Writing a reproducible protocol is an essential skill that all scientists must have. Here are some tips for writing successful protocols that readers of various education levels or backgrounds can follow. When it comes to protocol writing, one size does not fit all.

Getting started writing a protocol can be a difficult task. You want your reader to be able to reproduce your lab work—whether your reader is in the lab down the hall or someone doing similar research on the other side of the country—so details are important. However, you also want to keep your protocol concise. Knowing what details to include and which are better to omit because they can be implied or are common sense to someone who works in the same field to you is essential and often the most challenging part of writing a protocol, but it doesn’t have to be.

Whenever you write a protocol, there is a specific purpose for your writing. If you’re working in the lab, you may be writing a protocol in your notebook so you can look back and remember each step you took. Other protocols might be written as instructions for students or as part of a manuscript you would like to publish. These two protocols are serving very different purposes and will be read by very different audiences. Even if you are writing these protocols over the same exact experiment, they will be different because there are different requirements for a protocol based on if it is intended for publication, teaching or writing your own notes. I’ll discuss writing protocols for each of these unique purposes and this will make more sense.

Lab Notebook Protocols

Let’s start with the protocol that has the most flexibility—your lab notebook. Chances are you’ve written many protocols in your lab notebook without thinking twice about it. This information is generally for your own records and won’t be reproduced directly for others to see. Some institutions, however, may have lab notebooks that are accessible by colleagues and supervisors. For this reason, there are still guidelines that you should follow, which will help when writing other types of protocols based on your experiments later on.

First and foremost, your notebook should include the purpose of your experiment, the question you are trying to answer and have the procedure you intend to follow laid out. You should also have any tables used to record data and observations ready before you begin your experiment. Then, as you are carrying the experiment out, you will only have to record additional details, observations, data and any changes you make to the protocol. Having a record of any changes you make to your protocol—no matter how minor—is crucial to the reproducibility of an experiment. If you later decide you want to publish results you obtained, you will need to be able to go back and have the detail you need to meet the requirements of the paper you wish to publish in, but we will discuss more on that later.

Teaching Assistants’ Protocols

If you’re working as a teaching assistant during graduate school, writing protocols for your students will be very different from what you’re used to. These protocols are meant to be more instructional since most of your students will be encountering these procedures for the first time. One of the best ways to boost the confidence of your students and help them perform a successful experiment is to provide them with a very detailed protocol.

I can think back to my undergraduate days and remember some professors providing protocols that were very vague or purposely left out some of the details necessary so I could try to work through them on my own, but often times, this led my lab partner and me to ask many questions and feel like we weren’t able to run the experiment on our own. I learned better when all of the steps were laid out and I could make sense of why each step occurred in a certain order and why each was necessary.

It is important to remember that students will have less of a background in the topic than you so giving more instruction is necessary. While experienced biological scientists would know exactly how to pour a gel without laying out the individual steps, students would need the steps to doing this written out as part of the protocol. This applies to many techniques commonly used in labs; while a scientist would not want every step of a common technique explained in detail, protocols written for students will need to include this information.

Some teaching assistants even include visual aids in their protocols. Whether it be the set -up of certain equipment or an example of what the experiment should look like at each step, having this available for students to check if they are on the right track can make a big difference. It can increase confidence as well as efficiency within the lab.

When writing for students, it is really important that the experiment goes beyond the basic setup and procedure. Math and statistics are very much a vital element within the scope of a project. So if your students are pouring a gel, what calculations do you expect from them? What formulas can you provide to aid in their problem solving? How about measuring their results, what are good statistical calculations they need to include? Going beyond statistical calculations, preparing your students to think critically about them is also going to better prepare them for the real world of science.

Protocols for Publication

Writing protocols for publication varies greatly based on where you plan to publish. Many scientific journals have their own requirements for publishing protocols. Identify where you plan to submit your paper and look up the requirements or guidelines each journal has for submissions. This is usually found as an “instructions for authors” page or a similar page.

For example, if you want to publish in “BioTechniques,” there is a downloadable PDF of instructions for you. This journal publishes many protocols and states, “each protocol should be detailed and organized so that a researcher could print out the protocol and perform the experiment using only that document.” The also encourages the author to include any helpful details such as tips, data tracking methods, etc.

However, other journals have very different requirements. For example, “Nature” does not publish a methods section of experiments in the printed version of their journal. Rather, the methods will be published online and should be “written as concisely as possible but should contain all elements necessary to allow interpretation and replication of the results.” Nature states that methods should not exceed 3,000 words, but that authors can upload their more detailed protocols to their Protocol Exchange.

In addition to looking at the guidelines for authors page on a publisher’s website, you can also obtain a copy of the journal and look at examples of protocols that have been accepted and published. This will give you a good example to follow along with following all requirements of the journal itself.

Standard Operating Protocols/Procedures (SOPs)

Standard Operating Protocols or Standard Operating Procedures are written to ensure the step-by-step procedure carried out in certain experiments remains the exact same despite having different scientists performing the protocol. They are commonly used for quality control and quality assurance. In research, SOPs guarantee that sample preparation, analysis methods, etc. were carried out the same way each time. When a result is not what was predicted, the investigator should not have to question whether his materials or certain parts of his methods are the source of variance if standard operating protocols were used.

Writing SOPs should always be done based on company procedure. There will even be an SOP for writing an SOP at some institutions. Check out your company’s template for writing this type of protocol before getting started. Your company may also have guidelines for who is approved to write an SOP and what approval procedures are necessary for the SOP. Remember that you will have a varying audience ranging from colleagues to regulatory auditors reading the protocols you produce as SOPs. It is best to keep SOPs uniform and informative while keeping in mind the variety of people who may access it.

For most companies, SOPs will include the detailed protocol itself, a purpose, date and author’s name. They will have some background information as well as a materials section which lists the specific suppliers of the products used in the protocol. SOPs are tested and reviewed by someone who is not familiar with the protocol prior to testing. Remember that this is what standard SOPs contain, but the best practice is to follow your company’s policies for writing an SOP. Here is an example of a SOP for PCR.

Once you have written your protocol based on what its purpose and audience is, it is a good idea to have a colleague look over it and see if there are any areas that need clarification. Of course, if it is for your lab notebook, this wouldn’t be as necessary as if you are getting ready to submit a manuscript for publication. You can see how what you plan to do with your protocol really guides you in the way you prepare and write it. Ultimately, you want to make sure that your readers get what they are looking for and cater your protocol writing to fit their needs.


Instructions for Authors. (n.d.). Retrieved June 30, 2016, from http://www.biotechniques.com/multimedia/archive/00...

Formatting Guide to Authors. (n.d.). Retrieved June 30, 2016, from http://www.nature.com/nature/authors/gta/

Rebecca Talley
GoldBio Staff Writer

Rebecca is a medical student at the University of Missouri.
She previously worked as a lab technician while studying
biology at Truman State University. As an aspiring
reproductive endocrinologist with an interest in global
health, Rebecca has traveled across Central America on
medical mission trips. With a passion for the life sciences,
she enjoys writing for GoldBio.

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