What kind of data sharing do scientists want?

Posted by Rory on October 20th, 2010 @ 6:21 pm

In a recent article, Data Sharing:  Empty Archives, Bryn Nelson points out that although

“Some [scientific] communities have been quite open to sharing [data] . . . those discipline-specific successes are the exception rather than the rule in science. All too many observations lie isolated and forgotten on personal hard drives and CDs, trapped by technical, legal and cultural barriers.”

The communities where most data is not widely shared include disciplines like biology, chemistry, medicine and materials where the bulk of experimental data is generated by individual researchers and labs.  In this post I’d like to take a closer look at data sharing practices and attitudes in these ‘bottom up’ research disciplines.  Let me disclose my bias at the outset — this is that data sharing practices in these disciplines should be determined by the members of the community, not by funding bodies or other policy makers.  If data sharing is to become more widespread, it should be because the members of the community want that to happen, and it should happen in ways that they determine.

The starting point has to be existing attitudes to data sharing in the communities. A recent study of seven labs doing various forms of biology: Patterns of information use and exchange:  case studies of researchers in the life sciences came up with some interesting observations about those attitudes.  What the study found was that life sciences researchers

“are in principle in favour of sharing many kinds of information, and are remarkably willing to do so in order to facilitate each other’s research, without any apparent formal reward.  Thus information is extensively shared within research groups and laboratories, and informally across organisational boundaries through wider research networks, both before and after formal publication.  This may include sharing . . . standard operating procedures, plasmids, computer programmes, scripts and statistical analysis tools.”

So researchers are willing to share  information, but on their own terms.  Essentially they are willing to share information with people they are collaborating with, inside and outside the lab.  In other words, researchers are willing to share information with whom they the researchers want.

The study went on to report that

“Researchers are much more ready to share methods and tools than experimental data . . .  They are reluctant to share the data that makes up their ‘intellectual capital’.  In particular, they are wary of giving away their data for someone else to analyse and get the credit.  “

Researchers are willing to share experimental data, but only subject to two provisos

  • “First they are concerned that they need sufficient time to complete the analysis and, in some cases, to explore intellectual property rights . . .
  • Second they want to publish their results before or simultaneously to publishing their data — and they want to be the ones to publish the data.”

So researchers are also willing to share experimental data, but again only on their own terms.  And those terms are that researchers want to decide what data gets shared and when it gets shared.

Seven labs is hardly a representative sample of the hundreds of thousands if not millions of labs in ‘bottom up’ research disciplines like biology, chemistry, medicine and materials.  And yet the attitudes noted by the study have a strong feeling of familiarity about them, and it’s not implausible to assume that they are  broadly representative of  attitudes that are widespread throughout these disciplines.  The message from the scientists interviewed  in the study is loud and clear:  they are willing to share their data only when they can decide which data to share, whom to share it with, and when.

In the next post I’m going to discuss why many existing ‘top down’ data sharing initiatives have failed to take off because of lack of interest and support from the communities, and speculate about what kind of application, tool, or environment would be needed to enable scientists in bottom up research disciplines like biology, chemistry, medicine and materials to share their data in the controlled fashion they seem to prefer.

Enhanced by Zemanta

What are electronic lab notebooks for?

Posted by Rory on October 6th, 2010 @ 4:23 pm

1.  Introduction

Electronic lab notebooks 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

Electronic lab notebooks differ from other tools used in recording experimental data, like paper lab notebooks and electronic media such as word documents, spreadsheets,and wikis, in that they enable researchers to carry out all four of these functions in an integrated, ideally online, environment.

2.  Recording experimental data and other information

Electronic lab notebooks enable recording of experimental data, and other information like meeting notes and protocols, in two ways. First, they allow import of data which has already been captured elsewhere — e.g. in word documents, spreadsheets and images.  Second, they permit direct recording of data in various forms — text, tables, images, etc.

3.  Adding structure to data and information

Like paper lab notebooks, but unlike other electronic media such as word documents, spreadsheets, and wikis, electronic lab notebooks enable research groups to bring structure to their data.  They do this in a variety of ways:

  • By providing the ability to use records which, unlike the blank page of the word document or wiki, themselves have structure.  This is illustrated In the example below, where the record has a series of fields; Alternative name, Source, Lab, etc.

  • With preformatted template records likely to be of use to many researchers, e.g. for experiments, antibodies, protocols,and  inventory
  • By providing the ability to create records with a structure desired by the user, and including a range of field types, such as strings, radio buttons, dates, etc.

The structure which is added to the research record is invaluable not only in terms of immediate organization, but also in terms of later search and archiving.  The field structure make it possible to conduct fine grained searches which go below the record level.  In the above example, the lab might have thousands of antibody records; taking advantage of the field structure it would be possible to search on all the’ validation status’ fields containing the term ‘No signal’.

