Your personal research assistant

Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share research.

Available for Mac, Windows, Linux, and iOS

Just need to create a quick bibliography? Try ZoteroBib .

Meet Zotero.

Collect with a click..

Zotero automatically senses research as you browse the web. Need an article from JSTOR or a preprint from A news story from the New York Times or a book from a library? Zotero has you covered, everywhere.

Organize your way.

Zotero helps you organize your research any way you want. You can sort items into collections and tag them with keywords. Or create saved searches that automatically fill with relevant materials as you work.

Cite in style.

Zotero instantly creates references and bibliographies for any text editor, and directly inside Word, LibreOffice, and Google Docs. With support for over 10,000 citation styles, you can format your work to match any style guide or publication.

Stay in sync.

Zotero can optionally synchronize your data across devices, keeping your files, notes, and bibliographic records seamlessly up to date. If you decide to sync, you can also always access your research from any web browser.

Collaborate freely.

Zotero lets you co-write a paper with a colleague, distribute course materials to students, or build a collaborative bibliography. You can share a Zotero library with as many people you like, at no cost.

Zotero is open source and developed by an independent, nonprofit organization that has no financial interest in your private information. With Zotero, you always stay in control of your own data.

Still not sure which program to use for your research? See why we think you should choose Zotero .

Ready to try Zotero?

SCI Journal

30+ Essential Software for Researchers

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Essential Software for Researchers

Are you stuck with inefficient research tools? Discover the best essential software for researchers to revolutionize your work.

Academic research can often feel like a complex puzzle. Every researcher knows the struggles of data crunching, project coordination, document writing, and intensive note-taking. 

But here’s the good news: online tools for researchers can turn these challenges into manageable tasks.

Table of Contents

Academia has transformed from a domain dominated by a survival-of-the-fittest mentality into an inclusive sphere of shared knowledge, growth, and discovery.

This paradigm shift signifies the evolution of academia from a space where only the intellectually elite thrive, to a nurturing environment that promotes intellectual curiosity and learning for all.

We encourage researchers to try out the tools mentioned below to find the perfect research tool.

Essential Software for Researchers

#1. google scholar: best for scholarly literature search and keeping up-to-date with research in your field.

Credits: Wikipedia, Essential Software for Researchers,

  • One of the top academic search engines
  • Enables users to keep up-to-date with the latest research in their respective fields
  • Provides citation data for each article, contributing to the ease of referencing

In the quest for identifying pertinent research problems and gaps, Google Scholar acts as your invaluable companion. This search engine is your lens into the cutting-edge developments in your field. 

It helps you pinpoint where your investigation could contribute to the existing body of knowledge. Here are other academic journal discovery platforms that can help you at this stage of research .

How much does it cost?


#2. NVivo: Best for Designing and Conducting Qualitative Research

Credits: Scalar, Essential Software for Researchers,

  • Provides robust tools for data organization and analysis
  • Encourages meaningful insights from qualitative data
  • Promotes efficient coding, making it easier to sift through mountains of data

NVivo stands as a beacon of hope for qualitative researchers in the data fog. Its unique features categorize, analyze, and draw connections like a seasoned detective, unearthing meaningful insights with ease. 

With an intuitive interface, NVivo transforms complexity into a rich tapestry of knowledge. It empowers researchers to capture nuances, emotions, and subtleties, illuminating the essence of their study. 

As a guiding light, NVivo enhances the rigor of research and reveals profound insights that resonate with human experiences, making the journey through the data fog an exhilarating quest for wisdom.

  • Free trial available
  • Academic version costs $849 yearly

Source: Lumivero

#3. Qualtrics: Best for Survey Design and Distribution

Credits: Qualtrics, Essential Software for Researchers,

  • Comes equipped with sophisticated features for survey creation and distribution
  • Includes advanced data collection methods
  • Simplifies analysis with powerful analytics tools

When it comes to creating and distributing surveys, Qualtrics stands as the gold standard. This essential software is akin to having a personal survey consultant, streamlining every step of the process, from crafting engaging questionnaires to collecting and analyzing meaningful data. 

