PhD Toolkit

Applying to Grad School

A list of software and organization tips I used to apply to graduate schools. 

Step 1: Decide where to apply

To narrow down my list of schools, I used the following factors: 

1) Financial Support: I only applied to PhD programs with guaranteed stipends. 

2) Location: I wanted to live in a state that was easy to travel home from. 

3) Professors: I only applied to programs that had at least 4-5 professors I wanted to work with

4) Previous experience: If I had been there before in a research internship, I gave these schools priority. 

5) Program requirements: Programs have different course and TA requirements. I only applied to those that seemed reasonable and flexible to me. This is personal preference.

6) TOEFL requirement**: As a Puerto Rican, I am not required to take the TOEFL since we are part of the USA. Any school that told me I still had to take it was taken off the list. **The test has a sordid history of discrimination, and I refused to take it, especially as a native English speaker. 

Step 2: Organize your applications

I kept track of all the information gathered in Step 1 using two tools: 

1) Google Sheets: Here is an example of how I organized my sheet and the additional information I would save from each school. I also had another tab to keep track of potential letters of recommendation. 

LINK TO GOOGLE SHEET TEMPLATE

2) Trello: This is a dashboard app, where you can make cards and lists to keep track of projects. I loved using it to apply to schools. I made a separate list for each step of the process, added a card for each school. Each card had all the essays, transcripts, checklists to hand in and due dates. 

LINK TO TRELLO BOARD TEMPLATE

Step 3: Preparing for Interviews

Disclaimer, my interviews were during the pandemic and were all on Zoom. There will be differences between in-person and virtual interviews. Though, as someone that has now gone through both experiences (as a student and interviewer) they are mostly very similar prep-wise. 

To prepare for my graduate school interviews, I did the following

1) Research the Program and Faculty: I prepared a Word document for each school that invited me for interview. I listed all the faculty that I was going to be interviewing with and I researched their labs, school appointments and any other public information. That way, I had an idea of where the conversation might go with each one. 

2) Prepare a List of Questions: I used my research on each school to prepare some questions tailored for each faculty member, as well as general questions for students & program directors. Don't stress if you don't get to ask them all. They are meant to serve as a guide and help you avoid drawing a blank due to nerves. 

3) Practice Answering Common Interview Questions: If you want to avoid the "umms" and awkward pauses, it's best to practice a general answer for each of the most common questions. Indeed and Bemo have great guides to start with. 

4) Review Your Application Materials: Make sure to have a copy of your essays for that school on hand and to re-read it before you start your interview day. Your application should always be tailored to the school, so it's bound to change slightly between them. Make sure you know HOW you changed your application and refresh yourself on what your goals were when you submitted it.

5) Rest the Day Before: Get enough sleep, food and rest the day before your interview. This is a stressful time and it's important for you to prioritize caring for yourself. I found preparing food and my clothes the night before helped me be a little less stressed the day of. 

6) Ask Current Grad Students for Help: If you can, reach out to grad students before or during your interviews. Ask them how they feel about the program or advice about professors you are interested in. They are where you hope to be! Be kind and grateful for their advice. 

7) Practice your speaking skills: A new tool by Google called Interview Warmup, let's you practice having a conversation with an interviewer and answering questions succinctly. It records and transcribes your answer, so you can read back what you said and adjust your answers as needed. 

Bonus tip: 

After your interviews, you can send a personalized email or note to the professors that interviewed you, the program directors, program manager, grad students or anyone that you wish to thank for their time! This is polite and many people forget to do it. I had several professors say they were shocked to receive a note of thanks from me and were grateful.  

Step 4: Navigating Program Acceptances 

If you are lucky, you will receive more than one acceptance to the schools you applied for!

Congratulations!!

......Now what? 

Well, this is when decision time happens. Remember, you will always be given a time period by which you can decide whether to accept the offer of admission. Usually this will be at least 2 weeks time (usually more). 

In that time, you can go over all your research + what you learned during the interview process. Have your opinions about the school changed? For better or for worse? I found making a pros and cons list helpful. 

