The Comprehensive Guide to Electronic Lab Notebooks:

How to select the right ELN software for your research

1. Introduction

Hello, my name is Simon Bungers, and I’m the founder and CEO of labfolder. After spending years in the lab at the Max-Planck-Institute of Experimental Medicine in Germany, frustrated with the archaic methods of recording experiments in a paper lab notebook, I decided to dedicate my career towards the advancement of the paperless lab.

Although I usually spend my days being the chief promoter of the electronic lab notebook our team created, this article is NOT about labfolder. Instead, it is an attempt to create a comprehensive buyer’s guide to the electronic lab notebook or ELN, in the hope that it would make it easier for research organizations to switch from paper to digital infrastructure, regardless of the preferred ELN software provider. After all, the intelligent lab of the future is a digital one.

Watch: How will the smart laboratory of tomorrow work?

Digital lab books are not just at the center of the modern lab, but are essentially a prerequisite. If you want to introduce and fully leverage clean data, robotics, automated processes, integrated surfaces and modular design, you will need a connected platform to connect all the tools.

The digital notebook is finally becoming more commonplace in the lab after years of obscurity, but there are still very few useful guides that help researchers navigate through the different options. That’s why I decided to interview several labfolder customers (as well as non-customers currently considering an ELN) and ask them about how their decision process worked, in order to document it here in a best practice guide.

And yes, while I do hope that you give labfolder a try as one of the options for your lab, I will also aim to be candid and point out that it is not always the ultimate solution for every lab. Every scientist and research organization has its own unique needs, and it would be a lie to state that we, or any other laboratory software provider, can do everything for everyone.

In a nutshell, if you are currently considering moving your laboratory processes to an electronic lab notebook, and want to make sure you have reviewed all the important consideration factors, then this guide was written for you. Please note that this is a very long article due to its comprehensive nature, therefore I would recommend you to bookmark this page, so you can always refer to it later.

2. Is there really a need for a digital solution?

There are many obvious and rational arguments to make the decision to invest in an electronic lab notebook for your organization, be it in academics or commercial research. In fact, it’s not even a new idea. Already in 1985, electronic notebooks had their own dedicated chapter in Howard Kanare’s Writing the Laboratory Notebook.

As for my personal experience that shaped the creation of labfolder, I can look back and identify a couple of frustrating moments that convinced me of the necessity to move towards recording and organizing your research digitally.

The struggle to retrieve information as a PhD student

When I started as a PhD student back in 2007, I had a lot of questions to my lab mates – “How to do a mini prep?”, “How to prepare the Tris buffer for my western blot?”, “Where to find the spin columns for the DNA purifications?”, and so on. A lot of valuable information was stored on paper back then, which was difficult to share and even more difficult to retrieve sometimes. The neatly written paper cards with step-by-step protocols I got from a technical assistant (“please return it asap!”), the paper printouts retrieved after a long search in a stash of folders from a post-doc (“couldn’t find the word file, but the printout needs to be somewhere here…”). Imagine my frustration then, when I struggled with collecting all the information, retrieving all the knowledge I needed to get started.

Despite the initial opposition of my supervisor back then, I started to write protocols in Word, print them out before doing an experiment, recording my ad-hoc changes, observations and calculations on the printout while performing an experiment and transcribing the handwritten notes into the document at the end of the experiment. I started to set up a well organized folder with protocol templates you could easily adapt to your little changes, and for recording your findings. I was intrigued by the fact that over time, more and more people from the lab requested those protocols and I was able to send them by email in no time.

My first failure to reproduce an experiment

I can vividly recall a painful experience when my boss told me to look up experiments a researcher did, who had left the lab a few years ago. First, I had to find the right notebook amongst the several she had left in the lab. In fact, the description of the experiments stretched over two of her notebooks, and were not written down in one piece of course. There was a page here, a page there, from which information had to be combined to get an idea on how the experiments were done.

After having assembled the pages, it was really hard to organize the information. A lot of details were missing, and I couldn’t even decipher the handwriting in some cases. I ended up setting up most of the methodology from scratch, and of course I wasn’t too much surprised that my experiments showed different results than those she had observed.