Electronic lab notebooks also make it possible to build in a second level of structure through the ability to create links between records, for example between a record of an experiment and a record of an antibody used in the experiment.  Links are useful at this one-to-one level.  Moreover, by creating a series of links it is also possible to build databases, as reflected in the visualization below of a series of linked records.

class-diagram.png

4.  Sharing data and information

Electronic lab notebooks are designed to facilitate collaboration among a group of researchers. They do this with a permissions system that permits some records to be accessed by the entire group, some records to be accessed by subsets of the group, and some records to be kept entirely private.  In addition, they provide different kinds of access to different records or sets of records.  For example, the PI and the student conducting an experiment might have view and edit permission on the experiment record, so that the student could document the experiment and the PI could comment on it, and other members of the lab might have view only permission, so that they could observe and learn.

Electronic lab notebooks also permit permissions to be inherited by ‘child records’.  So, once the permissions are set on a particular project folder, all the experiments created within that folder have the same set of permissions, and it is not necessary to reset permissions each time a new experiment is set up.

Electronic lab notebooks also allow the creation of groups of users.  Typically there is an ‘all users’ group, and groups of smaller sets of users working together on particular projects.  Again, this makes setting permissions more streamlined.  For example, on records which everyone is to have access to, permissions are set for the all users group, and since everyone is a member of that group, it is not necessary to set permissions for each individual.

5.  Communicating

It’s pretty hard to collaborate if you can’t communicate, so good electronic lab notebooks include a messaging system.  This acts as an internal email capability, but it should also do more.  Ideally there should be the ability to make links in messages to other records in the ELN, so for example when a student sends a message to their PI to say that a particular experiment is ready for review and comment, the student can put a link in the message to the experiment record, so that all the PI has to do to access the record is to click on the link.

Online electronic lab notebooks are accessible 24/7 through any web browser, so they allow a new level of flexibility in communication between lab members.  No need to make an appointment during offfice hours to look at someone’s paper lab notebook.  You can now view it, and comment on it, at a time that is convenient to you, for example at home in the evening.  And when you are on the road you can stay in touch with the work that’s going on back in the lab because you can login over the internet, in the evening, between meetings, or whenever it suits you, and see what people have been doing.

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.

Communicating in electronic lab notebooks

Posted by Rory on September 7th, 2010 @ 10:40 pm

People usually think about electronic lab notebooks as tools for documenting research.  Fair enough since people also usually think about them as replacements for paper lab notebooks.  But ELNs are more than just paper notebooks that have ‘gone electronic’, as Andrew Lemon pointed out in an interesting post called The Electronic Laboratory Notebook Trap.  Andrew views the ELN

“as a product idea that hasn’t yet solidified. Think the Internet in the late 1980s or online advertising in the late 1990s . . .  [This is] for the simple reason that scientific organizations are still in the early stages of exploring what can be done when each of their scientists can (passively) connect with the activities of every other scientist, in real time, independent of geography and possibly – organization . . .  Even the term ‘Electronic Laboratory Notebook’ implies a way of thinking about the concept that may not hold up well over time. To me, this term implies something that does what I’m already doing as a scientist with my paper notebook – just in a new medium.”

But with the new medium comes new opportunities, capabilities and demands. Scientists still need to document their research when they move from a paper lab notebook to an electronic lab notebook.  But an electronic lab notebook is also an online environment  (or at least soon will be; ELNs that are not browser based are rapidly being overtaken by the new generation of online ELNs).  And an online environment opens up new possibilities for collaboration and communication.  Talking about one use for ELNs — student-supervisor interaction — Dave Lunt at the University of Hull makes the point that “paper lab books are a source, not method, of student-supervisor interaction“.  You can talk about paper lab books with other members of your group, but you can’t talk together in the paper lab book.

But talking together is exactly what people expect to be able to do in online environments.  In response to  a recent post exploring the question of how ‘social’ ELNs should be, messages were one of the social features that people wanted in an ELN.  It’s not hard to see why.  An electronic lab notebook that includes a messaging capability allows communication to take place when, where and with whom you like. The paradigm of PI and student agreeing a time to meet in an office or the lab to look over the student’s lab notebook so that the PI can comment on it is replaced by the PI being able to keep in touch with and comment on everyone’s work from anywhere, anytime.   So one to one communication is liberated from the confines of meetings in the lab.

That’s a revolution in itself, but it’s really just the tip of the iceberg.  Focussing on the PI – student relationship brings to mind Andrew Lemon’s comment that,  “Even the term ‘Electronic Laboratory Notebook’ implies a way of thinking about the concept that may not hold up well over time. To me, this term implies something that does what I’m already doing as a scientist with my paper notebook – just in a new medium.”  The bigger change that an online ELN with communication capabilities makes possible  more effective ways of  communication within the group, and that has the potential to transform the way labs operate.

