If you are in a science-based Ph.D. program, you will need to write a proposal at some point. Whether it’s for a class, a qualifying exam, or a fellowship application, knowing how to formally propose experiments in writing is a key skill to develop in grad school. Unfortunately, it’snot a skill that is often taught as explicitly as it should be, and many students are thrown to the wolves if they can’t figure it out fast enough. Even if you have written one before, did you feel frantic or rushed towards the end? Were you not happy with the way you prepared and with the final product? If you answered “yes” to any of those questions, this article is meant to help with some of the issues you may have experienced. Here, we will just cover the writing aspect of the proposal. Stay tuned for related future posts on how to give a chalk talk, how to make figures, and more!

Photo by Glenn Carstens-Peters via Unsplash, CC0 




Table of Contents


Choosing A Topic

The Writing Process

Choosing An Advisor

The Timeline

Citation Management

In Conclusion




Choosing a topic

If you’re already in a lab, you may have an easier time with this step because you have the lab’s general field of study as a launch point. However, half of the battle will be deciding which specific question to delve into. You don’t want to sink all your time reading papers for a topic that’s a dead end, but you also need to know when  to bite the bullet and get started. It can be a tricky balance to find, but these points should help guide you:


1. Read Reviews

Find the most recent review on a topic that interests you or that fits the proposal guidelines. Then, simply follow the unknowns! Always check the discussion section for future directions (the experts on the subject have done the work for you – take advantage of that!).

*Note: if you want to keep track of papers while skimming and following links without putting them all in a citation manager, try the Google Chrome extension “Tree Style Tab”

2. Pick a Topic that is feasible

At this point, you may find yourself in a PubMed rabbit hole, but that’s okay! Just keep asking yourself if these questions could be answered in 2-4 simple experiments. Do you have experience performing those experiments? Could you perform them in your current lab setting or with a possible collaborator? If you’d like to use a newer or more complicated method, make sure you understand it thoroughly before proposing it!

3. Pick a Topic with a ‘goldilocks’ scope

There should be enough unknowns that you could probe with experiments, but you don’t want to make assumptions about the system. Your background should lead cleanly and logically to your aims. This can be challenging but can be successfully executed depending on how you phrase your hypothesis.

4. don’t be afraid to switch topics

When you’ve sunk hours into researching something, it can be painful to tear yourself away from that “lost time.” But if things just aren’t working, you’ll save yourself way more time if you cut your losses and start again. This is much easier the earlier in the writing process you do it (see Timeline section).

5. Ask for help!

If you’re struggling to find a solid topic, or you want to make sure the one you have will work, talk to your professor or advisor! Part of their job is to help train you in skills like these. Feel free to brainstorm with classmates and labmates as well – someone may lead you to the perfect question without even trying.



The writing Process

Now that you have your topic, it’s time to get writing! Below are some more tips about the layout and logic each section and some important things to remember.


Include only what is necessary to understand your aims. Start broad and end narrow: I like to introduce the system by tying it to a broader significance (i.e. disease models, evolutionary developments, etc.), then ending the section by clearly stating my hypothesis in bold. Depending on your page restrictions, you can (should) include a figure or two for clarification.


Make this section as clear as possible – if the reader is confused by the basic question you are asking, they won’t understand your proposal.


Depending on the proposal type, you’ll likely want 2-3 aims. These can include subaims (i.e., Aim 1.A, 1.B, etc.), especially for longer proposals like qualifying exams that may need more details. Reiterate the gap in knowledge you are addressing and describe your experiment clearly but succinctly. You don’t want to make one aim dependent on any others, nor do you want too much uncertainty. You should be able to account for all possible outcomes of your proposed experiment, state them in the aim, and interpret them.


Each aim should be able to stand on its own and not rely on any other pending experiment.


Every word should count here – reiterate why these experiments are important and what we could learn if you perform them. Additionally expand the next steps and future directions for the models you have proposed.


Connect back to the broader significance you describe in your background. Why are these experiments worthwhile? Why should a funding source support them?



choosing an advisor

It is incredibly important to have an advisor, especially the first few times you write a proposal. If you have already chosen a lab, your advisor is probably just your PI. However, if you are not in a lab yet or your PI can’t help you for some reason, you have the flexibility to choose someone else. This should be a professor that A) you enjoy working and communicating with, B) has some expertise with your general topic, and C) has the time to meet with you, send you edits, etc. They should be able to steer you away from dead ends and keep you on track. Plus, establishing arbitrary deadlines can be very motivating for some people if another person is waiting on your progress!


Having other people read and edit your proposal can also be helpful. However, it is critical to not overload on other’s edits. Like that saying about too many cooks in the kitchen, too many opinions will freeze your progress. To be safe, I identify my primary advisor and 1-2 additional readers who are usually people in my lab or another mentor. If anyone else ends up reading my proposal (classmates, friends, my mom’s cousin’s niece), I ask for general impressions instead of specific edits.



The Timeline

Establishing and sticking to a realistic timeline is critical to the writing process. Deadlines vary drastically depending on the type of proposal, but you can roughly divide your time in quarters:

Q1 – Reading & Thinking

Give yourself the time to go down those rabbit holes and follow big questions in the field.

Q2 – Rough writing

Just start writing – you can always edit it later! (Pro tip: I find it easier to write my aims before writing the background.)

Q3 – revising & editing

Finalize your aims with your advisor and edit your draft for grammar and clarity.

Q4 – the last lap

Use this time for polishing or trimming text to fit the space limit.

For shorter or longer deadlines (or if you are a faster or slower writer), each step may not take 25% of your time exactly. BUT you should still send your progress regularly, even if sections aren’t finished! If you need to scrap a whole aim or hypothesis, you want as much time as possible to catch up. It’s important to know yourself and your writing style to give yourself enough time to get through each step.



Citation Management

Download a citation manager if you haven’t already! One common mistake when writing is thinking you’ll only have five or six references in a short proposal, so you try to note everything by hand. However, you’ll probably read 3-5 extra papers for every main citation you have, and those will start to add up. If you don’t have a citation manager, you WILL have a browser open with millions of tabs (and if that’s something that stresses you out, you should be extra motivated to get organized!). You’ll also thank yourself later when writing papers and your thesis. Here are some common managers that you can download for free:

  • Zotero – Free software with fairly convenient apps for desktops and tablets, but additional storage costs extra. I am currently using this system.
  • Mendeley – Free citation manager run through the larger Elsevier publishing company. This may be convenient if you tend to read papers via Elsevier, but the plugins for Google Chrome and Word can be a bit buggy. I have used this system in the past.

Here are some additional citation managers that are paid and may contain additional features. You can check with your institution’s library to see if they have site licenses for students:



In Conclusion

Writing a proposal can be stressful, but it doesn’t have to be if you’re prepared! As you plan your writing schedule, don’t forget about other preparations you might need to consider. Do you need to give a talk or defense? Send a personal statement? Ask for recommendation letters? I’ll be sure to cover all of these and more in future posts.



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Writing Resources

Good source of fellowship proposal examples: https://www.alexhunterlang.com/nsf-fellowship

More resources coming soon


Organization Resources

Tree Style Tab extension: https://chrome.google.com/webstore/detail/tree-style-tab/oicakdoenlelpjnkoljnaakdofplkgnd?hl=en

Comparison of citation managers: https://www.g2.com/categories/reference-management

Zotero: https://www.zotero.org/

Mendeley: https://www.mendeley.com/

EndNote: https://endnote.com/

Papers: https://www.papersapp.com/





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