It does not matter if the documentation of your PhD journey is in a single master document, whether it is Google Docs, or LaTex, or scattered across several apps and platforms. The how is less important. The key insight is to document the essentials of your PhD journey in the first place.  

In the following, we share some key insights that are important to note down – namely reading, meetings, experiments, networking – with minimal overhead while reaping many benefits.  

When planning and organizing the timeline for a 5-6 year PhD, there are two effective ways to structure it: by academic years or by specific semesters. In the year-based approach, you can divide your PhD journey into stages like “Year 1,” “Year 2,” and so forth, with each year representing the progression of coursework, research milestones, and dissertation work. Alternatively, you can organize it by semester or term—for example, “Fall 2022 to Summer 2023” for each academic cycle. This semester-based structure can offer a more granular view of goals and timelines, helping to outline specific objectives and tasks for each term. Either approach allows you to track your progress systematically, adapt to any shifts in your research trajectory, and clearly mark the completion of various phases within your PhD journey. 

Each semester can be further organized into sub-categories to keep track of specific academic responsibilities and activities. Key sections might include Coursework (for classes and academic assignments), Research Projects (for ongoing experiments, data analysis, and findings), and Undergraduate Projects (if mentoring or assisting undergrad students) and TA-ship (for classes you are assisting as a teaching assistant). Additional categories could cover Collaborations (joint work with other researchers or labs) and Mentorship (guidance provided to younger students or peers). This structure ensures that every academic aspect of the semester is systematically organized and easy to access. 

Coursework 

Coursework can be organized into subfolders to keep track of specific academic requirements and milestones. Key subfolders might include Core Coursework (for essential classes and materials related to the field), Qualifying Exam Prep (study materials and notes for comprehensive exams), Proposal (documents and drafts for research proposals), and Defense (resources for preparing the final dissertation defense). This structure helps streamline access to critical documents and keeps the academic journey well-organized. 

• Core coursework 

• Qualifying exams 

• Proposal 

• Defense 

The Core Coursework subfolder includes all essential curricular requirements mandated by the program. This folder houses key documents such as the Program of Study Form, RCR (Responsible Conduct of Research) Certificates, and the student-Advisor Matching Form. It also contains individual folders for each course taken during the semester, allowing for easy organization and access to course-specific materials. This setup ensures that all mandatory academic documents are systematically managed and readily available. 

Research projects 

The second major heading under your yearly or semesterly organization should be dedicated to Research Projects. While best practices for organizing research tasks and projects are covered in detail in another section, we’ll briefly introduce a simple method for structuring your research files. For the main Research Project heading, it’s helpful to include the project duration, grant number, and project title in the header to easily identify the work. This main project folder can then be divided into various subheadings for specific aspects of the project. There’s flexibility in how you structure these subfolders, but some useful categories might include Literature Review, Data Collection, Analysis, Results, Manuscripts, and Presentations. This approach helps keep all components of a project organized, making it easy to locate information and track progress. 

Project 1: 2020-2025_Grant #_Chemotherapy based cell Sorting 

• References & Readings: all research projects start with a literature review to evaluate the existing body of evidence and to develop ideas worth investigating which can be documented in a sub-folder 

• Meetings & Decisions: Documenting the regular meetings where research progress and goals are discussed in a dedicated folder helps keep a record of project milestones & agreements, ensuring all team members are aligned. This sub-folder can include meeting notes, action items, and any significant decisions that impact the direction of the project. 

• Experiments: This section can be further organized with sub-folders based on either the instrument used (e.g., Microscope Data, Spectroscopy Results) or the theme/hypothesis being tested. Structuring by instrument allows for easy access to all data collected with a specific tool, while organizing by hypothesis enables streamlined tracking of progress and findings related to each research question. This flexibility allows you to adapt your experimental organization to best suit the nature of your project. When grouping by theme/hypothesis, some example names can be as follows: 

• 09.23-03.24_Drug induced biomechanics 

• 02-34-ongoing_microfluidic sorting 

Project 2: 2024-2025 Grant # Natural Killer cell grant 

• Proposal draft: If you contributed to writing a grant for the project, a dedicated grant proposal sub-folder can help organize all related materials. This folder might include initial drafts, funding agency guidelines, budget documents, submission timelines, and correspondence with collaborators or funders. Keeping these files in one place allows for quick access to the grant application and its details, helping you stay aligned with project goals and funding requirements. 

