How to share and store data in an electronic lab notebook

Posted by Rory on September 23rd, 2010 @ 5:16 pm

In this blog I usually look at data sharing from the point of view of the core research unit, the lab.   That was the perspective I adopted a couple of weeks ago in a presentation, Electronic lab notebooks in biomedical research, at the Storing, Accessing and Sharing Data: Addressing the Challenges and Solutions event co-hosted by the Scottish Bioinformatics Forum and S3 in Edinburgh.  I’ll come back to that perspective in a minute, but first I’d like to contrast two very different institutional perspectives on data management described at the conference.

Sanger Institute:  centralized institutional data management

Phil Butcher, head of IT at the Sanger Institute, started with a high level overview of data management issues at Sanger.  He focussed mainly on the rapid growth in the amount of data generated at Sanger, and the other institutes with which it has large scale collaborations, and the issues relating to storing and finding data when there is so much of it.  The impression I came away with is that at Sanger data is viewed as an institutional matter, not something that individual labs or scientists manage or, apparently, have much of a say in.  That makes sense, because the research projects Phil mentioned were all large scale, involving large numbers of scientists, and the generation of huge amounts of data.  The title of Phil’s talk, Scaling up Science and IT: Sanger Institute’s Perspective, reflects the centralized approach.

London Research Institute:  decentralized institutional data management

The next speaker, Jeremy Olsen, head of IT at the London Research Institute, started by saying that based on Phil’s description of Sanger, the London Research Institute was very different indeed, more  a collection of individual research groups.  In describing his LRI  perspective Jeremy said that he would be sticking up for the “little guy”.  He proceeded to briefly overview how research is carried out at the LRI, introducing the various research groups and their research interests.  The LRI represents a very different paradigm from Sanger; at the LRI decentralization rules, as reflected by the title of Jeremy’s talk, Data Growth and Management in a Diverse Life Sciences Environment.  At the LRI there are fundamental issues relating to getting a handle on what research the various groups are involved in, what data they generate and how they manage it. Progress would need to be made on understanding  these issues before it would be possible even to consider a centralized approach to data management and what that might entail.

The lab: bottom up data management

When it came time for my presentation, I started by saying that if Phil was representing the centralized  institutional approach, and Phil was looking at  the “little guys” from an institutional perspective, I was going to look at the issue of data management and sharing from the point of view of the little guy him/herself, i.e. the PI.  In the academic context, it’s important to note that the Sanger model is the exception and the LRI  decentralized model is the rule.  In fact it is almost certainly the case that the LRI, decentralized as it is, is still towards the more organized and centralized end of the spectrum of academic biomedical institutions. That point was reinforced to me when speaking recently with the IT director of a medium – large biomedical research institute in Australia (800 people including 700 scientific staff).  His description of the issues he faced with getting a grip on what data there was in the labs at the institute, how they managed it (if they managed it all), and uncertainty about how to help PIs get a better handle on their data was uncannily reminiscent of Jeremy’s description of the situation at the LRI.

From the perspective of IT managers tasked with, among other things, trying to bring some order to the data generated by the research groups at their institution, to store it in a cost effective fashion and have it archived in a way that is useful in the future, multiple PIs generating ever increasing amounts of data may be a ‘problem’ to be managed or dealt with.  But from the PIs’ point of view it is their data and theirs to manage (or not) as they want.  There is a pretty fundamental difference in outlook here.

Electronic lab notebooks — part of the solution?

In my presentation I asked where electronic lab notebooks might fit into this picture, and whether they could have a role to play in crafting better data management solutions that meet the objectives of both PIs and IT directors.

ELNs tick some of the key boxes IT directors look for in best practice in data storage and sharing, including:

  1. Storing metadata in a structured fashion and ensuring controlled access.
  2. Effectively managing different data types, including attachments and imports.
  3. Allowing improved indexing  and search, through the use of structured metadata.

Electronic lab notebooks can also solve  the key data management problem facing many PIs:  coordinating a wide diversity of data type sets generated by a large number of people within the lab.  They can, that is, if they meet the following key requirements of today’s PIs:

  1. The ELN is flexible and can be set up the way the PI and their lab want it set up.
  2. It’s easy for the lab to transfer to the ELN.
  3. The ELN facilitates better exchange of information between members of the lab and, over time, better archiving.
  4. the ELN is web based and hence accessible anywhere, anytime.