Historically it’s fair to say, I think, that the majority of academic labs fall into the category of  ‘collections of individual researchers’ rather than ‘groups focussed on joint research’.  The film Naturally Obsessed:  The Making of a Scientist depicts the paradigmatic traditional lab which revolves around a series of one to one relationships between the PI and individual students.  Research in the Shapiro lab portrayed in the film, not surprisingly given that it was filmed 2004 – 2007, was documented using paper lab notebooks.  In a recent post I speculated about how the research dynamics in the lab might have changed had the lab been using an electronic lab notebook.  One of the key things an ELN could do is to open up new channels of communication beyond the traditional PI – individual student relationship.

There are various aspects of the possible new group orientation.  One is that, with even a simple messaging system, PI’s can communicate from anywhere, at any time, not just with individuals but with everyone, from anywhere, anytime. Of course they can already do that with email.  But with a messaging capability in the ELN they can link their communication to specific bits of research and to other pieces of information such as protocols, lab meeting notes, etc., which all now reside  in a single integrated environment.

A second aspect of the new ‘group focus’ is the potential for enhanced communication between lab members.  If two or more people are working on a project together they can communicate just with each other, or with each other and the PI, about the project, again with the ability to link to experiments, samples, and other items relating to the project. And they can do this from home in the evening just as easily as in the lab during the day.

ELNs are still in an early phase of development, and have only been adopted by a tiny percentage of academic labs, so it would be premature to predict what they might evolve into.  But given the advantages that come with more convenient and accessible means of communication that takes place within the same integrated environment where members of the lab are documenting their research, it will be surprising if communication capabilities like messaging and chat do not play an increasingly important role in the development of ELNs going forward.  And it will be equally surprising if this in  turn does not help to stimulate a shift from academic labs being collections of individual researchers to being groups of researchers working together.

Enhanced by Zemanta

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.

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.

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 III: the benefits of structure

Posted by Rory on July 21st, 2010 @ 8:43 pm

The last post and the one before that looked at different views on who electronic lab notebooks are for — individuals or the lab — and how wikis measure up as environments that  enable lab members to enter and share experimental data.  Notwithstanding their attraction as convenient online tools for sharing general information, wikis lack structure, and it is primarily this which has kept even labs that use wikis wedded to the paper lab notebook for documenting experiments.

In this post we’ll look at why the ability to add structure to research data  is the key enabler permitting the transition from paper lab notebooks to electronic lab notebooks.

Paper lab notebooks support as much structure as you like.  You can create sections, paste copies of images, make notes in the margin, draw diagrams — the only limit to adding structure to a paper lab notebook is the scientist’s imagination.    Unlike a wiki, an electronic lab notebook allows you to replicate the structure that you put into a paper lab notebook.  Why?  Because an electronic lab notebook allows the creation of records with different kinds of fields.  This supports structuring your research data in two ways. First, the different types of fields support entry of information in differing ways, e.g. by date or time, by entry of text, by number, with radio buttons signalling  series of mutually exclusive options, etc.  Second, different classes of records can be put together with different combinations of various kinds of fields, so creating types of records that are appropriate to different aspects of research, e.g. a CHiP experiment, a freezer, a particular protocol,or an antibody.   This is in stark contrast to the wiki, which has only one type of record — the wiki page — and an undifferentiated one at that with no support for separation into different fields.

The benefits of this structure extend further to the other  things you use in your research like images and spreadsheets.  Like wikis, electronic lab notebooks have the advantage over paper lab notebooks of being able to make links to images and spreadsheets, which can also be inserted into the electronic repository — wiki or electronic lab notebook.  But electronic lab notebooks offer superior structuring capabilities in this respect too, because with an electronic lab notebook, unlike a wiki, you can associate a spreadsheet, image or other electronic item with a particular field of a particular kind within a record.

Making use of an electronic lab notebook’s ability to create records with different kinds of fields allows you to put structure into the record of your research in an online electronic environment much as you did with a paper lab notebook and at the same time gain the benefits of associations between bits of information which can only be made in an online environment, so they actually enable taking structuring of research data to a new and higher level.  It is this element – the ability to add structure to research data – which explains why that electronic lab notebooks — and not wikis — provide the best platform for labs  wishing to move from paper to electronic recording and management of their research data.  This is the unstated driver that lies behind wikipedia’s definition of electronic lab notebook as “a software program designed to replace paper lab notebooks“.    And so, I would revise that definition and say that an electronic lab notebook is an online environment that provides a sufficient capability for structuring research data to enable scientists to document and share their research data in that environment without the need to also resort to a paper lab  notebook.

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.