• Illustrations: A dedicated sub-folder for Proposal Illustrations can be highly useful for organizing all visual content created to support your project proposal. This folder could contain diagrams, figures, flowcharts, or any other graphics that visually convey your research concepts, methods, or anticipated results. By storing these illustrations separately, you can easily access, update, or repurpose them for presentations, reports, or future proposals. 

Undergraduate mentorship 

Mentoring undergraduates as a grad student can be very rewarding and manageable with the right structure. To stay organized and ensure smooth collaboration, you can create dedicated folders for each undergraduate, tailored to the specific project they are working on. These folders can include sections for learning goals, research timelines, weekly research updates, and relevant resources, making it easy for both you and the undergraduate to track progress and expectations. Using collaborative tools like Google Drive, Dropbox, or shared institutional folders allows everyone to access important documents such as meeting notes, datasets, protocols, and code in real-time. These platforms enable updates and changes to be instantly visible to everyone involved, promoting transparency and accountability. A structured, shared folder system helps undergraduates stay organized, encourages them to keep their work documented, and makes mentoring and feedback more efficient. 

Collaborations 

For effective research collaborations, it’s essential to establish a structured system for organizing and sharing resources, ensuring everyone stays aligned on goals and progress. Creating dedicated folders for each project or sub-team within tools like Google Drive, Dropbox, or shared institutional drives can be highly effective. These folders can contain project objectives, timelines, task assignments, and communication records, enabling collaborators to access and update critical information as needed. Additional subfolders for meeting notes, raw and processed data, protocols, analysis scripts, and manuscript drafts help to keep the workflow organized and transparent. Real-time collaboration tools allow team members to make updates, comment, and provide feedback seamlessly, enhancing coordination across all stages of the project. Such a structured folder system not only fosters accountability but also simplifies the process of tracking contributions, setting milestones, and managing the project’s progress efficiently. 

Mentorship 

Organizing mentorship materials into subfolders can greatly streamline the mentorship process, making it easy to track progress, share resources, and provide feedback. Within a primary mentorship folder, you can create subfolders dedicated to specific areas, such as Learning Goals, Development Plans, Meeting Notes, Progress Updates, and Feedback & Reflections. A Learning Goals folder can house initial assessments, skill-building objectives, and target competencies, while a Development Plans folder can outline key milestones and timelines. Meeting Notes and Progress Updates folders help both mentor and mentee stay aligned on goals and achievements, with regular updates providing a documented record of the mentee’s journey. The Feedback & Reflections folder is valuable for storing constructive feedback and self-reflections from the mentee, fostering a growth-oriented approach. Using shared platforms like Google Drive or Dropbox allows both parties to access and update these folders in real time, facilitating a collaborative and structured mentorship experience. 

Meeting minutes: AMA citation, keep the instructions generic and universal 

• Health & Wellness 

The Health and Wellness Folder can include resources and materials aimed at supporting physical, mental, and emotional well-being. Subfolders can be created for various aspects of health and wellness such as Mental health (counseling resources, mindfulness guides, journaling prompts), Physical health (Exercise routines, meal plans, health check-up records), emergency resources (contact information for on-campus and local health services, crisis hotlines) etc. 

Career advancement 

All materials and activities related to building your professional profile can be organized under a Career Advancement folder. This includes essential documents like CVs and resumes, as well as applications for conferences and fellowships. You can also keep track of opportunities such as internships, networking events, and seminars that contribute to skill development and professional growth. Having a centralized folder for career-related advancements ensures that your achievements and ongoing efforts are organized, making it easier to access and update as you progress. 

Conferences 

Under the Conferences sub-folder, you can keep a detailed record of each conference you applied to, including abstracts, agendas, your presentation or poster, travel itinerary, and notes on interesting projects or researchers you encountered. This organization helps you track both your contributions and valuable insights gained, making it easier to reference and build upon in the future. 

Fellowships 

In the Academic Fellowships sub-folder, you can organize all relevant materials for each fellowship application, such as application documents, recommendation letters, project proposals, and important deadlines. This setup allows you to efficiently track your progress and maintain a comprehensive record of each application, helping streamline the process for current and future fellowship opportunities. 

