Biologists, software and ELNs

Every few months, my colleagues decide that electronic laboratory notebooks (ELNs) are a good idea. I go through the ritual of searching the web, bookmarking some resources and where possible downloading, installing, configuring and running packages to see how well they work. I know in advance that I’m wasting my time, because I’ve tried them all and there isn’t one free/open-source ELN that works for me.

The problem here is that my colleagues don’t think about software. They just assume that something exists which fulfills all their requirements – but they haven’t even thought about what those requirements are. I call this Microsoft syndrome – the belief that software means a bloated, resource-guzzling software suite with a nice GUI which can do anything. The problem with that kind of software is that trying to do everything means doing no one thing very well. MS Word is a perfect example – it can’t decide if it’s a word processor, a desktop publisher, a graphics editor or an email client and as a result, it’s rubbish at all of those things.

The Linux philosophy is different – you have a choice of many small tools, each of which do one thing very well and you achieve impressive results by gluing them together. Not only does this result in better software, but it forces you to think about your workflow – inputs, processes and outputs and how it fits with your computational needs. If we ask “what goes into a laboratory notebook?”, we see a series of problems each with their own computational solution. For example:

  • User management. I own my notebook, but I’d like to look in yours.
  • Privacy. Are my data private? Do I want to share it with the lab, other labs, the world?
  • Data entry. Do I want a generic template: name, date, experiment title, aims, results? Or the ability to design my own templates according to the experiment?
  • Data management. What items do I want to store? Plain text, images, spreadsheets, graphs, raw data from lab equipment?
  • Data retrieval. Search my experiments by date, title, keywords, tags. Generate reports in various formats from an experiment.
  • Version control. I need to modify entries but also see old versions so as my modifications are not misconstrued by others.
  • Links. I want to link my experiment to related resources: protocols, MSDS data, risk assessments, plasmid maps, PubMed entries, tagged data in social networks (del.icio.us, Connotea, CiteUlike).
  • Legal issues. If my research might lead to IP, patents or commercial application I need digital signing, verification of dates, witnesses?

When we think about notebooks in this way, it’s clear that there are lots of suitable tools with which to build ELNs: blogging software, content management systems, wikis, CVS/subversion. It also becomes clear that the private, paper laboratory notebook is just a ridiculous concept for the times in which we live.

I can see an ELN coding project in my near-future.

11 thoughts on “Biologists, software and ELNs

  1. kevin

    Cool I be waiting for that ELN to dl and use!
    am also looking for a good system to intro to my colleagues who might be averse to steep learning curves…

  2. Roland Krause

    I wonder why no major focus group (NCBI, EBI, MPG, EU) has ever started a serious project on ELNs. It would bring so much to help scientists organizing data in the days of genomics, to secure reproducibility, etc. However, you probably need a strong group to get the project to some serious stage.

  3. Ryan Castillo

    I agree that there needs to be some kind of new system for lab journals, but how many of your colleagues feel comfortable with using such a tool or more specifically computers in general? Its like you said, “they don’t think about the software”. Every biologists who is in Bioinformatics starts to envision these beautiful tools that can be built for them but do not realize the time and work necessary for their development. Plus they do not realize commitment on their part to learn and faithfully use such a tool to further progress its development and functionality. I agree that we should be looking into such tools for the further progression of our respectable fields I just want to emphasize that when these tools are built Biologists who desire the tool should be included in every step of the development process.

  4. nsaunders Post author

    biologists who desire the tool should be included in every step

    Absolutely. What’s missing most at the moment in computational biology/bioinformatics is dialogue between the “computer people” and the “wet lab people”. We need more people who can speak both languages and who have the enthusiasm to keep prompting the biologists to participate; they are notoriously reticent ;)

  5. nsaunders Post author

    I wonder why no major focus group (NCBI, EBI, MPG, EU) has ever started a serious project on ELNs

    I wonder too. The closest that I’ve found is the EMSL Collaboratory, which is DOE-funded. Unfortunately their efforts at an ELN require an advanced degree in Apache Tomcat administration before use.

    Similar problem with structural genomics – lots of people with the same requirements (target selection, workflows, data storage) – yet no one standard software solution.

  6. Curtis

    Very nice post. I agree that paper notebooks are ridiculous in the computer age. While nearly every aspect of the modern research enterprise changes quickly, the lab notebook hasn’t changed in over 100 years.
    A labmate and I have also been spending a fair bit of time trying to come up with a good ELN solution. Your points are exactly what we have been thinking about, how would we design one from scratch? A key aspect of the modern electronic notebook should be data sharing and communication. Everyone involved in a project should be able to view and comment on recent results. One of the first steps we have taken is to get into the Web 2.0 arena by starting a social networking and social bookmarking website for scientists. We are hoping this site will start to improve communication among researchers. It’s at JeffsBench.com, please check it out. Maybe we will try to do an ELN next.

  7. Deepak

    In a lot of companies, ELN’s are becoming mandatory. What is missing is grassroots levels ELNs which can be used in academic research labs, etc. It’s important for any number of reasons. Back in the day, I maintained a simple HTML notebook. If things like Rails existed, would probably have written something that could be more extensible.

    I know any number of wet lab scientists who would like ELN access and are sufficiently computer savvy to work with the coders to get something decent done. That would be a good place to start.

  8. Joerg Kurt Wegner

    Do you have the time for creating an overview of the ELN tools you compared? This would be very useful for being able understanding the detailed arguments.

    Cheers, Joerg

  9. nsaunders Post author

    Do you have the time for creating an overview of the ELN tools you compared?
    No :)
    It would be nice to have some data though, rather than just me saying “they’re all rubbish”. Good project for wiki collaboration.

  10. Pingback: ConnectedBases :: Electronic Laboratory Notebooks don’t work in the Wet-lab

  11. nsaunders Post author

    Brian makes some good points – follow the link in the comment above this one. Question: is “freeform” good, or should biologists strive to bring structure to their wetlab data, even before doing the experiment?

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