Who are electronic lab notebooks for?

Posted by Rory on October 13th, 2010 @ 10:48 am

In last week’s post I looked at what electronic lab notebooks are for, and said that they enable groups of researchers to conveniently carry out four central aspects of the research process:

  • Record experimental data and other kinds of information
  • Add structure to the data and information
  • Share the data and information
  • Communicate about their research

The answer to the question, ‘who are electronic lab notebooks for?’ is implied within that statement, namely ‘groups of researchers’.  This week I’d like to zero in on the makeup of a typical group of researchers in an academic lab, and ask the question, among that group, who benefits from use of an electronic notebook and why?  Just the PI?  Postdocs? Graduate students?  Research assistants and technicians?

PIs

Lets start with the PI.  In most cases the PI drives the decision to adopt an electronic lab notebook.  PIs benefit from their lab using an electronic lab notebook in lots of ways — some of the things they like include:

  1. Having everyone in the lab working in an integrated environment.
  2. Having everyone using common structures to document their research, e.g. for experiments and protocols.
  3. For online electronic lab notebooks, the ability to access their own work, and that of other members of the lab, 24/7, from any web browser, when they are at home in the evening or on the other side of the world at a conference.
  4. The ability for lab members to conveniently work in groups.
  5. The ability to link experimental data with other kinds of information, e.g. protocols, and with physical things like reagents.
  6. Having an integrated searchable archive of the lab’s work that allows them and other lab members to find and make use of work done by existing lab members and those who have already left the lab.

Postdocs

Postdocs don’t have the same global view on the lab’s needs as PIs, nor do they have the PI’s long term interest in the efficiency of the lab or creating a usable, searchable archive of its research.  But they almost certainly will be working closely with others in the lab — the PI, one or more graduate students, and perhaps a research associate or technician — on their own projects and other projects involving lab members.  For that they will benefit from many of the same group advantages of using and electronic lab notebook that are valued by PIs:

  1. Having everyone using common structures to document their research, e.g. for experiments and protocols.
  2. For online electronic lab notebooks, the ability to access their own work, and that of other members of the lab, 24/7, from any web browser, when they are at home in the evening or on the other side of the world at a conference.
  3. The ability for lab members to conveniently work in groups.
  4. The ability to link experimental data with other kinds of information, e.g. protocols, and with physical things like reagents.

In addition, PIs are likely to particularly appreciate the benefits an electronic lab notebook brings in terms of documenting their own research, including:

  1. The automatic introduction of structure into their research record.
  2. Ease of use.
  3. Having data well organized in a form that it can conveniently be incorporated into presentations and papers.

PhD students

PhD students, and other graduate students, are likely to value these last three benefits just as highly as postdocs.  And they, too, benefit from the group aspects of the electronic lab notebook. For example,with an electronic lab notebook they can share information and ideas online with others in the lab — the PI and other students whose brain they want to pick or whose experiments they are keeping up with.   An electronic lab notebook means easier access to the PI — it’s no longer necessary to corral the PI during office hours to look at your paper lab notebook — with an electronic lab notebook you can send the PI a message with a link to your latest experiment and ask the PI to comment when he or she has time.

Unlike the PI and postdocs, at the end of the day graduate students are focussed on getting a degree, and that means their own work is of paramount importance.  In this respect they are likely to particularly appreciate the fact that electronic lab notebooks provide the flexibility for some records to be shared and others to kept entirely private.  So graduate students (and of course others in the lab) benefit from the group and sharing capabilities of the electronic lab notebook while at the same time having their own private space.  They can keep some records private forever, and other records private until they are ready to be shared, or reviewed, by others in the lab.

Research associates and technicians

What makes the life of research associates and technicians different from that of PIs, postdocs and graduate students is that their focus  is not their own research but  the work of  others.  They are supporting others, and  helping to organize the lab and ensure that the lab and its equipment, computers, and systems are running as well as possible.  In that regard they will from the enhanced structure, organization, and communication the introduction of an electronic lab notebook brings to the lab.

