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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 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 organize your lab with the electronic lab notebook eCAT

Posted by Rory on September 20th, 2010 @ 10:09 am

Background:  research in the lab

The electronic lab notebook eCAT can be configured in many ways.  One of the most common configurations is for the single lab, typically including a lab head, postdocs, students, support staff and possibly  visitors. In this post I’m going to show you a typical model for how to set up eCAT for a lab.  We’ve made a video that covers the same ground, so if you’d rather watch the video, here it is!

http://www.axiope.com/electronic-lab-notebook/video/ecat_3.3.0/tutorials/research/research.flv

Lab information basically falls into two categories. First, there is public, i.e., lab-wide, information, such as protocols, supplies, reagants, etc. This can include research data that everyone should have access to. Second, there is information generated by one person and typically thought of as private, or at least only available to others at the discretion of the author. There is a third kind of information, research data related to activities of a group — I’ll consider that later.

Basic eCAT set up

Data in eCAT can be organised to look like this diagram  from Mike Shipston’s lab:

At the top level there are two folders for the two different kinds of information:  Users contains the “private” information, and Lab Resources contains the “public”, i.e., lab-wide, information.

Within the “Users” folder there is a subfolder for each lab member. The lab member can put whatever they want in there, but there will always be a set of folders named for the projects that person is working on, and within those project folders a set of experiment records for each of the experiments that person has done.

Within the “Lab Resources” folder there are subfolders for each of the different types of resource, such as protocols and molecular tools, and within those further subfolders, for examples constructs and oligos in molecular tools.

Sharing

One of the important aspects of this organization of information is the way sharing is set up.

By default, everyone can see inside the Users folder.

Within that folder, the permissions on the individual lab member’s folders are set so that only approved people can see what is in the folder and its children – the individual themselves, and perhaps the lab-head or other supervisor as well. Records below that, such as Projects and Experiments, are set to inherit permissions from their parent records – so they have the same permissions as the individual lab member’s folder.

The Lab Resources folder  does not come preloaded in eCAT and needs to be created. All subfolders of Lab Resources need to be viewable by everyone. Depending on how you want to run the lab, selected people or anyone in the lab will have permission to add records and edit records. For example, permissions on the the Constructs folder can be set so that anyone can add to it or edit records in it, while permission on  the Oligos folder can be set so that only a few users can add to it or edit records contained in it. Again, lower-level records are set to inherit their permissions from their parent record so that they have the same behaviour as is set at the higher level.

Groups

We’ve seen how eCAT can work with individual users. You can  use Groups to make sharing even simpler. For example, you may want to create a group for the members of the lab working on a specific Project.

You might want all the work for that Project to be placed in one folder, with any member of the group able to add records and edit records in that folder. In that case you’d establish a folder Project X in the Projects folder. And for permissions you would create an eCAT group with all the people working on project X in it, and set the Project X folder to give permission to that group to add and edit. An advantage of having the group is that you don’t have to set permissions for each individual.  When someone joins the lab or leaves you can simply  add them to the group or remove them from the group.

Customizing eCAT

So that’s an example of a structure you can use to get your lab working with eCAT. There are also various ways to customize eCAT so that it better fits your work pattern. One simple way to do that is to customize the Favorites menu on the Dashboard page.

The Dashboard lets you quickly see records you have been working on and the Favorites menu lets you filter the Dashboard. So clicking on “My Projects” shows you just the Projects you can see.

You can customize the Favorites menu by clicking on “Customize menus” in your Preferences. You are taken to a page which shows the classes in the system. For example, if you always work with Lab Protocols and want to be able to quickly see them, you can add them to your Favourites menu.  When you return to the Dashboard My Lab Protocols is now visible, and clicking on the My Lab Protocols link shows you just your protocols. This is just one example of how you can customize eCAT by using Preferences!

So that’s a quick overview of organizing lab research information in eCAT. eCAT is incredibly flexible, so an almost infiite variety of  variations are possible.  Why not sign up for a free trial and explore what set ups makes sense for your lab!

The eCAT electronic lab notebook: a time saving technology for labs

Posted by Rory on September 14th, 2010 @ 8:51 pm

Last week eCAT was featured in an article called Time Saving Technology in the Nexxus News Autumn 2010 edition. The other companies featured in the article were:

  1. Actual Analytics, whose technology takes video footage of animals used in scientific research and automatically identifies specific behaviors.  This ensures that data about the animals is captured in an objective fashion, improving the quality of the data on which decisions are made, and significantly reducing the time involved.
  2. Lab901, whose ScreenTape provides a fast solution for automated electrophoresis of DNA, RNA and proteins.

Actual Analytics is about more efficient data capture, and Lab901 is about automated, hence faster, data processing.  The time saving element of each of these solutions is pretty obvious, more or less self evident.  Lab901, for example, says that “On multiple protein and antibody analysis, SDS-PAGE and full analysis can be completed within minutes instead of hours.”  The ROI is readily quantifiable there.  But what about eCAT?  Why did the folks at Nexxus(the Scottish life sciences networking group) decide to include an electronic lab notebook in the company of these two time saving technologies for labs?  I asked Kate Fink, and here’s what she said:

“One of the most consistent things we hear from people and small science businesses is how incredibly busy they are.  Something that saves them time can be a huge benefit . . . so I thought the article could be useful to them . . .  Turns out what tied the [three companies] together to form a cohesive article was their ability to improve efficiency.”

ROI on electronic lab notebooks

It’s a lot harder to quantify the efficiency gains which result when a lab adopts an electronic lab notebook than with the Actual Analytics and Lab901 examples.  Yes, some vendors have done studies concluding that in pharma labs which have adopted an ELN scientists produce and analyze the same amount of data in 80% of the time.   But without being involved in the study it’s hard to know how accurate these conclusions are, and in any event this kind of analysis is not that relevant to PIs in academia, who just don’t think about their labs or their students in these terms.

