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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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.