It was my first direct encounter with the “reproducibility problem” and led me start to question the sustainability of empiric research data in general. If the methods (the experiments) are so complex, and the ways to record this complexity are missing and prone to error (paper, transcribing, retrieving), so that reproducibility of “results” cannot be guaranteed, how could you ever be sure you’re dealing with real insights and not random information? It all came down to missing infrastructure for data recording and retrieval, and data integrity.

Digital proficiency is no longer optional

I still find it difficult to explain to non-scientists that research labs, which are supposed to be at the forefront of scientific and technological breakthroughs, still run on a largely analog infrastructure. Every day millions of scientists, students and technical assistants are shaking Erlenmeyer flasks, setting parameters on a laboratory device, asking a colleague where to find an important reagent they need for an experiment, before finally noting down observations or data via pen and paper.

It is now exactly 10 years since my start as a PhD student, but the landscape hasn’t changed much since. I bet that you’ve experienced similar frustrations with all these outdated, manual laboratory processes during your research work. Quite possibly, those very moments have led you to this article, trying to finally find a suitable solution that could dramatically change the way you work. In 2007, there were not that many useful solutions out there, but nowadays there seems to be plenty of ELNs to choose from. So let’s discuss how you should structure your search to find the most suitable electronic lab notebook for your laboratory.

3. What even the most basic ELN should do

The first obvious pain point that electronic lab notebooks try to solve, is that research data often gets lost. According to a 2013 study published in Current Biology called “The Availability of Research Data Declines Rapidly with Article Age“, up to 80% of raw data from scientific papers published twenty years ago is unobtainable. The study shows that the likelihood of finding an existing data set falls by 17 percent per year, which is mostly attributed to outdated data storage methods.

This is certainly a big problem when you consider the importance of replicable data, reproducible data and reproducible research. But what’s even more frustrating, is when this sort of data misplacement happens within one’s own research team, or even worse, with your own notes!

Typical scenarios include:

  • I need to find raw data from an experiment I performed years ago but do not recall exactly where I stored that information.
  • I want to replicate an experiment from a colleague, and need some additional information, but that person has already left our organization.
  • I cannot use the data needed to continue a group project, because the person who holds the specific data set went on holidays without a full handover, or unexpectedly took ill.

 

In our day-to-day lives, this problem has almost disappeared. I can now retrieve an email I wrote to a colleague years ago, or the pictures I took at a research conference, within seconds thanks to the search functionalities of my mobile phone, Gmail and Dropbox. To achieve the same in the research environment, most ELN software providers provide similar solutions.

Data Creation, Storage & Retrieval

  • Create, import and store all important data types in digital format. Important examples include:
    • A text processor which allows you to write notes and format them, as you would do with Microsoft Word. Ideally, the ELN should allow you to import existing Word documents and keep editing them within the tool, and vice versa when exporting from your digital notebook to a Word file.
    • A spreadsheet tool that at the very minimum allows you to create tables, enter data, perform some basic formatting and common calculations within the ELN, as well as import from and export to Excel. Additional advanced features would typically require an integration with Office 365.
    • The ability to import images and add annotations (through text or sketching). For example, you can annotate your western blot with the molecular weights of the ladder and even highlight the specific bands that strengthen your hypothesis. You need to assure that the annotations are created as an image overlay and do not alter the raw data that you uploaded.

 

  • Make it easy to retrieve using tags, smart filters, and search functionality. No matter how organized your lab team is, finding that one piece of information you need by looking through volumes of paper lab notebooks will never be faster than a searchable, digital record, stored on a single platform used by the entire research group. As a researcher or team leader, you should be able to quickly look up notebook entries by:
    • Author
    • Unique IDs or Tags assigned to the entry
    • Entry Title, Description or Text Content
    • Timestamps such as created date, last modified, or even custom dates
    • Structured data queries (for example, “find all entries where the test subject’s age is between 25 and 35”)


Tip
: to better understand the sophistication of a digital notebook’s search functionality, try testing whether the ELN can handle scientific unit conversions. If you can tell an ELN to search for all entries which reference 5 microliters of DNA solution, and the search query also returns entries which have recorded this as 0,005 milliliters, then you know that the search functionality has really been built with scientists in mind.