Decision making in academic labs

So what’s different about academic labs? Here’s a hypothesis:  it has to do with the decision making process.  In pharma labs, although the scientists may be consulted about the possible adoption of an electronic lab notebook, at the end of the day the decision is made by managers and supervisors, not scientists.  Once the decision has been made, training and mentoring will be provided to make the adoption process as painless as possible, but the scientists have no choice but to learn how to use the new system.

In most academic labs, it doesn’t work that way.  Many academic labs are really collections of individual researchers.  In these cases the decision whether or not to adopt an ELN is likely to be truly democratic and collective.  In other cases the PI exercises greater control and there is more of an orientation towards common research.  Even in these cases, however, it’s highly unlikely that the PI will make a unilateral decision about adopting an ELN.  It may be a managed decision, but there will still be strong collective input.

Joshua Shaevitz at Princeton makes the point that “the whole lab has to seriously embrace the new use of technology or the system will fail. Before implementing our wiki system, I setup a mock wiki ELN on my laptop and presented it during lab meeting to show everyone the benefits firsthand. I especially wanted to convince them that the new system would not generate extra work, but would instead make their lives easier.”

Academic labs:  ROI on the process of adoption

This means that for academic labs a key consideration in thinking about ELNs has tobe the the ROI on the process of adoption.  It’s fine to think about the productivity gains — for both individuals and the lab — that will come after the ELN has been adopted.  But these are a pipe dream unless adoption takes place in the first place.  And PIs know that adoption is not going to be easy.  A scientist in a regenerative medicine lab pointed out a typical attitude when he said:

“What amazes me is how little lumpiness there has to be in the use of something for everyone not to want to use it.”

With that attitude to adopting new tools so prevalent in academic labs, PIs know that it will be highly unproductive to attempt to coax, much less coerce, lab members into adopting an electronic lab notebook unless it not only is easy to use but also is easy to learn to use.

Electronic lab notebooks: easier than you think!

Electronic lab notebooks are often perceived to be hard to use, difficult, non-intuitive, and/or things which are only used in commercial settings.  That perception is itself a barrier, but it’s not necessarily a difficult barrier to overcome — with appropriate supporting evidence! — and hence need not be a big drag on the adoption process.  The comment made by Professor Mike Shipston at Edinburgh University (a PI) that

“It was a major surprise; transferring to an electronic lab notebook is actually very easy.”

captures both the typical perception that ELNs are difficult and the reality that adoption of  (in this case) eCAT was very easy.  Andreas Johansson at Lund University (a graduate student), makes the additional point that being easy to get started with eCAT makes it easier to encourage adoption among the lab as a whole:

“The main reason I chose eCAT is because it’s really easy to get started with and use.  If something is hard to get started with and easy to use a lot of people will just have a look at and never get around to starting the first experiment.  eCAT is easy to use; it also means I can ask my colleagues to use it as well.”

Electronic lab notebooks:  a time saving device whose time has come?

I have to say that even I was surprised recently when a new eCAT user, starting from scratch with no prior training or coaching, and completely on his own, created and filled out more than 40 new records, many of which he designed himself, in less than two days, involving only a few hours of work!  When word gets around about experiences like that, perceptions are bound to change, and that means a lower barrier to adoption and a higher ROI on the adoption process.  That’s good news if you’re a PI who is considering adopting a PI for your lab — time saved during the adoption process and time saved once adoption has taken place.

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.

Preparing for patent filing with an electronic lab notebook

Posted by Rory on August 12th, 2010 @ 7:00 am

One of the questions that often comes up when people are considering adopting an electronic lab notebook is whether ELNs generally and the particular ELN being considered can be used to record research which may be used in a patent filing.  Often people get caught up in a theoretical conundrum about this question, but thankfully an increasing amount of practical guidance is available on the web from knowledgeble sources, i.e. practicing IP attorneys and legal scholars.  In this post I am going to highlight two recent examples.

The first is a recent blog post byJohn Boger.  He makes the following recommendations for groups  using an ELN to record research for use in patent filings:

“(1) institute a written policy for electronic record-keeping that is distributed to all involved employees; (2) establish a firm schedule for creating permanent back-up copies of all electronic lab notebooks.  All electronic signatures should be completed prior to the back-up process.  “Write-once” media should be used for the back-up; (3) number all discs (in progress and back-up) in consecutive order with permanent labels that note the disc number, start and end date; (4) validate the computer system used to ensure that it is operating properly and is free of viruses or other malicious applications; (5) all daily entries should be dated or time-stamped via a separate server.  Consistent use of electronic signature is a must with encryption software; (6) any commercial software package or bundle purchased should use “write once, read many times” technology; and (7) access to the computer and/or computer system should be restricted with screen and keyboard locks and password protection in place.”

The second is a webast by Professor Lisa Dolak at the Syracuse University School of Law titled, Establishing First to Invent and Electronic Lab Notebooks.  Professor Dolak echoes John Boger in making the point that in the case of both paper lab notebooks and ELNs, to prove admissibility, credibility and corroboration of evidence submitted in support of patent claims courts will scrutinize what SOPs have been put in place, for example relating to signing records, and whether those SOPs were followed in practice.

The point that strikes me about the perspectives brought to bear by both Professor Dolak and John Boger is their focus not on the ELN, but rather on the SOPs that need to be put in place to support a patent filing.  For many small labs, considering the adoption of an ELN should therefore be the beginning, not the end, of the process of thinking about putting in place a robust patent preparation strategy.