How to Master Electronic Lab Notebooks: A PhD Guide to Automated Methods Writing

Hello. My name is Thomas Bertelsen, and I want to share with you a discovery that changed how I approach methods writing during my PhD. Like many PhD students, I spent 30-40% of my writing time struggling with methods documentation - constantly rewriting sections, hunting for missing details, and trying to remember research decisions I had made months earlier.

When I first started my PhD, writing methods sections felt like an endless cycle of frustration. I would sit down to document my research procedures only to realize I had forgotten crucial details about why I chose certain approaches. Sometimes I would find incomplete notes scattered across different notebooks and computer files, making it nearly impossible to reconstruct what I had actually done. What frustrated me the most was spending hours writing methods sections that my supervisors would ask me to completely restructure because they didn't match the conventions in our field.

After considerable trial and error, I discovered that electronic lab notebooks could solve most of these problems. Instead of treating them as simple replacements for paper notebooks, I learned to use them as structured systems for methods writing. This approach goes beyond basic documentation - it creates a workflow that makes writing easier for your future self.

The solution I developed uses two main strategies. First, I learned to select model articles from my field and use them as templates within my electronic lab notebook. Second, I maintained a research diary to capture the reasoning behind my methodological choices as they happened. Together, these approaches ensure that when it comes time to write, I have both the structure and the content ready.

I hope that you can benefit from this approach and avoid the somewhat overwhelming process of trying to reconstruct your methods from incomplete notes. Whether you have just begun your PhD or have been working for some time, these techniques will help you document your research in a way that makes writing your methods sections straightforward rather than stressful.

What Electronic Lab Notebooks Actually Do for PhD Students

To understand why electronic lab notebooks work so well for methods writing, you need to know what they actually are and how they differ from the tools most PhD students currently use.

Electronic vs. Paper Notebooks: The Real Differences

An electronic lab notebook is software that replaces your physical research notebook. The basic idea is simple - instead of writing on paper, you document experiments, protocols, and research data on your computer or mobile device. However, the differences go far beyond just switching from pen to keyboard.

Paper notebooks have obvious limitations. They get damaged by coffee spills, pages tear out, and your handwriting becomes illegible when you're tired or rushing between experiments. I have spent countless hours trying to decipher my own notes from months earlier, wondering what I meant when I wrote something that looks like "test w/ weird sample."

Electronic lab notebooks solve these practical problems while adding capabilities that paper simply cannot match. You can include text, data, images, equations, links, videos, and even connect directly with laboratory equipment. More importantly, ELNs feature built-in search functions, the ability to create stable URLs, and permission-based access control—capabilities impossible with paper documentation.

Why ELNs Matter for PhD Research

Electronic lab notebooks address specific challenges that PhD students face during their research journey.

The most obvious benefit is collaboration efficiency. Scientists save an average of 9 hours per week using ELNs, particularly when preparing for meetings and communicating with advisors. This time savings becomes crucial when you are working with multiple supervisors or collaborating across different research groups.

Data security represents another major advantage. Your research data remains protected through password protection, backup methods, and often end-to-end encryption. This protection prevents the kind of information loss that could set your PhD progress back by months. I have seen PhD students lose entire semesters of work due to damaged notebooks or misplaced files.

How ELNs Support the Model Article Approach

Electronic lab notebooks excel in the area where most PhD students struggle - systematic methods documentation. Their structured nature makes them ideal for implementing the model article approach I described earlier.

You can create templates for protocols and standard operating procedures within your ELN, making it straightforward to establish your methods section framework based on exemplary papers from your field. The process involves copying sections from model articles, marking them with curly brackets as I will explain later, and gradually replacing template content with your own research details.

The research diary component works naturally within ELNs through real-time documentation. As you make decisions throughout your study, you can immediately record your reasoning. This ongoing commentary becomes essential material when writing your methods section and reflecting on your research choices for your thesis.

ELNs also help maintain consistency across your documentation through standardized entries and experiment linking. This consistency ensures your methods section remains coherent throughout your multi-year PhD journey, even as your understanding of your research evolves and deepens.

The combination of structured templates and reflective journaling within a single, searchable system creates an ideal environment for the two-pronged approach to methods writing that I will walk you through in the following sections.

Find Your Model Article

Your first step in creating a good lab notebook is finding a model article. A good model article will help you regardless of whether you are writing a qualitative, quantitative, methodological, or systematic review article. Following a model article will ensure that you adhere to the conventions in your field and avoid overlooking essential aspects of your research.

Ask your supervisor for recommendations

To find a suitable model article, ask your supervisor or other experienced researchers in your field if they can recommend an article with a study design similar to yours. It doesn't have to be on the same subject. Still, it must be an article where the method section resembles what your supervisor wants your method section to look like. Additionally, it would be a good idea to share this model article with other supervisors or co-authors to gauge their agreement on whether this is a suitable model to follow.

When considering a model article, it is a good idea to look at how your co-authors have written similar articles and how similar articles that are widely cited in your field are structured. To find ideal candidates:

1. Review articles published in your target journal
2. Examine papers from prominent researchers in your field
3. Study well-cited articles with methodologies comparable to yours
4. Consider articles written by your potential co-authors

Different co-authors may make other suggestions, and you may end up with 1-3 model articles. Read these and note how they differ.

