Social networking sites — threat or boon to science?

Posted by Rory on December 16th, 2010 @ 5:13 pm

Social networking sites and science

Sir Tim Berners-Lee recently argued, in Long Live the Web:  A Call for Continued Open Standards and Neutrality, that social-networking sites pose a two-fold danger to the web. First,

“Social networking sites assemble. . . bits of data into brilliant databases and reuse the information to provide value-added service—but only within their sites. Once you enter your data into one of these services, you cannot easily use them on another site. Each site is a silo, walled off from the others. Yes, your site’s pages are on the Web, but your data are not.”

A second danger “is that one social-networking site . . . gets so big that it becomes a monopoly, which tends to limit innovation.”

In the last post I took issue with Sir Tim and argued that, on balance, social networking sites add rather than subtract to the flow of information, and stimulate rather than suppress innovation.   In this post I’ll look at the impacts social networking sites are having on science.  I’ll look focus on two large generic social networking sites, Facebook and Twitter.  In a future post I’ll look at social networking sites aimed specifically at scientists.

Facebook

Scientists, like everyone else, use Facebook, but generally they don’t use it in relation to their research.  Rather, like most people, scientists use Facebook to keep in touch with family and friends.   As I have argued previously, the serious problems with privacy — or rather lack thereof — in Facebook put scientists off from using it for research.  An even more fundamental problem is the lack of support in Facebook for adding structure to data, which makes it unsuitable for recording experimental data.

Twitter

In contrast to Facebook, Twitter is used extensively by scientists to discuss issues related to scientific issues.   Importantly, this discussion usually does not reach down to the level of active research projects that individuals or labs are carrying out. Rather discussion centers around things like research techniques and trends, approaches, technology, publications and publishing, and the research process. Twitter is not viewed as a good place for discussing active research because of concerns about confidentiality held by the majority of scientists, who are not open science advocates, and limitations on the nature of the content that can be included, which are of course far more severe than even in the case of Facebook.

Science and social networking sites

So that’s how scientists are using, and not using, Facebook and Twitter in relation to their research.  Facebook is largely irrelevant as an environment or space for conducting scientific research and scientific discussion.  I would argue, however, that Facebook is indirectly playing an important role, (a) by shaping the way  younger scientists think about how to communicate, which in turn will impact on the way they carry out science as new collaboration and communication tools become available, and (b) in stimulating scientists to think about what these tools might look like, as Cameron Neylon did in an interesting post called, What should social software for science look like?.

Twitter is already an important  environment for conversations about science, so it is more than just a model or a stimulator of new ideas.  Twitter is already making a positive contribution to science in that (a) it facilitates conversations between people who probably would not have been in contact or found each other were it not for Twitter, (b) the conversations it stimulates probably would not have taken place without the Twitter platform, and (c) the conversations are useful adjuncts to other forms of scientific communication, e.g. those which take place in academic journals and blogs.  Like Facebook, Twitter is also a model and a stimulator of new ideas about ways of communicating that will over time  find their way into specialized resources developed specifically  for scientists.  An example is the powerful stimulus that Twitter provides to the spontaneous formation and rapid development of micro communities of interest.  This has led to the growth of these communities around specific areas of scientific interest on Twitter, and there is no reason to suppose the same thing will not happen on social networking tools developed specifically for scientists.

Overall:  thumbs up for social networking sites

So the story so far is pretty positive.  Twitter is already making a significant contribution to communication between scientists, and Facebook is stimulating lots of thought about how its  new communication model can be adapted and tailored to science.

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Are electronic lab notebooks for individuals or groups?

Posted by Rory on November 11th, 2010 @ 5:51 pm

I wrote a post last week over on Bitesize Bio comparing electronic lab notebooks to other collaborative tools like wikis and Google Docs.  What was interesting is that most of the people who commented on the post were looking not for a collaborative tool but for something they could use to document their own research, i.e. an individual tool.  This lack of clarity about whether electronic lab notebooks are intended for group or individual use dogs much of the discussion about  ELNs, which tends to get bogged down in debates  about particular features people would like to see in an electronic lab notebook.   See for example the discussion currently going on here.

I thought I’d try to unpick some of the confusion by separating out what elements are essential in electronic lab notebooks used by both groups and individuals, from features that are useful only for groups.

Features for groups and individuals

I have argued previously that the ability to add structure to the research record is the key distinguishing feature of an electronic lab notebook.  That’s because with structure you can replicate online what has traditionally gone in a paper lab notebook, and so the electronic lab notebook can become a replacement for the paper lab notebook.  So in my view neither simple online note-taking devices nor wikis qualify as electronic lab notebooks because they don’t let you add structure to the record of your research.  In the majority of cases people who have adopted note-taking devices or wikis use them along with, not instead of, paper lab notebooks.

Putting structure into the research record is equally important for both groups and individuals who are documenting their research.  And for individuals, that’s it!  The ability to create an online structured record of their research is really all they need.