You can also reach out to other schools you are waiting an answer for and ask them directly. You can be honest and say something like: 

"I recently received offers at other schools, but since you are my top choice school, I would like to know where I stand in the applicant pool. This will help me make a final decision."

Schools that are actively trying to recruit you will let you know where you stand and schools that have ruled you out usually will let you know too (or ghost you). 

This is a stressful time, so always make sure to talk about this with someone you trust and get feedback! Of course, take time for yourself too and just check-in with your goals and which school will help you get there the easiest. When you have done your soul-searching, the answer will usually reveal itself! 

Step 5: Navigating Rejections

If you receive rejections from the schools you applied to, remember you are not alone. This is a very competitive process and rejection is super likely. That DOES NOT mean you are not fit for grad school. It just means that the particular program might not be the right fit for you. 

So, what should you do now?

First, allow yourself some time to process and feel your emotions. It's okay to be disappointed, but don't let it define your self-worth or your future prospects.

Next, use this as an opportunity to reflect and regroup. Look back at your applications and identify areas for improvement. Did you get any feedback from the schools? Consider revising your statement of purpose, seeking more relevant experiences, or strengthening your letters of recommendation.

Reach out to mentors, advisors, or friends who can provide support and guidance. They might offer valuable insights and encouragement during this time.

You can also contact the schools directly and politely ask for feedback on your application. This can give you a clearer picture of what areas need improvement for future applications or perhaps what they felt they were unable to provide you (interests weren't aligned, for example).

Consider alternative pathways. Maybe there's a master's program, post-bacc program, a research position, or relevant work experience that can enhance your qualifications and prepare you for the next application cycle.

Remember, persistence is key. Many successful professionals faced rejections before achieving their goals. Stay focused on your long-term aspirations, and use this experience to fuel your determination and resilience.

Step 6: Other Options: Gap Year, Post-Bac, Job

Every grad school journey is different and rarely linear. While I went straight from undergrad to the PhD, this is not the only way. There are many options that you can do between undergrad and applying to PhD programs. Which one you choose will depend on what skills you want to strengthen and what your needs are during that time. Here are examples of opportunities: 

1) Master's Program: A one to two-year advanced degree to hone your research skills, improve your GPA and increase your chances of getting into a competitive PhD programs. 


2) Post-Baccalaureate Program: Designed for graduates to enhance their academic record and gain additional experience before applying to graduate school. Some of these programs are funded and provide a salary for the year. 

See here for examples: NIH PREP, Columbia Bridge to the PhD Guide


3) Gap Year: A break from formal education to travel, work, or pursue personal interests, providing valuable life experiences and clarity on future goals.


4)Post-Undergraduate Job: Gaining professional experience and practical skills in the workforce, which can strengthen your resume and make you a more competitive PhD candidate. These can be entry level positions in industry or government for example. I personally know several PhD students who worked in industry for at least 1-2 years before applying to grad school. 

Again, these are all options, none of them are more "correct" than others. Choose whatever is right for your goals! 

Step 7: Explore Inspiring Websites & Other Guides

No single person is an expert in STEM careers. Our strength is always found in community. For that reason, I want to highlight some other blogs that have inspired me: 

1) Academic Memories: a collection of STEM guides, stories and useful articles about neuroscience topics. They also provide opportunities for undergrad volunteering. 

2) The Illustrated Explanation for a PhD: Matt has a wonderful sense of humor and honestly, this illustration is something I find myself coming back to when nothing is working. It is reassuring to remember that we exist at the edge of knowledge. 

3) Anderj Karpathy's Guide: This is lengthy and detailed guide. I have found it to be a "take what you need" type of document. The guide has a lot of advice, some which resonates, but some that doesn't. Yet, it might for you! So I recommend checking it out.

Starting Grad School

A list of software and organization tips I currently use to make grad school a bit easier. 