So, electronic lab notebooks can help to solve the key data management  issue faced by  the core unit in academic institutions — labs.  And they provide a platform for data management that IT directors looking at the problem from an institutional perspective can work with.  As such they can be part of a solution which benefits both PIs, who are concerned with the research done in their group, and IT directors, who are concerned with the data generated throughout their institution.

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.

What’s the best time to implement an electronic lab notebook in your lab?

Posted by Rory on September 1st, 2010 @ 7:00 am

It’s September, and the new semester has started or will be starting soon. With new people coming into the lab, new courses to teach, and the start of the new academic year, it’s a good to think about ways of making your lab more productive.  One of the most obvious ways of doing that is to implement an electronic lab notebook for people to record and share experimental data in.  But is this actually the best time to do that?  This post discusses the pros and cons of adopting an ELN at three different times.

1.  When setting up a new lab

The three  biggest advantages of implementing an ELN at the same time you’re setting up your lab are:

  1. Since the ELN is there from the beginning, you will have a single, integrated and  complete record of all the research that has been done, by everyone in the lab, from day one.  And the corollary of this is that you won’t have to worry about integrating data from other sources, as you would if you waited to adopt an electronic lab notebook at a later date.
  2. Having everyone work in the same environment that the electronic lab notebook provides should have a beneficial impact on collaboration and communication, between you and other lab members and also among themselves, and hence will play a useful role in bringing the lab together and creating a positive lab culture.
  3. People are likely to be most open to initiatives at the start of something new, so you are likely to encounter less resistance to implementing an electronic lab notebook when a lab is starting up rather than later, when individual and group work patterns are already in place.

Those are very big wins and it’s hard to argue against them.  But it’s important to be aware of considerations which might make you inclined to do a bit more preparation before introducing an ELN.  These include:

  1. Are you ready to embrace an electronic lab notebook for yourself and your lab and what that entails — working with your IT support to get the system in place, and then administering the system yourself or working with the person who is going to administer it for you?
  2. Have you thought about how to get other lab members on board with the idea of implementing an electronic lab notebook?  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.”
  3. Do you have the necessary IT infrastructure in place for an electronic lab notebook?  With a service where someone else is hosting the electronic lab notebook, there is less to think about, but you still need to make sure that the network speed on the computers your lab members will be using to access the service is not too slow, and that they are able to use an up to date browser — like Firefox, Safari, Chrome or Internet Explorer 8.  If you are setting the electronic lab notebook up on your own server you’ll also need to make sure that your IT support is aware of your plans and willing to help, that the servers you will be using have sufficient capacity for the data that will flow through the electronic lab notebook, or if you will be using  a new server, the specs that will be required for running the ELN.

2.  At the start of a new academic year

The same considerations apply if you decide to set up an electronic notebook at the start of a new academic year, and some additional pros and cons also come into play.

On the plus side, a new year, possibly with some new members of the lab, is always a good time to introduce new ‘things’, be they pieces of equipment or software, or new practices, because people are more likely to be open minded about trying them out.  Also on the plus side, unlike setting up a new lab, with an established lab you will have a good read on people’s work practices, including who is likely to be in favor of adopting and electronic lab notebook, and who is likely to be opposed, so you should be able to design an effective evaluation period, where for example you might have several enthusiasts test out a new system and, if it meets with their approval and yours, assist in mentoring other members of the lab when it comes time for implementation.  Or you might have a research or administrative assistant take on the task of evaluation, again by this time someone you have worked with and trust.

The biggest downside of adopting an electronic lab notebook at the beginning of the term or semester is that you — and others in the lab — will probably be even busier than usual, and evaluating the ELN may either get lost in the shuffle or not receive the attention it needs.

3.  In connection with starting work on a new grant

Adopting an electronic lab notebook to coincide with work on a new grant is probably even easier than adopting at the beginning of a term or semester.  With a new grant you have an identifiable, and probably a large, project, which in any event will require thought about who is going to be involved, the division of labor, how the project is going to be organized, how data will be captured and recorded, possibly how data needs to be organized and archived to satisfy the requirements of the granting body, etc.  So, it’s very natural to introduce the idea of adopting and electronic lab notebook as a vehicle for documenting the work done in connection with the grant, and, beyond that, other work as well.

A second benefit is that the grant will have a starting date, a schedule, and deadlines, so there will be an impetus which everyone will feel to actively push through an evaluation and then, when the electronic lab notebook has been adopted, to push ahead with implementation.

There are no obvious cons to adopting an electronic lab notebook in conjunction with the start of a new grant, but an additional consideration may need to be taken into account.  This is whether the ELN will be used just for the research associated with the grant or for all the lab’s research.