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.

Naturally Obsessed: What if the scientists had used an electronic lab notebook?

Posted by Rory on August 25th, 2010 @ 7:00 am

The film

Over a year after it was released, the award winning film,  Naturally Obsessed:  The Making of a Scientist, continues to attract praise and stimulate discussion. The film chronicles the experiences of three PhD candidates in the laboratory of molecular biologist Lawrence Shapiro at Columbia University Medical Center.  Here’s the plot, as summarized on the Memorial Sloan-Kettering Cancer Center website

“In the film, shot mostly in Dr. Shapiro’s lab, the students are trying to beat worldwide competition in identifying the molecular workings of the protein AMPK, which controls whether fat is burned to produce energy or is stored as fat. The three scientists struggle with various personal challenges: Robert Townley has a history of rebellious behavior; Kilpatrick Carroll questions whether he should leave academia for industry; and Gabrielle Cubberley wrestles with self-doubt about succeeding in such a competitive environment. At the end of the film, Townley achieves success in his project and publishes the results, with Dr. Shapiro as the only other co-author, in the journal Science.”

Naturally Obsessed has been called “the best film ever to depict what goes on inside a real science lab — period.”  In my view it deserves all the accolades it has received;  gritty, realistic, entertaining, etc.  So it’s well worth watching.   Understandably, it’s the human dynamics of life in the lab that seems to have captured the imagination of most people who have commented on the film.   In this post I’d like to focus on an aspect of the film which has not received a great deal of attention, but IMHO is just as interesting as the human dynamics.  That is the light the film sheds on the research process in a lab, on the ‘research dynamics’ if you will.

Research dynamics in the Shapiro lab

Richard Rifkind, M.D.  co-producer/co-director of Naturally Obsessed: the making of a scientist (and Chairman Emeritus of the Sloan-Kettering Institute and founding Chairman of the New York Structural Biology Center,  observed in commenting on why he was inspired to make the film

“Scientific research . . .  is an investigation that starts with curiosity about a question that can only be answered by the collection of data, and  . . . must find the story in that data that resolves that original question. For the scientist, that story is buried somewhere in the myriad experimental data points collected in a lab notebook.”

Sure enough, Robert Townley’s lab notebook even features in the film.    Since  Townley and Shapiro’s paper was published in 2007, the period of filming must have been roughly 2004 – 2007.  That was before collaborative research tools like electronic lab notebooks were widely available.  If the film was remade today, and the Shapiro lab was using an electronic lab notebook rather than individual paper lab notebooks, how might that impact on the research process and the research dynamics in the lab?

Three kinds of research relationships are depicted in the film:  between Larry Shapiro, the lab head, and each graduate student, between the graduate students themselves and between each graduate student their own research.

Relationships between the lab head and individual graduate students

The key research links in lab appear to be a series of individual relationships between Larry Shapiro and each graduate student.  Although Larry says, “I don’t tell the students what to do, we are trying to train independent scientists,”, he also says, “As a PhD, you are an apprentice to the advisor,” and he clearly is closely involved with his students’ research.  So closely that Robert says at the end of the Science paper, “This is me and Larry’s paper.  Together we have solved this structure of this really important molecule.”

Relationships between the graduate students

There are close links in the Shapiro lab between at least some of the graduate students.  And these are not just social links.  Kil sums it up when he says, “It’s not just my data that enriches the experience, Rob has been sitting across from me, working here, and has done many experiments that I never would have thought to do, and they’ve turned out to be really useful.”

Relationship of each graduate student to their own research

This of course is the ‘obsession’ in the film’s title.  Some quotes give a flavor of the experience:

“Two and a half years of doing experiments and having them not work.”

“We did an experiment a year ago, the crystals were too disordered.  We went back to the drawing board.”

“You learn so much from failure, nothing from success.”

The lab

As depicted in the film, this lab appears to be more a collection of individuals each working independently on an aspect of a problem rather than a group working together on the problem.  So there isn’t — or at least does not  appears to be — a strong common research agenda.

How might the research dynamics change (improve!) if the Shapiro lab adopted an electronic lab notebook?

Relationships between the lab head and individual graduate students

If everyone in the lab was using an electronic lab notebook Larry would find it much easier to keep track of each student’s research.  He could, for example, check their records of their experiments — any time, from anywhere — and leave comments.  The students would also find it easier to communicate with Larry.  They would not need to track him down or wait until he was available to ask a question about a procedure or an experiment in progress.  They could simply send him a message, with a link to the experiment, protocol, etc., posing their question, and expect to get an answer back promptly.

Relationships between the graduate students

With an electronic lab notebook opportunities for exchange of experience and learning from each other –something the students value highly — would be massively increased.  They could if they wanted give selected of their fellow  lab members view or even edit permission on their experiments, so that their colleagues would be able to comment on experiments as they progressed, and in their own time.  Communication would no longer be limited to chance encounters in the lab.

Relationship of each graduate student to their own research

The organized, searchable record of their research that would come with an electronic lab notebook would prove a major plus for the students in the two biggest challenges they describe:  how to learn from failure and how to manage the mass of data they accumulate as years of experiments pile up.  With an electronic lab notebook their past research would be immediately available — to themselves, to Larry and to other lab members — and searchable.  It would be much easier to keep track of what worked and and what did not, and to understand why.  And the chance of ‘making progress’ more quickly by applying lessons learned to future experiments would be materially increased.

The lab

In the absence of an electronic lab notebook, the Shapiro lab appeared to consist of a series of one to one relationships, between Larry and each student, and between individual students.  An electronic lab notebook would provide a convenient environment where the lab, as a group, could share their research and ideas about their research.  Since they are all working around the common theme of better understanding the workings of AMPK, the lab as a group and also each individual would benefit from access to a greater base of knowledge.  Even better, this base of knowledge would accumulate over time, so future members of the lab, and Larry, would have convenient access to the work not only of current, but also past, members of 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.