Step 1: Preparing for Classes

Many programs have different class requirements. Here are some tools I used during my grad classes to make things easier: 

1) Time Management Excel Sheet: Best tip I ever received from a professor was to organize all my assignments for every class at the beginning of the semester. It only takes an hour to prepare and it saves you SO much worry during the semester. 

ASSIGNMENT TIME MANAGEMENT EXCEL TEMPLATE

2) Desktop Folders: I like to keep my desktop clear to avoid digital and mental clutter. I usually make a folder per semester and within that I make folders per class. This also is useful for keeping your assignments organized. You would be surprised how often you can refer to some assignments to help you with your thesis work! Some classes will be directly related to your topic and it will save you a headache if you can easily find relevant files.

3) Plan Out Semesters in Advance: During my first semester, my program had us meet with our Program Directors to discuss what our plans were for the PhD. This included the classes we wanted to take. Taking this step early was essential in helping me plan out my first two years! Ask your program if there is a set list of courses you can take, or if you can pick them yourself. Go from there, but make sure you plan WHEN you want to take them and check any course requirements early. Some classes can have waitlists, so ask other grads in your program who have taken the course you want for any tips or how to get enrolled.

Step 2: Preparing Backpack, Tech & Other Supplies

For those that are going to be working on a large campus, preparing yourself for long days is important. For that reason, there are a few things I made sure I had before I started grad school: 

1) A Good Ergonomic Backpack: You will likely be hauling around a computer, books, notebook, snacks and any other trinkets you will need throughout the day. It's important that you have a sturdy backpack that will last you at least 5-6 years. I recommend looking into Jansport, they have a great history of quality bags and they also do great accessibility work. This is not sponsored, I just like my backpack from them. 

2) Durable Water Bottle: You will be working long hours and will need to stay hydrated. It's worth looking into a water bottle that you can refill on campus and will keep your water cool! Please don't go out buy a Stanley. 

3) Stable computer: I often find myself doing a lot of work from home during my PhD. It's useful to have your own laptop so you can easily work from anywhere or take it to take notes during classes. This is one of the few items I think is worth investing in as a new graduate student. Especially if you don't already own one or the one you have is very old and incompatible with new software. I won't recommend any specifics, but I will say to be aware of what system requirements you will need for your research area. This is something you could ask your advisor or fellow grad students about. Additionally, many bigger schools have loaner programs through the IT department. Check with them about getting a loaner laptop if you can't afford one right away. 

4) External Storage Drive: This might not be necessary if you don't work with big files. However, as someone that works with sequencing, images, and just bulky data, I like having an external drive I can use to backup my computer or transfer bigger files. I have a 1 TB Seagate hard drive that I got in 2020 that still works great! 

5) Comfy, lab-appropriate clothing: You are going to be spending every day in a lab setting (STEM PhDs). This means always having to wear long pants, shirts with sleeves and closed-toe shoes (even during the summer!). I found that buying several, simple shirts and pants allowed me to put together simple outfits every day, that didn't make me feel like I was always repeating clothes. I also felt comfortable working and doing experiments in them. I highly recommend thrifting to save money. However, if you are like me and need plus sizes or sensory friendly items, I recommend Old Navy!

6) GOOD SHOES: If you run experiments, you will definitely spend lots of time on your feet. Even if you don't, if you work in a large campus you will probably do a lot of walking. Invest in a good pair of shoes that will support your feet and be comfortable to wear all day. I personally use Hokas. Not an ad and they are expensive, but they last and are incredibly comfortable. 

For everything on this list, PLEASE don't buy yourself everything new. Shop in your own home first, see what you have and decide from there if you need something. Grad school stipends are tight enough as it is. 

Step 3: Tips for Neurodivergent Grads 

As someone with late-diagnosed ADHD and anxiety, I am familiar with the struggle that academics can go through managing symptoms. Here is a list of accessibility things I have done to try and make my life easier

1) Glean (Recording & Notetaker software): This app records meetings or lectures and allows you to supplement with notes in real time. Super helpful in case you miss anything by getting distracted, you can just listen back again. Glean usually has subscriptions with universities, ask your Student Accessibility Services about what options are available to you. 