  1. With the structured records you can set up in  an electronic lab notebook it is much easier to get buy in from everyone to use common forms and formats for things that everyone in the lab needs to use, like protocols.
  2. With an electronic lab notebook lab members can document their experiments in the same online environment that is used to store and share general information like meeting notes and protocols — that makes for much better organization.
  3. With the electronic lab notebook’s messaging system technicians and research associates can communicate with lab members 24/7, and do this in a targeted way — for example if they have a question about a protocol someone has submitted, they can send a message with the question and insert a link to the protocol, making it easier for the recipient to respond quickly.

The bottom line?  Everyone in the lab benefits from the introduction of an electronic lab notebook!

7 Things to consider before adopting an electronic lab notebook for your lab

Posted by Rory on September 16th, 2010 @ 8:43 am

Adopting an electronic lab notebook for your lab is not a decision to be taken lightly. It will take time and effort on your part and is likely to meet with mixed reactions from other lab members — delight/relief from some but also suspicion/hesitancy from others.  It will involve at least some changes in working practices for everyone. So, what things should you consider before you begin the process of looking at what’s out there and what kind of ELN suits you and your lab?

1.  You!

There’s no better place to start with than yourself.  Lab heads/PIs who successfully introduce ELNs in their labs tend to be:

  • Comfortable with computers and software
  • Not afraid to try out new software applications
  • Strong leaders within their labs
  • Well organized
  • Interested in improving collaboration within the lab
  • Interested in the benefits deriving from the lab working together more effectively as a group, such as more research data being captured and archived in a way that it can be found and used in the future.

2.  Other lab members

Let’s assume you’re ready to drive the process of adopting an ELN, but what about the rest of the lab?  There are a couple of things to consider here.  First, are there one or two lab members who are likely to be positive about adopting an ELN and prepared to help you with testing a system and rolling it out?    You will want to test the ELN yourself, but you probably will not want to do all the work involved in bringing others up to speed.  So someone — a research technician, a lab admin person, or just an enthusiast — who is willing to take on that role could be invaluable.  Second, what is the range of attitudes to ELNs among the lab members?  If the general attitude is neutral to positive, you’re in good shape, but if there are significant pockets of resistance you and your ‘allies’ will need to work out a strategy for bringing the sceptics along, e.g. by pairing them up with a mentor.

3.  IT infrastructure

In addition to considering the people side of your lab, you need to consider the IT environment. Do you have a computer system which is reliable and available to host the ELN?  If not, are you or your department in a position to purchase a new computer to host the ELN?

4.  IT support

How good is your IT support and how good is your relationship with them?  Are they available and happy to help with installing the ELN?  If the answer to this question or the previous one  is no, you may want to consider adopting an ELN which is hosted by the provider, who will take care of the system and backup.

5.  Your lab’s data

What kind of data does your lab deal in?  Do you have lots of images?  Where is the data currently stored and how is it managed?  Do you have a shared file system?   Do lab members use paper lab notebooks for experimental data?  You will need to think about these issues because the ELN you adopt will need to be integrated with your data storage set up, and will require some changes in data management, e.g. experimental data can now be kept in the ELN rather than spread around in everyone’s individual paper labbooks.

6.  Lab working practices

Adopting an ELN may prove to be a lot easier than you imagined (or feared!), but it still is going to require some changes of working practices in the lab.  So it would be useful to think about just what current working practices are, and what areas can be improved by adoption of the ELN.  For one thing, with everyone working in the same online environment there is a lot of scope for (a) increased flexibility, and (b) better and more focussed collaboration.  as an example of flexibility, you will  no longer need to arrange a specific time to look at individual paper labbooks, instead you can view and comment on experiments lab members are working on anytime, from anywhere, when you’re at home in the evening or away at a conference.  Adopting an ELN also opens up new ways of collaborating and communicating about research.  Of course people will still chat at the bench or around the coffee machine.  But with an ELN a particular group can work on documenting a single experiment or a broader project together, again from anywhere, any time and if you like other lab members can be given view (but not edit) permission on the experiment or project, so that they can follow the course of the group’s work.

7.  Timing

Last but certainly not least, you’ll want to introduce the ELN at a time that makes sense in terms of your own schedule, the lab’s overall workload, and movement of people in and out of the lab.  I’ve written another post discussing the pros and cons of adoption at different times.

That’s quite a lot to consider, but if the circumstances are right — they don’t need to be perfect of course — the benefits of adopting an ELN for both you and your lab can be substantial, even transformational, and adoption itself is very likely to be a lot easier than you imagined in advance.