Additional desirable features

  • Protocol templates which you can re-use to save time on repetitive tasks.
  • User interface in multiple languages to allow researchers to work with ELN software in their own native language.
  • Mobile and tablet apps, as well as responsive design, allowing researchers to use their preferred device to record their experiment notes.
  • Strong onboarding materials, user manuals, and a dedicated support team which is available via different communication channels, such as email, live chat, and online webinars. Make sure to test the service levels of your digital lab book provider – you don’t want to be stuck using a piece of software where no one will support you in case you are not sure how to use some functionality or discovered a product bug.

Conclusion for individual researchers and small teams

If you are an individual researcher, or part of a small team, and are mainly looking for a simple, cost-effective solution to record experiment notes in digital format, without any requirements in terms of team management, compliance, communication tools, etc., then you can probably already stop reading after this section.

To a certain extent, you can make use of generic notebook software solutions such as Evernote or Onenote. These note-taking apps tend to cover many of the features described in the above section, but it can take a lot more time and effort to customize them to your needs than selecting a dedicated digital solution for your lab.

Many ELN software providers, including labfolder, offer a fully free electronic lab notebook with limited features that should suit your needs.

List of all electronic lab notebooks (ELN) with a free version:

 

ELN
Free version Academia
Free version Industry
Cloud Version
Local server installation
Benchling
Yes
No

Yes
No
eLabFTW
Yes
Yes
No
Free
Hivebench
Yes
Yes
Yes
No
Labarchives
Yes
Yes
Yes
No
Labcollector
Yes
Yes
Yes
Paid
labfolder
Yes
Yes
Yes
Paid
RSpace
Yes
Yes
Yes
Paid
Scinote
Yes
Yes
Yes
Paid

 

For researchers who intend to use an ELN for their entire research group or institution, I would recommend moving on to the next chapter as there is a lot to unpack.

4. Features and structural considerations for teams

When it comes to working as part of a research team, selecting the right electronic lab notebook gets a bit more complicated, and you’ll need to consider the structural needs of your team. In the following section, I will discuss what those are and which features are to be considered to meet those needs.

Team communication, collaboration, and administration

There is always this fine balance between sharing information in a collaborative environment, and protecting your data. On the one hand, developing innovative solutions is complicated and requires teamwork between experts with diverse and highly specialized expertise. Failure to collaborate can lead to wasted time, effort and funding. On the other hand, many scientists are ambivalent about how open the research process should be, fearing an increase in mistakes, misunderstandings and vulnerabilities.

Electronic laboratory notebooks can offer a balanced solution to this conundrum, by offering the following:

  • Flexible group structures and robust team administration functionality that allows you to define who should have access to what.
    • Creating subgroups and hierarchies to reflect the organizational structure of the entire research institution, not just an individual team.
    • Defining administrators (and sub-administrators) that can invite team members, assign user rights, and determine which information can be accessed, exported or removed.
    • Revoking access to team members without losing the information they created.
  • The ability to share and discuss research notes and underlying data.
    • Sharing notes, projects and protocols with specific team members.
    • Adding notes and comments to entries.
    • Sending messages to colleagues and project collaborators.
    • Managing projects and assigning tasks to team members.
    • Multi device and browser compatibility.
  • Security features to safeguard your data’s integrity
    • Time stamps to record data creation and modification.
    • Audit trail that records an accessible version history of every change to an entry
    • Modern encryption standards to ensure your files are protected from malevolent access attempts.

Cloud vs. On-premise Server

Perhaps one of the most crucial questions to consider in advance, is what your organization’s policies are about data storage. Cloud-computing solutions are rapidly becoming the norm for most industries, but scientific institutions are slower to adapt in this case and often prefer to operate on an on-premise, self-hosted server. Here is an overview of the most common options:

Cloud hosted solution

Most ELNs would store your data on a cloud server as the default option, often hosted on Amazon Web Services or Microsoft Azure.