Internships 

In the Internships sub-folder, you can store all materials related to internship applications, including cover letters, CVs, interview notes, and offer letters. Additionally, you can keep documents from the internship itself, such as project summaries and mentor feedback. This structure provides a clear record of each internship experience, supporting both professional growth and future applications. 

Networking events & Seminars 

Networking Events & Seminars: Similarly, you can create dedicated folders for Networking Events and Seminars to keep all relevant materials organized in one place. These folders can include event schedules, speaker information, presentation slides, and any papers or resources shared during the sessions. Additionally, notes on key insights or follow-up actions can be stored here, as well as contact information for new connections. This setup ensures that valuable resources and connections made during these events are easily accessible and well-organized for future reference and professional development. 

Extra-curriculars 

All extra-curricular activities and commitments can be organized into dedicated folders such as Student Clubs, Mentorship Programs, and Competitions. This structure helps keep track of each activity type, making it easy to locate important documents, event details, and accomplishments. Grouping these activities ensures a well-organized overview of your involvement outside of academics. 

Student Clubs 

The Student Club Folder is designed to organize all the student clubs you are a part of. Each club will have its own dedicated subfolder, making it easy to keep things streamlined. Within each club’s folder, you can create additional subfolders based on your needs, such as Finance, Marketing, Event Planning, Meeting Notes, or Membership Details. This structure ensures all club-related materials are accessible and neatly organized. 

Competitions 

The Competitions Folder is designed to keep all the competitions you participate in as a graduate student neatly organized. Each competition can have its own dedicated subfolder, such as Poster Competitions, 3MT Thesis, Hackathons, or Case Competitions. Within each competition’s folder, you can create additional subfolders for Submission Materials, Guidelines, Practice Sessions, Feedback, or Results. This structure ensures all competition-related resources are easily accessible and well-organized. 

Finances 

This can include resources and materials to help you manage your personal, academic, and professional finances effectively. Subfolders can be created for various financial aspects, such as Budgeting and Planning, Income and Earnings, Tuition, Investment and Savings, Taxes, Financial aid and Loans etc. 

Budgeting and Planning 

This section can include monthly or yearly budget spreadsheets to track your income and expenses, financial goals to guide your savings and spending habits using tools like budget templates, financial calculators, and reminders for recurring payments or deadlines. 

Investment and Savings 

This section can include records of any investments, such as stocks, bonds, mutual funds, or retirement accounts, as well as documents related to savings accounts or emergency funds. You can also store plans for long-term financial goals, such as buying a home or building wealth, along with strategies to achieve them. 

Taxes 

You can organize all your tax-related documents such as W-2s, 1099s, or 1098-Ts, as well as receipts for deductible expenses like tuition, books, or charitable contributions here. You can also store completed tax filings, records of refunds or payments, and important deadlines. Additionally, this folder is a great place to save any correspondence with tax authorities or resources for filing, such as software guides or accountant contacts. Keeping this subfolder up to date helps ensure a smooth and stress-free tax season. 

Templates/apps/Platforms that you can use: 

OneNote

OneNote is a versatile tool for organizing research activities, with notebook and section layouts that allow you to categorize projects, notes, and data efficiently. The digital handwriting feature is ideal for annotating papers or jotting down ideas, while tagging options make it easy to highlight important points and track to-dos. Plus, with cloud syncing, you can access your research notes across devices, keeping everything organized and readily available. 

Notability

Notability offers several features that are excellent for organizing research activities. Its folder structure allows you to categorize notes by project or topic, while handwriting and PDF annotation capabilities make it easy to mark up research papers and add detailed notes. The audio recording feature is also useful for capturing key points during meetings, and with cross-device syncing, you can access your research materials anytime, keeping everything organized and accessible. 

Notion

Notion is highly effective for organizing research activities, with its flexible database structure allowing you to manage notes, tasks, and project timelines all in one place. Customizable templates make it easy to create dedicated spaces for literature reviews, experiment tracking, and data analysis. Additionally, Notion’s collaborative features allow for seamless teamwork, making it a powerful tool for managing and sharing research progress.