5 Things PIs want in an electronic lab notebook — other suggestions?

Posted by Rory on July 28th, 2010 @ 7:00 am

What PIs want in an electronic lab notebook is often different from what postdocs and graduate students want because PIs are looking for a tool for recording the entire lab’s work, rather than an individual note taking tool.  I looked around the web at recent discussions of what PIs are looking for in an ELN, and identified five common themes:

  1. Something that’s easy to learn and easy to use in order to ensure (relatively stress free) lab-wide buy in and take up.  Joshua Shaevitz, at Princeton, has a good description of the considerations that went into adopting an ELN, and the adoption process, in his recent  post on My Lab’s Wiki-based Electronic Lab Notebook System.  He says, “Before implementing our wiki system, I setup a mock wiki ELN on my laptop and presented it during a  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.”
  2. Something that’s flexible in terms of providing for, on the one hand, common structures for group records and records that need to be accessed by multiple members of the group, and, on the other hand, scope for individuals to ‘do their own thing’ in terms of both research style and having their own private space.  Joshua Shaevitz again: “I didn’t want to impose too much structure on each lab member, as I think notebook style is very personal thing. But, I also wanted to ensure that the results would be compatible with features such as search and would work well with our archiving strategies.”
  3. Something that facilitates integrated handling of  experimental data (i.e. the lab notebook function) in the same environment as other information the lab deals with, e.g. protocols, meeting notes, etc. Alex Swarbrick at the Garvan Institute: we use our electronic lab notebook “to compile the diverse collections of data that we generate as biologists, such as images and spreadsheets, and to take minutes of meetings.”
  4. Related to the previous point, something that provides the capacity to manage physical inventory as well as data in electronic form, and the ability to link the two together.  This point is brought out by Cameron Neylon in a thread accessible in a great recent discussion started by Jonathan Eisen at U.C. Davis, Possible electronic lab notebook systems – update.  In discussing what kinds of data a system needs to able to handle, Cameron says, “generating, storing, analysing and publishing research objects, explicitly including samples and other physical objects.”  And Alex Swarbrick again: “the ability to link records, reagents and experiments. For example, to connect an experimental mouse with the tube containing its tissues in the freezer, to the 6 different experiments (conducted over a year) that analysed those tissues in different ways. Managing this kind of ‘metadata’ is absolutely essential to our work.”
  5. Something that can “help to deal with information and data overload (sorting and filtering)” — a scientist interviewed in a recent study of the research practices of seven life sciences research labs Patterns of information use and exchange:  case studies of researchers in the life sciences.

How does this list sound?  Is it an accurate reflection of what others want in an ELN? Is it comprehensive?  Are key requirements missing?  Comments welcome!

What is an electronic lab notebook II — how do wikis measure up?

Posted by Rory on July 14th, 2010 @ 7:00 am

In the last post I poked a bit of fun at the wikipedia definition of  electronic lab notebook — “a software program designed to replace paper lab notebooks”.  Since that could mean just about anything, beauty is in the eye of the beholder.  The big dividing line is between people — like postdocs and graduate students — looking for a note taking tool for themselves, and others — like PIs — looking for a collaborative research tool for the lab.

This time I’m going to take a look at wikis — how do they measure up to the challenge faced by PIs looking for a collaborative research tool:  organizing and keeping track of a wide range of types of research data generated by lab members, present, past and future?   The first point to make is that there are all sorts of wikis, with varying degrees of sophistication, power and capabilities.    I’m going to use the most developed wikis as a point of comparison here — Confluence and PBWorks are good examples — wikis with a fully developed feature set.

As a recent study looking in depth at the work practices of seven life sciences research labs pointed out, a growing number of labs have turned to wikis as convenient environments for storing and sharing general information like meeting notes and protocols.  Wikis have a number of attractions to labs, in that they are easy to learn and use, online, and provide good support for sharing and collaboration.  In addition, the more sophisticated wikis have integrated messaging systems and some, like PBWorks, even have voice conferencing capabilities.

At the top end, then, wikis are becoming fully fledged knowledge management tools.  But features like voice conferencing are aimed at businesses, not labs.  For labs the key issue is managing their data. The study notes that notwithstanding the trend towards organizing general information in wikis, all the labs studied still maintain paper lab notebooks.  Paper lab notebooks stand out as an island of tradition in the midst of a growing ocean of online information sharing.    An island perhaps but a pretty big island, Australia rather than Fiji if you will, because paper lab notebooks are the repositories for the most important information labs deal with, their research data.