Features for groups

Groups of researchers need two additional things in an electronic lab notebook, the ability to:

  • Share research data and information, and
  • Communicate about their research

Sharing research data and information

By definition a group of researchers needs to share data and information.    An electronic lab notebook needs to allow the group to do this in a controlled way.    It therefore needs a permissions system that allows some records to be kept private and other records to be shared with everyone or with selected members of the group.  To do this it needs to have an administrator.

Communicating

In order to collaborate effectively groups of researchers need to be able to communicate about their research. Obviously there are plenty of ways to do that outside the electronic lab notebook.  But that’s limiting because it’s not possible, or at least not convenient, for members of the group to communicate about the research they are undertaking in the context of the research itself.  Therefore to be fully effective an electronic lab notebook should include an internal means of communication, e.g. a messaging or notifications capability, and this should include the ability to link the messages or notifications to the record of the research, e.g. experiment records.

Conclusion

In conclusion, electronic lab notebooks can be useful for both individuals and groups. Both individual and group users need the structuring capability electronic lab notebooks provide.  And groups in addition need to use the collaborative and communication capabilities of ELNs.  Beyond that it’s all about features, which are important, but I think it’s useful to separate the woods from the trees, and diving in to a discussion about features without thinking about these broader issues often proves to be unproductive.

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What kind of application would enable controlled data sharing among scientists: Google Docs? Facebook? Something else?

Posted by Rory on October 27th, 2010 @ 9:49 am

In the last post I looked at a study which concludes that researchers in the life sciences are willing to share their data, but only on their own terms:  they want to decide which data to share, with whom, and when. My starting point was a recent article by Bryn Nelson lamenting the fact that data sharing is the exception rather than the rule among scientists.  In the article he gives a number of examples — some successful and some not — where top down data storage/sharing repositories have been established for particular disciplines and particular kinds of data.

Are these kinds of repositories a model for what might encourage widespread data sharing by scientists in bottom up research fields  like life sciences?  I think not, because these top down, centralized repositories generally remove control from the individual or group who is contributing the data.  They are really focused on data storage rather than data sharing. In most cases, moreover, once the data has been contributed it is open for all to see — that is the point of the exercise.  So it’s not surprising that when databases like these are offered to the researchers in the bottom up fields, they usually opt not to contribute their data.  There are few incentives to make contributing their data  an attractive proposition, and it’s yet another administrative burden.

An environment (or system, application, call it what you will) that would stand a better chance of attracting large numbers of scientists is one that does what they want — i.e. lets them  share that part of their research  data they want shared, with whom, and when.  The only kind of environment that will maks that possible is one that puts individual scientists, and groups of scientists, at the center, and in control. That is a bottom up application, not a top down, centralized application like the ones noted by Bryn Nelson.

Google Docs

Is there a model for the kind of application that might work?   How about Google Docs, which is already used by many scientists to share documents, spreadsheets and presentations? Google Docs allows users to share information in a way they control. However, it  lacks a number of necessary capabilities  to enable scientists share their research data when and with whom they want.  These include:

  1. The ability to create records with structure — i.e. the kind of structure scientists are used to putting into their paper labbooks to record experimental data
  2. The ability to link between records
  3. An audit trail of changes made to records
  4. A messaging capability

Facebook

What about Facebook?  Like Google Docs, Facebook permits sharing of information in ways the user controls.  Facebook, moreover, has the ‘social’ features that Google Docs lacks, particular the ability to communicate with other users.  But Facebook has its own set of shortcomings as a potential tool for sharing scientific research data. First, it is viewed as a tool for communicating with friends and family about social rather than work matters.  Second, there are serious problems with the privacy — or rather lack thereof — of data people put in Facebook, which might be acceptable for personal data but is not for scientific research data.  The most fundamental problem, however, is that Facebook, like Google Docs, does not provide support for recording and sharing experimental data because it does not provide the ability to create records with structure.

Essential elements of a data sharing application for scientific research

If neither Google Docs nor Facebook looks like a suitable candidate for a general data sharing application/environment for scientists in bottom up disciplines like biology, chemistry, medicine and materials, the above discussion does provide an idea of the capabilities such an application/environment would need to have:

  1. An individual, user-centric focus
  2. The ability for individual users to control with whom they share data, and when
  3. The ability to create records with structure so that experimental data can be recorded
  4. The ability to create links between records
  5. An audit trail of changes made to records
  6. A messaging capability

If and when an application with these elements becomes available, it would stand a good chance of being taken up by large numbers of scientists in bottom up disciplines like biology, chemistry, medicine and materials.  And that would bring benefits not only to the individual scientists themselves and those with whom they are directly collaborating, it also would lead to a far greater percentage data that is generated being, first, captured electronically, and, second, shared.

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.

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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!

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.

Privacy versus sharing: electronic lab notebooks, Facebook and wikis compared

Posted by Rory on September 29th, 2010 @ 9:08 am

Common misconceptions about sharing and privacy in ELNs

A couple of weeks ago I fielded the following question (assertion, really) at a conference on data sharing and storage in biomedical research:

“An electronic lab notebook is not useful because everyone can see everyone else’s work — there’s no privacy.”