The advantages of a public cloud solution:

  • You will not have to pay any setup costs, and any ongoing maintenance costs (if any) will be usually include in the license fee charged by your ELN provider.
  • No setup or maintenance is required from your side.
  • Your documents are easy to access, from anywhere, as long as you have a working internet connection. Make sure to test compatibility with different browsers.
  • Most leading cloud-computing providers will virtually guarantee reliability. For example. Amazon’s Service Level Agreement promises at least 99.95% uptime.

 

The disadvantages of a public cloud solution:

  • You do not have full control over data security and privacy, but are reliant on the cloud provider. Although Amazon Web Services boasts more than 1,800 security controls, including encryption capabilities, there are never any guarantees that your data will be 100% safe.
  • If set up on a public cloud, your data will be stored on a multi-tenant environment, meaning that other organizations also ‘rent’ space on the same server. Your data is segregated and protected from other server users through authentication protocols, but despite these security measures some organizations simply prefer to not share servers with anyone (see private cloud and on-premise server).
  • You are dependent on having a reliable, fast internet connection (usually should not be a problem for research institutions but exceptions exist).

 

For those organizations that would consider a cloud solution, but prefer to not share servers with other organizations, a private cloud may be the best solution. Ask the ELN provider you’re considering if this is possible, as not all companies offer this.

On-premise Server

The more conservative but still popular approach is to select an on-premise server.

The advantages of an on-premise server:

  • Your IT admin has full control of all your settings and security protocols.
  • Dedicated server only for your own organization.
  • Can also be accessed offline.

 

The disadvantages of an on-premise server:

  • Higher cost of deployment and maintenance.
  • Requires IT resources to set up and maintain on ongoing basis, and will likely to be slower to roll out compared to “plug and play” cloud solutions.
  • Your IT team is responsible for the reliability, speed and service performance. Having full control is nice but it is difficult to compete with Amazon or Microsoft for performance, even with your own servers.
  • Can also be accessed offline.
  • Less frequent software updates (bug fixed and feature releases) for the server version, as server deployments are more complicated and require assistance from your IT staff.

 

Your organization’s policy regarding data storage will be the key decision maker here. Large organizations with a big IT department often prefer to have an on-premise solution to be in full control, and are willing to pay extra for that reassurance. Smaller companies and research institutions are generally more willing to take advantage of the capabilities offered by cloud computing, especially those provided by Amazon or Microsoft.

Additional desirable features

  • A material database which allows research teams to track which materials have been used in each experiment, as well as the exact quantities.
  • Stock inventory management that updates the available quantities of chemicals and supplies when used in experiments. Other relevant product attributes could include locations and expiration information.
  • Advanced data archiving options , such as XHTML exports.
  • Domain-specific features, such as a chemical structure drawer or a DNA/RNA/Protein sequence aligner.

Conclusion for academic research teams

For those research teams, especially in academia, that are mostly research-focused as opposed to production-focused, all the features and considerations listed above should suffice to make an informed decision about the best ELN for your needs. Please refer to the below list of the most popular digital lab books for academia.

For R&D labs with the goals to also develop commercial products, let’s move on to the next section, to learn about all the important considerations around compliance and data governance.

 

List of electronic lab notebooks (ELN) suitable for academic research teams:

 

ELN
Free version
Paid version
Cloud Version
Local server installation
Benchling
Yes
?

Yes
No
eLabJournal
No
$$
Yes
Yes
Hivebench
Yes
?
Yes
No
Labarchives
Yes
$$
Yes
No
Labcollector
Yes
?
Yes
Yes
labguru
No
$$
Yes
No
labfolder
Yes
$$
Yes
Yes
Mbook
No
$$
Yes
No
OpenLab ELN
No
$$$
Yes
Yes
PerkinElmer Signals
No
$$$
Yes
Yes
RSpace
Yes
$$
Yes
Yes
Scinote
Yes
?
Yes
Yes

5. Compliance, Data Governance & IP Protection

Research laboratories which look to patent and commercialize their inventions, also have additional responsibilities, and undergo more scrutiny,  in terms of complying with standards, regulations and best practices. Some of the most important ones include GLP Compliance, FDA 21 CFR Part 11, and ISO certification. We wrote plenty of blog posts and white papers on these topics, which allows me for the purpose of this article to jump right into the topic of which features ensure your electronic lab notebook is compliant with all these regulations and standards.