With its user-friendly interface and robust features, Qualtrics empowers researchers to gather valuable insights effortlessly. This powerful tool ensures that the journey from survey creation to data interpretation becomes a seamless and rewarding experience.

In the world of survey research, Qualtrics is your steadfast ally. It not only simplifies the process but also empowers you to glean meaningful insights from the data, adding immense value to your research. You can also check out other survey tools.

  • Free version available
  • Premium starts from $2,500 per year


#4. SPSS: Best for Statistical Analysis and Data Interpretation

Credits: SPSS, Essential Software for Researchers,

  • Provides comprehensive tools for statistical analysis
  • Simplifies data interpretation with an intuitive interface
  • Supports a wide range of statistical tests

If statistical analysis is your battleground, SPSS becomes your formidable armor. This software doesn’t merely crunch numbers; it possesses the alchemical ability to transform them into comprehensible insights, making data interpretation a breeze rather than a battle. 

With its robust toolkit and advanced analytics, SPSS empowers researchers to extract meaningful patterns and correlations from complex data sets. 

SPSS takes the intimidation out of data analysis. With this robust software, you’re not just analyzing data; you’re demystifying it and transforming it into actionable insights that can drive your research forward. Here are other top data analysis software for researchers.

  • Starts at $99


#5. Tableau: Best for Data Visualization and Reporting

Credits: FusionSpan, Essential Software for Researchers,

  • An industry-leading tool for creating interactive, insightful data visualizations
  • Empowers users to turn complex data into easy-to-understand, actionable information
  • Streamlines reporting with customizable dashboards and real-time updates

Tableau dominates the field of data visualization and reporting as a true titan. It serves as a personal data storyteller, adeptly converting intricate raw data into visually captivating and easily comprehensible narratives. 

With its powerful features and user-friendly interface, Tableau empowers users to unlock valuable insights and make informed decisions from data that might otherwise be overwhelming. 

From interactive dashboards to dynamic charts, its versatility and effectiveness make it a go-to tool for businesses, analysts, and anyone seeking to extract meaning from data in an engaging manner.

  • Starts from $180 per user yearly to $840 per year


#6. Overleaf: Best for Collaborative Writing and LaTeX Editing

Credits: Wikipedia, Essential Software for Researchers,

  • A powerful platform for creating and editing LaTeX documents
  • Enables seamless collaboration with real-time syncing and shared access
  • Simplifies LaTeX editing with a user-friendly interface and pre-made templates

As your LaTeX guru, Overleaf offers an efficient, collaborative workspace tailored to crafting and editing LaTeX documents. Whether you’re a researcher, engineer, or academic, this platform empowers you to produce polished and professional papers effortlessly.

Say goodbye to the complexities of document preparation and welcome a seamless, intuitive experience that enhances productivity and fosters collaboration among peers.

Overleaf facilitates collaboration and simplifying the editing process, making crafting complex documents less daunting and more productive. You can learn more about LaTeX tutorials here.

  • Standard: $199 per year
  • Professional: $399 per year


#7. Grammarly: Best for Checking Grammar and Improving Writing Clarity

Credits: Grammarly, Essential Software for Researchers,

  • A sophisticated tool for real-time grammar and spelling checks
  • Enhances writing clarity and eliminates errors
  • Provides personalized suggestions to improve your writing style

Grammarly is more than a proofreader; it’s your personal writing coach. This software is designed to guide you towards impeccable grammar, clear writing, and a refined style, ensuring your academic work shines.

With Grammarly at your side, you’re not just writing; you’re crafting compelling narratives. This tool helps ensure that your ideas shine brightly, unmarred by grammatical errors or unclear writing.

  • $25 per monthly


#8. Turnitin: Best for Plagiarism Checking and Originality Reports

Credits: Turnitin, Essential Software for Researchers,

  • A plagiarism checker tool
  • Provides detailed feedback to maintain academic integrity
  • Supports multiple languages and file formats for broader accessibility

Turnitin stands at the forefront of safeguarding academic integrity. As a vigilant watchdog, this software diligently ensures the authenticity of your work and detects any inadvertent plagiarism, guaranteeing its originality. 