To which I responded that good ELNs have a permissions system that allows records to be kept private.

The person who asked the question, still on the attack, then said something to the effect of, that’s no good because people can’t share their data.

To which I responded that the permissions system in a good ELN allows fine level controls so that any record can be completely private, completely public to the entire universe of users, or accessible only to a particular group of users.   In other words, it supports privacy and sharing.

I was a bit taken aback by the aggressiveness of the questioner, and felt quite pleased with myself in that I had, I thought, successfully countered both lines of his attack  on ELNs.  But reflecting on the exchange afterwards, I began to have second thoughts.  The questioner said that he was in a research support role with a group of academic biomedical researchers.  So presumably his comments reflected concerns/preconceptions the researchers he works with have about ELNs.  And judging by the tack he adopted, the prevailing view about ELNs is not positive — they don’t allow privacy, or they don’t allow  sharing, and in any event they are inflexible.

ELNs:  neither Facebook nor wiki

I don’t know how representative these views are.  Since ELNs have yet to be widely adopted by academic scientists, it’s probably the case that few people have first hand experience with them, so whatever the prevailing view is, it will be based on vague impressions rather than a good set of information.    Many labs have adopted wikis for sharing general information like meeting notes and protocols, and most of these wikis will be inflexible, and not offer scope for keeping private records.  So it’s quite possible that people just assume that electronic lab notebooks are beset by the same restrictions.  It’s also possible that people assume ELNs are only capable of replicating the crude and inflexible privacy/sharing regime you get with your Facebook account.  In other words, many people probably project on to ELNs concerns they have with information sharing applications they are familiar with without any understanding of how sharing actually works in ELNs.

Fine-grained and flexible sharing in ELNs and the benefits it brings

In fact there are some key differences between the sharing/privacy system of Facebook, wikis, and ELNs designed for documenting and sharing experimental data. Here are three of them.

1. Sharing and privacy in ELNs is simpler than on Facebook, and more flexible than in wikis.

When you think about it, sharing on Facebook is very complex!  You’ve got three categories of things you can share — things you share, things on your Wall and things you’re tagged in, and then within each of these a whole variety of subcategories.  And then you’ve got a variety of categories of people you can share with — everyone, friends and friends of friends.    Most people ignore most of the sharing  functionality — the system is just too unwieldy.  It’s also very inflexible — the categories of what you can share and what kinds of groups you can share with are decided by Facebook, not you!

Sharing on wikis is at the other end of the spectrum:  exceedingly simple, but it’s even more limiting.  The way most wikis are configured you are part of one or more groups and the pages in that groups or groups can be viewed by everyone in the group.  In other words, there is no privacy!  And of course no flexibility, since the decision about what group(s) you are in is made by the administrator, not you.

In contrast to both Facebook and wikis, sharing and privacy in the best ELNs are (a) simple, and (b) flexible.  They are simple because they don’t require distinctions between different kinds of things that can be shared or between different categories of people that are involved in the sharing.  For any record in the system sharing is set in the same way. They are flexible because a record can be shared with one other person, with everyone, or with any subset of people  using the system at the discretion of the person setting the permissions, and a different sharing regime can be set for each record if so desired.

2.  ELNs give equal weight to individuals and groups

Facebook, like most social media, is designed around individuals — sharing is about individuals creating groups centering on themselves.  Wikis are just the opposite — they are designed around groups — individuals are slotted in to an environment which is focussed on achieving group objectives.  Neither of these extreme orientations is appropriate to  labs.  When you think about what makes a scientific research lab tick, it’s the fact that it is designed to facilitate both group and individual objectives.  So what a lab really needs is a collaboration and communication tool that has been designed with both individuals and the group in mind. Enter the ELN!  As noted, ELNs allow for some records to be completely private.  So a PhD student, for example, can have their private space where their experiments are accessible to no one but themselves.  But ELNs also allow for the flexible sharing described above, so records which everyone needs to see, e.g. lab protocols and meeting notes, can be made accessible to everyone, and the records in certain projects can be restricted to a specified set of users, e.g. just to the group of students working on the project and the PI.

3.  ELNs  enable  sharing of a particular kind of information — experimental data — in the same environment as other general information.

ELNs bring another kind of benefit to labs engaged in creating and sharing scientific data that is not supported by the sharing regime in either wikis or Facebook.  This is that they are specifically designed to handle sharing of experimental data, the bread and butter of labs engaged in scientific research.    They do this by making it easy to put structure into the research record.  And with structure comes better organization, more targeted search, and better archiving.  So current and future members of the lab can more easily find and use data which they, and other members of the lab, have entered into the ELN.

So that’s a brief overview of how ELNs facilitate both sharing and privacy, and enable labs and lab members to record and share experimental data.    They are superior to wikis in these respects, and they don’t suffer from the sharing and privacy concerns people have as a result of their experience with Facebook.   That’s not too surprising since ELNs have been specifically designed with labs in mind!

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.

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