2) SAS: Student Accessibility Services is a great help if you have an official diagnosis! Reach out early so they can give you accommodations as needed. For my ADHD, I had extra time on quizzes or tests. I also had the permission to use the recording software to take notes. I did not have these in undergrad and I cried the first time I used them. It really is the world of a difference. 

3) Planning Experiment Days: Part of my ADHD means having very unpredictable energy levels on a day-to-day basis. This can make planning experiments very difficult. What I currently do to manage that is: planning experiments with intentional breaks as much as possible. If I know an experiment takes 4 hours, I leave 4 hours of my day intentionally free. That way, I can use them to rest, eat, nap or just recover. If I feel great, then I use that time to work on something else! But I love preparing for the worst because it means I can take time to myself, guilt-free. 

4) Find Community (Disabled in STEM): Over the past year, I joined the Disabled in STEM group as a mentor. It has been incredibly helpful to find a community of disabled scientists that I can reach out to for help or moral support. STEM can be isolating, so you need to be intentional about finding community, in whatever way that looks like for you. 

5) Meal Prep with Protein: By far the biggest "adulting" lifehack I have found. Meal prepping only takes a few hours on Sunday, but it ensures that I am fed for the whole week! Make sure to meal prep lunches and snacks. I sometimes even throw a dessert in there too. I have found that having a lot of protein in the morning (greek yogurt, meat, cheese, etc) helps my brain work better! However, I make sure to add plenty of protein and fiber to every meal. Of course, please don't base any nutritional advice from the internet. Consult your doctor if you have doubts about your needs. That being said, TikTok is amazing for finding new recipes if you are getting bored of your own. I also recommend the Food Network website! Always find fun recipes there too. 

Step 4: Preparing for PhD Stipend & Budget 

PhD stipends have notoriety for being incredibly low compared to normal corporate jobs that require an undergraduate degree. For many, starting the PhD will be the first time they need to adjust to living on a budget, especially in a new city. Here are some tips I found useful when I started. 

1) Become Acquainted with your Salary: Ask in detail what your salary will be each month, how much taxes will be withheld (if any) and when your university sends out payments. Often this is information you will have to reach out to the Financial Affairs office, but it doesn't hurt to ask Program Directors who you can contact for that information. 

2) Be aware of what your graduate student appointment is: Each semester, you will receive a letter about your "appointment" with the graduate school. This usually notifies you whether you will be on "Fellowship", "Research Assistantship (RA)" or "Teaching Assistantship (TA)". Each of these classifications determine your tax status. Usually, only RA and TAs have taxes deducted from their stipend. However, this doesn't mean that you don't owe. I recommend reading the Personal Finance for PhDs website for more details. You can also ask your university admins. 

3) Download a Budgeting App: I personally prefer Rocket Money, but there are loads of free apps out there. This will help you be able to track your spending and transactions without having to individually put them in an Excel sheet (which takes time). 

4) Set up a ROTH IRA: Just because we are in grad school and don't have a 401k, doesn't mean we have to waste 5-6 years of not preparing for retirement. Usually, since PhD stipends are low, we qualify for ROTH IRAs. Look into setting one up with your bank of choice and try to max out the contribution limit per year (if you can!). The limit as of 2024 is $7,000 for those under age of 50. 

5) Set up a High Yield Savings Account: Many banks offer a high yield savings account that will normally have at least 2% APY, sometimes as high as 5.3%APY. Open a HYSA account with an FDIC insured bank and try to set money aside each month. I like to keep my emergency fund in a HYSA so that it can keep accruing interest as it sits there!

6) Pay Yourself First: Once you know what your stipend will be (on average) and how much your average necessities are (rent, food, car, debt, etc.) you can determine how much you can set aside for savings and retirement. I usually do things in this order once my check comes in on the last day of the month: 

a) Pay Bills (Rent, Grocery Budget, Car budget, Debt Payments, etc.)

b) Transfer my allotted savings amount to a high yield savings account 

c) Transfer my allotted retirement amount to a ROTH IRA

d) AFTER all of that is done, then whatever is left over in my check can be used on fun (if anything)!