Feature requirements to ensure full compliance

Let’s start with the Good Laboratory Practices (GLP) which were introduced by the OECD. There are 3 principles in particular that apply to electronic lab notebooks, which mostly prescribe how data should be stored, secured and managed. Here are the features an ELN needs to have before you can be assured that you are GLP compliant:

  • Security: The ELN must be able to archive, securely store, protect and extract the data and notes you create. Make sure to ask your ELN software provider how often the data is backed up, how it protects it data center, and which exporting methods are available.
  • Confidentiality: Lab notebook software must employ procedures that keep all stored records protected from unauthorized parties. At a minimum, this includes strong user right controls (who can see what), robust encryption standards, as well as confidentiality procedures and agreements.
  • Authenticity: Your digital lab book should guarantee the reliability of data transfers through multi-level authentication processes, secure user identification, electronic signatures, and a migration plan.
  • Integrity: Few things are more important than ensuring that your data cannot be altered or deleted by unauthorised parties. This can be prevented through restricted management rights, a full audit trail including version control and timestamps, secure data transfer, and organizationally defined controls on data availability, data retention, and data deletion.

 

Next, if your lab is seeking to produce pharmaceutical drugs, vaccines, biopharmaceuticals or any other product or treatment regulated by the Food and Drug Administration (FDA), you will need to make sure that your digital records are considered as trustworthy and reliable to paper records. This is covered in Title 21 CFR Part 11 of the Code of Federal Regulations. To ensure this is the case, your ELN must do the following:

  • Your data must be digitally recorded using a closed system that restricts access, and ensuring that only authorized personnel can access your records. This is generally achieved by most commercial ELNs using a secure login with username and password, but do watch out for tools which allow for public sharing of documentation.
  • Your digital lab book must also be able to create readable copies of your notes at any time, for example in pdf format. In addition, these copies must also be archived for future retrieval.
  • Probably not very surprising, but the FDA also mandates that electronic notes have an audit trail with time stamps, which cannot be edit or deleted.
  • Finally, the FDA is also very specific about how electronic signatures should be instituted to prevent fraudulent use. For witnessing documents, it is required to securely record who is witnessing and at which date and time, in a manner that wouldn’t allow a signer to easily repudiate the signed record as not being genuine.

 

In an ISO certified environment, it is also important to make sure that certain standards are followed as to how documentation should be maintained. The ISO standards most relevant to laboratories are ISO 9001 (general quality management), ISO 15189 (medical and diagnostic laboratories), and ISO 17025 (testing and calibration laboratories). Concretely, this means that ELNs must:

  • Allow users to assign a title to documents.
  • Automatically create a timestamp for date creation and modification.
  • Assign a unique ID to each document.
  • Ensure that editing a document version can only happen by one authorized person.
  • Add serial page numbers when printing the digital notes.
  • Identify the authors of each document.
  • Have a full audit trail recording the nature, the date/time and author of changes.
  • Make it possible to invalidate documents.
  • List all documents in a master list.
  • Review and if applicable revise processes and SOP based on the latest guidelines.

 

List of electronic lab notebooks (ELN) enabling industry research teams to comply with FDA, ISO & GMP/GLP standards:

ELN
Free version
Paid version
Full Audit Trail
Sign &
Witness
Cloud Version
Local server installation
Benchling
No
$$$$

Yes
Yes
Yes
No
eLabJournal
No
$$
Yes
Yes
Yes
Yes
Hivebench
Yes
?
Yes
Yes
Yes
No
Labarchives
Yes
$$
Yes
Yes
Yes
No
Labcollector
Yes
?
Yes
Yes
Yes
Yes
labfolder
Yes
$$
Yes
Yes
Yes
Yes
RSpace
Yes
$$
Yes
Yes
Yes
Yes
Scinote
Yes
?
Yes
Yes
Yes
Yes

6. App integrations & Open API

At least until the ELN industry reaches a more mature stage, it is unlikely that every researcher can find the perfect ELN that suits the needs of their team. After all, there are so many people that are stakeholders in selecting an electronic lab notebook: the lab manager, the Head of R&D, the IT manager, the QA/QM manager, post-doc researchers, etc.  Every research team has unique preferences and procedures that it would like to be included in their new digital lab book.

