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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.

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 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.

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 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.

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.

4 things postdocs and graduate students like about the electronic lab notebook eCAT

Posted by Rory on July 22nd, 2010 @ 7:00 am

Last time some PIs told us what they like about eCAT.  This time its the turn of postdocs and graduate students.

  1. The thing I like best about eCAT is it’s very simple to use.  I looked at some other electronic lab notebooks and they were complicated or overly designed.  eCAT has a very simple interface.  It’s very flexible so I can just go in and immediately start writing my lab notebook the way I used to with a paper lab notebook.  It’s simple, I don’t have to spend any time figuring it out.” (Matt Nicotra, University of Pittsburgh).
  2. “It also brings structure to your experiments automatically.  Since you are working with project folders you have your own experiments, and you also add protocols, and you add the data and you add whatever electronic stuff you get during the experiments to that folder.  So everything gets sorted by date and time.  It’s much more structure, automatically. (Andreas Johansson, Lund University)
  3. “Members of our labs are starting to realize the power of allowing them to more natively integrate electronic sources of data (documents, images, web links, etc.), which was not something readily accomplished with a paper notebook.” (Morten Jensen, University of North Carolina, Chapel Hill, and Hoang Pham, Lawrence Berkeley Labs)
  4. “The great thing that we saw in eCAT was a system that could be suited to varying needs as they change over time. It had a nice architecture in place that could be well suited to our needs right now, but also one that was flexible enough to handle all kinds of different data needs as they emerge in the future.” (Trevor Covert, Washington State University)

Why not see for yourself?  Sign up for a  free trial of the Team Hosted or Install versions of eCAT, or get your own free Personal account!

10 reasons to try an electronic lab notebook — eCAT version 3.3!

Posted by Rory on July 6th, 2010 @ 3:59 pm

We’re launching a new version of the electronic lab notebook eCAT today.  Why is version 3.3 special?

First, the new features:

  1. a familiar dashboard modelled on Google Docs
  2. the ability to import spreadsheets, images and documents with a couple of clicks
  3. an extensive set of useful templates — experiments, antibodies, CHiP extracts, protocols and many more
  4. a notifications system
  5. a complete series of brief  ‘how to’ videos, embedded on each page of the application, describing the actions you can do on that page.

Second, enhanced support for people interested in learning about electronic lab notebooks and testing eCAT:

  1. The electronic lab notebook blog, covering everything you want to know about electronic lab notebooks
  2. A series of tutorial videos — such as eCAT for PIsGoogle Docs and eCAT, Wikis and eCAT, Patent protection with eCAT, etc.  —  available on our website
  3. An automatic installer that makes it a breeze to set up an eCAT trial
  4. This eCAT blog,  discussing how to get the most out of eCAT and answering questions from users

Third, a growing number of forward looking PIs are adopting eCAT because it combines ease of use, flexibility and the ability to add structure to their research data and enhance collaboration in the lab.  Here’s what Professor Mike Shipston, Director of the Centre for Integrative Physiology at the University of Edinburgh, has to say:

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