What makes a good methods section

When evaluating potential models, look for sections that provide sufficient detail for reproducibility—allowing other scientists to repeat your experiments and verify findings. The methodology should increase reader trust through transparency.

A high-quality methods section should:

• Follow a chronological structure (beginning with what happened first)
• Include clear subheadings that organize different procedural aspects
• Provide appropriate level of detail for your discipline
• Explain not just what was done but why certain approaches were chosen

According to methodological experts, an effective methods section clearly describes the study design, participants/subjects, procedures, and analysis techniques. The content should be straightforward yet comprehensive enough that readers understand both the procedural steps and the reasoning behind them.

Create a Frankenstein model when needed

If they differ only in how they structure information, you can pick one over the other. If they differ in content, you will help yourself in choosing the one that contains more content/details, as it will be easier for you later to remove unnecessary information than it is to add missing necessary details. If you have a situation where two articles contain more content than another but in different places, I would recommend creating a Frankenstein model article by copying the two together as accurately as possible to clarify where each type of information should be placed.

This is entirely okay, as the goal of the model article is not to be a readable article but instead to guide you in how to structure your methods and what you need to include. When creating this composite model, maintain logical flow between sections. Ensure that your combined template maintains coherent organization despite drawing from multiple sources.

Use the model for structure, not content

The most crucial aspect of using model articles is understanding they guide structure, not content. The idea is not to copy their content but instead to use the model article as an inspiration to understand what sort of information will be essential to present when describing the study in an article or thesis.

Within your electronic lab notebook, set up a template based on your model article, marking sections with curly brackets or another distinctive format. As your research progresses, replace these placeholders with your actual methodology details. This approach balances efficiency with academic integrity, giving you a clear roadmap without risking plagiarism.

Part 2. Setting Up Your Template in the Electronic Lab Notebook

Now that you have identified your model article, the next step is to create a structured template within your electronic lab notebook. This process may seem straightforward, but the way you set it up determines how smoothly your methods writing will progress.

2.1 How to copy your model article

Your first task is to copy the entire methods section from your model article into your electronic lab notebook, minus the data analysis section. In quantitative studies, this analysis section is often called "Statistical Analysis" or "Data Analysis." In qualitative work, it might be "Data Analysis" or "Analytical Strategy." The key is to exclude only the part that describes how you will analyze your data after collecting it.

When I first started using this approach, I made the mistake of copying everything, including the analysis section. This created confusion later because my analysis approach differed significantly from the model article. By focusing only on the data collection and procedural elements, you create a cleaner template that guides the parts of your methods that follow established conventions.

Create a new entry in your electronic lab notebook specifically for this template. This becomes your methodological foundation - a framework that includes all the standard elements your field expects while leaving space for your unique research details.

2.2 The curly bracket system

Once you have copied the model content, enclose all text within curly brackets {{ }}. This creates a clear distinction between what belongs to the model article and what you will add yourself. For example:

{{Participants were 90 adolescents aged 12–18 (M = 15.29, SD = 1.32) and their parents, recruited from two community clinics for child and adolescent mental health between 2017 and 2019.}}

I prefer curly brackets for several practical reasons. First, they are rarely used in scientific writing, making them easy to search for when you need to find sections that still need your input. Second, unlike color coding or highlighting, curly brackets remain visible regardless of which device or software you use to view your notes. Third, they create an obvious visual boundary that prevents you from accidentally submitting template text in your final manuscript.

Using this system consistently means you can search for "{{" in your electronic lab notebook and immediately identify any sections that still need your attention.

2.3 Filling in your research details

As your study progresses, you will gradually replace the bracketed sections with your actual methodological details. When you have information to add, break the curly bracket chain and insert your content between the existing brackets:

{{Participants were}} 58 adolescents aged 12-16 years (M = 14.3, SD = 1.2) {{and their parents, recruited from}} three university-affiliated clinics {{between 2022 and 2024.}}

This progressive approach offers several advantages:

1. You document methodological decisions as they occur, rather than trying to remember them months later
2. You can identify missing information early in your research process
3. You maintain consistent structure across your documentation throughout the entire study

Many electronic lab notebook platforms offer dedicated template-based approach functions that can further support this process. However, the curly bracket method works regardless of which specific software you choose.

The most important thing to remember is that your model article serves as a structural guide, not as content to copy. Your final methods section must be written entirely in your own words to avoid any issues with plagiarism.

Building Your Research Diary Within Your Electronic Lab Notebook

_{Image Source: Labfolder Electronic Lab Notebook}

The second part of your electronic lab notebook workflow involves maintaining a research diary alongside your structured template. This is the most challenging part of the system to execute correctly and the area where you are most likely to fail. This is okay, and I know that you are no worse than many academics who came before you.

The first piece of advice I received when I began my PhD was to keep a diary. I saw that this was a great idea and thought, 'Yeah, I should do that.' But I did not. So, I will give you the same advice that I was given and did not follow (and regretted) - keep a minimal diary where you try to write down every time you make a choice regarding your research.

