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.

Electronic lab notebooks: how ‘social’ should they be?

Posted by Rory on August 18th, 2010 @ 10:22 am

The web has gone social, with Facebook and Twitter leading the way.  And applications that were not designed with social networking as a core element are scrambling to add social features.  Often, however, that’s not as straightforward as it seems and can have unintended consequences, of which  Google Buzz is perhaps the highest profile example.  As Robin Wauters at Techcrunch pointed out, “Merging something designed for public broadcasting (Buzz) with something inherently private (Gmail) was just looking for trouble.”

The issue of how many and what kind of social features to include also faces developers of collaborative tools like electronic lab notebooks.  Although collaborative tools are designed to help people work together, they are not  necessarily ‘social’.   But how can something that is designed to help people collaborate not be ‘social’?   As a way into looking at that question, let’s examine what Tom Coates, until recently head of product at Yahoo’s Brickhouse lab, was getting at it when he was quoted in the August 16 issue of Fortune as saying,

“Google is very good at building these utility-type products — search, email, and messaging . . .  But what they lack is a sense of how people share and collaborate.”

When I read that I thought, hang on a minute, what about Google Docs?  OK, Google Docs is not Google’s highest profile offering, but it is used by millions of people, so it surely must be included when considering Google’s ability or propensity to build ‘social’ products .  Document sharing is clearly a social activity, and the express purpose of Google Docs is to facilitate collaboration, so it must be the way that Google Docs is set up that, in Tom Coates’ view, excludes it from the ‘social’ category.

The Fortune article goes on to say, “Coates’s point is that you don’t have friends on Google, you have contacts and tasks.  These services reflect an engineering culture that is all about utility, but one that makes it hard for the company to create something that’s friendly and social.”   So in Fortune’s view in order to be ‘social’ it’s not enough to involve a group, in addition there needs to be an element of ‘friendliness’, and a focus on utility is implied to be anti-social.  Whether or not that is correct, it does constitute an explanation for Coates’s apparent oversight about Google Docs.  Google Docs is very much a utilitarian tool, and it is not designed to be particularly ‘friendly’.  So, even though Google Docs is intended to be used by groups of individuals, for these reasons it is not ‘social’.

Collaborative research tools, including electronic lab notebooks, are like Google Docs primarily designed for a utilitarian purpose — in the case of ELNs, to provide a platform for sharing and structuring experimental data and other information of interest to the research group.  On the Coates/Fortune view, this is at least one strike against their counting as ‘social’.  But since they are used by people not only to collaborate, but also to communicate, would they not benefit from being more ‘friendly’ and ‘social’?  Here are some capabilities, found in Facebook, that Fortune describes as the ‘social layer’.  Which of them would make an electronic lab notebook more ‘friendly’ (and useful!)?

What social features should an electronic lab notebook include?











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.