permissions for those records.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Importing existing data is also covered in the following video

Importing documents, spreadsheets and images

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

You can now begin to edit the record!

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