Why You Need a Research Diary for Your PhD

A research diary forms a permanent record of thoughts, actions, and decisions throughout your research process. Unlike your structured template, which captures what you did, your diary documents the why behind your choices. When writing your thesis, you will be expected to reflect on your choices and why you conducted, analyzed, and framed your research as you did. However, if you haven't made any notes on that, it is doubtful that you will be able to remember why you chose to do things the way you did.

Research notes, failed experiments, and unresolved questions are all vital parts of your research data. Your electronic lab notebook protects intellectual property and provides evidence to defend research activities. Even experiments that didn't work as planned become valuable learning opportunities rather than forgotten dead ends.

Electronic lab notebooks excel at this reflection process because they allow you to search through hundreds of pages instantly—something impossible with traditional paper notebooks.

What to Include in Your Research Diary

Your research diary should capture information on the choices you make that you may use in the future. This includes:

• Research choices and their rationale
• Failed experiments and documentation of missteps
• Environmental observations and evaluations
• Background aims and specific scientific questions
• Data collection methods and processing approaches
• Detailed experimental protocols
• Problems and "unknowns" that may indicate knowledge gaps

Throughout your PhD, these entries create an evolving record that tracks not just what you did, but how it made you feel while conducting it—offering a personal perspective alongside objective documentation.

Making Diary Writing Work for You

My best advice for ensuring that you can do this is not to believe that you have to write in your diary every day, but rather to have a place to store information on the choices you make that you may use in the future.

Even if you use this diary for a little bit, it will be helpful for you later when you are writing your thesis. Consider designating specific times after experiments or meetings for quick reflections. Review entries weekly to identify themes and plan necessary actions. Design your setting to maximize consistency. After about 20 diary sessions, this practice may become a natural habit.

Remember that writing itself can be a learning tool to explore ideas and understand them better. Your research diary isn't just documentation—it's an active part of your scientific thinking process.

Part 4. Avoiding plagiarism and writing your methods section

The final part of working with your electronic lab notebook template requires careful attention to avoid plagiarism while creating your methods section. This is the most challenging part of the process and the area where you are most likely to make mistakes. This is okay, and I know that you are no worse than many academics who came before you.

How to rewrite your template content

When working with your bracketed template text, read each section carefully and then look away from your screen while thinking about how you would explain the concept to a colleague. This approach helps prevent accidentally copying sentence structures or specific phrases from the model article.

The key is to understand the underlying concept completely before attempting to write about it. For example, if your template says:

{{Participants were 90 adolescents aged 12–18 (M = 15.29, SD = 1.32) and their parents, recruited from two community clinics.}}

You might rewrite this as:

The study included 90 young people between 12 and 18 years old (average age = 15.29, standard deviation = 1.32) along with their parents. We recruited these families from two clinics in the community.

The idea is not to copy their content but instead to use the model article as inspiration to understand what sort of information will be essential to present when describing your study.

Using your electronic lab notebook to track changes

Most electronic lab notebook platforms include features that help you track your writing progress. You can search for remaining curly brackets to identify sections that still need to be rewritten. Many platforms also allow you to compare different versions of your methods section, which helps ensure you don't accidentally remove important information during editing.

Some electronic lab notebooks even allow you to "lock" completed sections, preventing further changes once you're satisfied with a particular part of your methods section. This feature proves helpful when working on longer documents where you might otherwise lose track of which sections are finalized.

Preparing your methods section for publication

Before submitting your article, search your electronic lab notebook for any remaining "{{" brackets to confirm that all template text has been replaced with your original content. Review your methods section to ensure it includes all essential elements: information about participants, materials, procedures, and how you collected your data.

The most important consideration is that other researchers should be able to repeat your study based on what you've written. If you find yourself uncertain about whether you've included enough detail, ask a colleague to read your methods section and tell you whether they could conduct a similar study using only your description.

Remember that this approach balances efficiency with academic integrity. You have a clear structure to follow without risking plagiarism, and your methods section will meet the standards expected in your field.

Conclusion

The electronic lab notebook approach I have shared addresses what I consider one of the most frustrating aspects of PhD work - spending hours writing methods sections only to have them rejected because they don't match field expectations. The combination of model article templates and research diaries creates a system that makes this process manageable rather than overwhelming.

This approach requires some initial effort to set up properly. You need to invest time in finding the right model article, learning to use curly brackets effectively, and developing the habit of maintaining a research diary. However, the time you spend establishing this system pays considerable dividends when you sit down to write your methods sections. Instead of staring at a blank page trying to remember what you did six months ago, you have both structure and content ready.

What remains consistent is the underlying logic: capture methodological decisions as they happen, use proven structures from your field, and create a system that makes writing easier for your future self. This approach helps ensure that you spend your time on research and analysis rather than trying to reconstruct forgotten details.

I hope that implementing these approaches helps you avoid some of the trial-and-error process that made my own PhD journey more difficult than necessary. The goal is not perfect documentation but rather practical systems that support your academic success.