Even if all you can contribute to savings and retirement is just a few dollars, it will still be a few dollars closer to securing your financial future! 

7) Make Finances Fun: I have found listening to the Financial Audit by Caleb Hammer podcast particularly useful for this topic. If you have debt that you are trying to pay down, I recommend checking him out! Of course, it is not meant as financial advice, but it's an easy way to listen to money conversations (which many people have never had).

8) File Taxes for Free with IRS: Please don't waste precious stipend money on TurboTax or other similar tax preparers. As students, we usually qualify for IRS Free File. This is a FREE tool created directly by the IRS for people to file taxes online for free. I have used it the past two years and I will never go back! 

Disclaimer: I am NOT a financial planner and this is NOT financial advice. This is simply tools I have used to make my PhD financial journey easier.

For International Students: The tools I provided mostly focus on U.S. Citizens, however reach out to your International Affairs department for more specific help with your tax status. I am also working on a guide for International students, and will update the website once completed. 

Step 5: Organization in and out of Lab 

Look, my neurodivergent brain can't be trusted to remember everything I need to do on a daily, weekly or monthly basis. For this reason, I have found ways to organize myself in and out of lab. Here are some examples: 

1) Google Calendar: I use my calendar to keep track of everything! You can use the calendar feature to create separate calendars within the same account. I prefer using separate calendars for my lab work, extracurriculars, meetings, etc. You can have them all enabled to ensure you never double-book yourself. Here is a handy how-to guide for using Gcal

2) Google Drive: If your university uses Google as their email system, you will likely have at least 1 terabyte of storage space in the Drive. First thing I did was set up Google Drive on my desktop, so now I can work seamlessly between my work and personal computer without having to transfer files back and forth. They are always available immediately after I hit save. This is great if you work from home often on data analysis or get snowed in. No need to come in and download data!

3) Trello Board: I already mentioned using a Trello Board to apply for Grad Schools. However, you can adapt your board for anything! I now use my Trello board as a virtual whiteboard where I can visually keep cards for each of my ongoing projects, as well as checklists, useful documents, protocols, etc. 

4) Electronic Lab Notebook: Check with your supervisor about their policies regarding electronic lab notebooks. My lab allows them and I have been using LabArchives. I have found that they can be super useful to keep organized notes about my experiments. I also keep protocols and instructions for repeating certain analyses for quick reference. It makes training new people in the lab super easy too! You can download pages as PDFs and share them or add your PI to your notebook so they can check on your progress! 

5) Appointment Calendar (especially for TAs): Now this is one of the best tools I have found to help me manage my time! As a TA, I had to have office hours available. Additionally, now as a Chair of a student organization, I often need to meet with undergrads to fulfill my role. Therefore, in order to avoid constant emailing to set up appointments, I decided to use the Google Calendar appointment feature! You can set your availability per day (down to the minute!) and also set a buffer between bookings. The calendar will also prompt the person to fill out a short form with whatever info you want, and then emails them with the meeting link you add.

Here is a tutorial on how to set it up and here is how my booking page looks like

Step 6: Preparing for Qualifying Exams

My program has a single qualifying exam which we take at the end of our second year. It consists of a written proposal for our thesis project and an oral presentation defending this proposal to our thesis committee. Requirements vary per program, so make sure that you ask beforehand in order to prepare adequately. Here are some resources I found helpful while preparing my quals: 

1) UC Davis Qualifying Exam Guide

2) Carnegie Mellon Qualifying Exam Guide 

3) University of Florida Guide

Additionally, here are something I learned in the process of developing my quals: 

1) No one wants you to fail: I was scared of getting "trick" questions or being bombarded. The test is meant to assess whether you are ready to function under pressure, but no one is going to be hoping you fail. In fact, your thesis committee should want to see you grow and push you in the right direction. So, don't see their questions as attacks, instead opportunities to learn something new. 