On this evidence wikis are falling short as a software program that replaces paper lab notebooks, and hence are not functioning as electronic lab notebooks per the wikipedia definition.  Why are labs staying with paper lab notebooks even as they adopt wikis to share information other than research data?  Inertia no doubt is a big part of the reason.  But the other big barrier to adoption of tools in labs — they have to be easy to learn and easy to use — is probably less of a factor.  Wikis  are coming into general use and it’s not the wiki per se that is being resisted, its the use of the wiki specifically as a place for entering and sharing research data.

Here’s a hypothesis:  the reason labs are sticking with paper lab notebooks for dealing with experimental data and not moving their experimental data into wikis along with general information like meeting notes and protocols is that wikis are unable to provide structure for the data.  With a wiki all you get is the wiki page.  It has no more support for structure than a Word document, and even less structure than a spreadsheet, without  doubt the most popular electronic repository for experimental research data.  Next time I will look in more detail at how electronic lab notebooks provide support for structuring research data and the benefits this can bring to collaboration and communication in the lab.

What is an electronic lab notebook?

Posted by Rory on July 6th, 2010 @ 9:30 pm

Welcome to the electronic lab notebook blog.  This will be a space for discussing electronic lab notebooks from every angle:  what benefits do they bring? how do they compare with alternatives? what kinds of features do they have and should they have? what issues do people face in using them?  how can you get the most out of them?

In this first post I’m going to start at the beginning:  what is an electronic lab notebook?

Wikipedia defines electronic lab notebook as “a software program designed to replace paper lab notebooks“.  That could be just about anything — beauty is in the eyes of the beholder!   I’ll take a look in a second at who the relevant beholders are and what each of them thinks, but taking wikipedia as the starting point it’s  fair to say first that all of them are looking to move away from this:

Postdocs and graduate students

So who are the relevant beholders?  They can be divided into two categories.  The first is people looking for an electronic note taking device for themselves.  They tend to be interested in convenience and simplicity.  Something which is easy to use and also helps them get organized.     But many postdocs and grad students want something which also provides  support for research.  Here is one description of the ‘dream app’ over on an Apple forum about electronic lab notebooks:

  • easy copy-pasting/drag ‘n drop
  • ability to re-open the files
  • metadata and search (tags, keywords, …)
  • possiblity to link to older notes and graphs
  • store PDF (or TIFF) representation of external files along with the original file: preview files without their originating application
  • automated backup mechanism
  • encryption on disk

The thread following that post contains a good discussion of the varieties of things people want in an electronic lab notebook for their own use, examples of what they have tried, what they like and dislike, and the limitations of the available tools.

PIs

The second category of people looking for an electronic lab notebook want a collaborative tool rather than one aimed at individuals.  They tend to be PIs, or in some cases others in the lab who’ve been asked by the PI to identify a suitable tool. Like those looking for an individual tool, PIs want something which is simple to use and easy to learn.  But beyond that their needs diverge from that of individual scientists. Professor Mike Shipston of the University of Edinburgh provides a good summary of the kinds of challenges that drive PIs to look at adopting an electronic lab notebook:

“We generate a wide variety of types of data sets, for example data from molecular analysis, quantitative analysis, for example quantitative RTPCR, gene cloning, through to electrophysiological analysis, for example from confocal images and total internal reflective microscopy right up to behaviorial assays in animals.  So its really about coordinating those types of data sets that fit together, keeping them contained within projects, because the data sets are derived from different people within the lab.  Also we have a very big extended network both in the UK and across Europe and the US.  It’s about keeping that information together. We have a large number of people coming in and out of the lab, the challenge is keeping track of that data and integrating it in with data from existing projects.”

Well that’s it for this first post — I realize I haven’t yet provided an answer to the question of what an electronic lab notebook is!  The next post is going to look at the tool that has been most widely adopted by labs looking for a collaborative tool, wikis.  I’ll discuss the strengths and limitations of wikis and whether they do – or should – qualify as electronic lab notebooks.  And don’t worry, I promise to come back with a specific answer to the question of what an electronic lab notebook is.