That’s why I strongly believe that software companies which serve the lab need to build products as a platform, not a tool or a suite. What does this mean?

Let’s take an example from Microsoft with its Office 365 Online Productivity Suite. Over the years, they have built a carefully crafted selection of productivity tools, such as Outlook, Word, Excel, OneNote, etc. Together, these form a productivity suite, offering you a well-rounded solution from one provider. However, there are some trade-offs. If the suite does not offer a particular feature you would like to have included, or does not integrate with a differ tool that you are already using, then you are most likely out of luck.

Given the complexity and diversity of research, there will always be a subset of organizations who end up finding that none of the ELN software solutions match exactly what they need. Luckily, a few lab software companies have recognized this challenge, and are providing a platform that allows research organizations to:

1) select a third-party plugin or app from an “ELN app store”,  whether generic integrations such a Dropbox or Gmail, or research-specific solution such as Mendeley’s reference manager or Figshare’s data management solution .

2) develop their own custom solution to interact with the ELN software environment, via an open API. This allows unlimited possibilities for what can be achieved with the ELN. For example, a research lab within a hospital could build a solution that automatically transfer patient files to their notebook, or a chemistry lab could be integrating balances and thermometers to automatically send data to the right notebook entry.

 

List of electronic lab notebooks (ELN) with third party integrations and/or open API:

7. Final Remarks

Welcome to the digital lab movement

The choice for which electronic lab notebook or ELN is the best for you, your team, and your organization, ultimately boils down to preferences around user experience, features, pricing, compliance environment, and so on. However, in my mind there is no doubt that the digital trend will accelerate and that we’ll see a lot more ELNs in the laboratory.

I still hold on to my old paper notebook as some sort of memento, to remind me of all the time I wasted printing, cutting and pasting all kinds of documents onto the pages of my lab companion. It didn’t matter whether I was working with Excel files, 3D models, plain text documents, metadata or proprietary information files, everything ended up going through this ritual.

My hope for this article is that it contributes, even if just a little bit, to the increased acceptance of the digital lab. Scientists are at the forefront of innovation, and should be supported at all times by the most advanced technology available. I strongly believe that the future will see connected laboratories which would enable clean and structured data, as well as artificial intelligence helping researchers better understand experiment results. Electronic lab notebooks are the first step in the right direction, and little by little they evolve into highly intelligent productivity and collaboration platforms that will support scientists all over the world in their quest to make groundbreaking discoveries.

Housekeeping notes

  1. First of all, I very much welcome feedback of any kind and would be happy to discuss your thoughts on this subject. You can reach me at simon@labfolder.com or on Twitter – I promise to respond to every genuine message.
  2. Since I tried to be as helpful as possible to the research community, I listed not just labfolder, but 15 other popular options for electronic lab notebooks. Those mentioned include: Benchling, elabFTW, eLabJournal, Hivebench, LabArchives, LabCollector ELN, labfolder, Labguru, Mbook by Mesterlab Research, OpenLab ELN by Agilent, PerkinElmer Signals Notebook, RSpace (formerly known as ResearchSpace), sciNote by Biosistemika, and even Onenote and Evernote which aren’t technically ELNs but “only” digital notebooks.
  3. It is possible that I didn’t include some other options that would merit mentioning. If this is the case, feel free to send me a note and I would happily consider adding it to the article (I do reserve the right to maintain a certain quality standard and to not include certain solutions if they would not provide value to the readers).
  4. Together with my team, I spent a lot of time recording the features and pricing advertised by each ELN software company. At the time of writing (August 2017), I am confident that my representation is fair and accurate. At no point did I provide a subjective opinion on usability and design, but rather I only summarized the facts published on each provider’s website. If you spotted any inaccuracies or now have updated pricing or new features, please send me a note and I will happily rectify any outdated or inaccurate information.