2) Ask Lab Members for Questions: Best advice I received was to ask the lab members of my committee members what type of questions they like to ask. What have they been researching or asking a lot about recently in lab meetings? What did they study in graduate school? What projects do they have ongoing? Knowing the answer to these will help you prepare for questions that might relate to your own project. 

3) Practice Your Presentation with Others: I am really grateful that my lab had me practice my qual two weeks before the big day. It not only allowed me to get feedback on my presentation, I was also able to relax once I realized I could answer most of the questions they asked me! This is a good sign because they are the people that know the most about my research area other than myself. If I can hold up against them, then that is a good sign for how I will be able to field questions from people outside my field! 

4) Make the Written Proposal Useful: If your program makes you write a proposal for your thesis, think of it as an opportunity to write the basis for a new grant! This motivated me to write meticulously and also to get a lot of feedback from trusted advisors. If I hadn't gotten the NSF GRFP, I would have used my qual to write a T32 or similar grant application!

Leaving Grad School

A list of how I am preparing to transition out to the career world.  This list is still a work in progress!

Step 1: Determine your Career Path

Figuring out what you want to do is difficult! When I decided to do my PhD, I wasn't fully clear on what career path I wanted. As I have progressed in the program, the decision has become clear! 

However, my first step was figuring out what I wanted my life to look like after. I recommend using the Science Careers myIDP tool to find career options for PhDs. 

Science Careers myIDP page

It will give you a survey to help you define your interests, skills and which careers they believe are a good match. Make sure to sign up for their weekly newsletter to get Job posting opportunities!

You can also reach out to the Careers office at your institution to get some more personalized options. 

Step 2: Building a Portfolio

Many people think that portfolios are only useful in creative or artistic careers. Yet, this is far from the truth. Whether you are interested in academia, industry, government or any other PhD field, having a relevant portfolio while applying to jobs will help you get a step ahead. 

Obviously, my own journey in this is still in progress, but here are some ways I am preparing a portfolio for myself (while still in grad school).

For context, I am interested in Science Communication and Science Writing careers.  

1) Website: Portfolios don't have to be dusty binders with a million pages. We live in a digital world, so we can use that for our benefit! A good way to do that is a website. 

You will notice that my website has a Portfolio tab with each of my pursuits (Science Writing, Science Illustration, Creative Illustration). This is something that I continue to improve as I grow and develop relevant skills. 

I also really like Riki's website, Jordan's website, and Dr. Valkanas's website.

I recommend that you Google the career you like and see what online presence people with those jobs have curated!

2) LinkedIn: I know, it's difficult to get on LinkedIn and read about B2B sales everyday. However, the reality is that it is an incredible tool to network with people in your field of interest. You can also make yourself available to recruiters and learn relevant skills with LinkedIn Learning. 

It's important to keep your profile updated with your accomplishments. This will help recruiters find you! Here is what my LinkedIn looks like as an example. However, I encourage you to search for those that have the jobs you want and see what their skill sets and accomplishments are. This will serve as a road map for you to figure out what you need to add to your CV.

3) Resume/CV: Having both a resume and a CV is important since they apply to different scenarios. In academia, your CV is essential. It must be jam-packed with everything that you have done professionally (projects, publications, presentations, extracurriculars, etc.). 

Meanwhile, your Resume should be one page long and only include the relevant experience to the job you are applying to! 

Here is a great guide from Cornell on how to prepare CV/Resumes. 

Step 3: Informational Interviews

Informational interviews can be a formal or informal chats about someone's role in their company and what steps they took to get there. This is a helpful way for you to build your network, while also learning more about your career options. Often times, your school will have some kind of alumni group or platform. Reach out to alumni that are currently working at companies and/or institutions you are interested in and ask for some time to discuss XYZ role they have at their company

You can reach out to people via email or connect with them on LinkedIn. If your school doesn't have a formal alumin group, you can search for your school on LinkedIn and it will pull up profiles of people that went there. Use that, along with keywords to identify alumni that are currently in roles you are interested in. 

For example: Search for "Brown University" and "Medical Scribe"