With Turnitin’s cutting-edge technology, students and educators can have the confidence that their academic pursuits maintain the highest standards of integrity and authenticity. 

By continuously refining its capabilities, Turnitin remains a trusted ally in upholding academic excellence and promoting a culture of originality in educational institutions worldwide.

Here are the best academic writing that can help you in your research.

  • $3 per student per year


#9. Mendeley: Best for Discovering New Research and Collaborative Work

Credits: Mendeley, Essential Software for Researchers,

  • One of the best reference management tools available
  • Provides a platform to organize, share, and annotate research papers
  • Facilitates easy referencing with a built-in citation tool

When navigating the extensive realm of academic research, Mendeley serves as your reliable compass. With its centralized hub, this tool facilitates the discovery of cutting-edge research, fosters collaborations among researchers, and efficiently organizes your ever-expanding library of academic papers. 

By offering seamless access to a wealth of knowledge, this reference management software empowers scholars to delve deeper into their fields of interest, stay up-to-date with the latest findings, and engage in meaningful academic endeavors.

You can compare collaborative writing tools here .

  • Starts from $4.99 to $14.99


#10. Zotero: Best for Collecting, Organizing, and Citing Research Sources

Credits: Zotero, Essential Software for Researchers,

  • A comprehensive tool for collecting and organizing research sources
  • Supports a wide variety of citation styles
  • Integrates with numerous browsers and word processors for seamless usability

In the bustling marketplace of academic resources, Zotero stands out as a first-rate organizer. It helps you collect, manage, and cite your research sources, transforming a haphazard collection into a well-organized library.

Zotero is your personal library architect, ensuring your wealth of sources is well-structured and easily accessible. It doesn’t just simplify source management; it elevates your research process to a new level of efficiency.


#11. Trello: Best for Research Project Management and Task Organization

Credits: Trello, Essential Software for Researchers,

  • A robust platform for managing research projects and organizing tasks
  • Facilitates team collaboration with shared boards, lists, and cards
  • Enables tracking progress and deadlines for efficient project management

Trello is one of the best project management tools. This platform boasts a visually appealing and intuitive interface, facilitating seamless organization of tasks, progress tracking, and team collaboration.

Trello optimizes efficiency, enabling researchers to focus on their work, not administrative hassles. With an array of intuitive features, it remains an indispensable tool for coordinating and executing successful research endeavors.

Learn more about task management tools here.

  • Standard: $5 per month paid yearly


#12. ResearchGate: Best for Connecting with Fellow Researchers and Sharing Publications

Credits: ResearchGate, Essential Software for Researchers,

  • A dedicated platform for networking with global researchers
  • Enables sharing and discovery of academic papers and publications
  • Provides a space for discussions, questions, and collaborative problem-solving

ResearchGate, a haven for those yearning for a community of like-minded researchers, offers a platform that facilitates connections among scholars. 

By joining ResearchGate, you can share your work, connect with fellow researchers, and discover new research that aligns with your interests. 

This dynamic environment empowers you to stay at the forefront of knowledge and contribute to the scientific community.


#13. Notion: Best for Comprehensive Note-Taking and Project Management

Credits: Notion, Essential Software for Researchers,

  • A versatile tool for both note-taking and managing research projects
  • Provides customizable templates for a tailored user experience
  • Facilitates real-time collaboration among research teams

Isn’t it just exhilarating when you find a tool that simplifies your academic life? Well, that’s exactly what Notion is all about: a revolutionary digital workspace designed to merge the realms of in-depth note-taking and sophisticated project management.

With Notion, the tedious becomes straightforward, the overwhelming becomes manageable, and the complex becomes clear. It’s about getting the most out of your A-level studies, fostering a sense of achievement while making the process enjoyable. So, buckle up and let Notion revolutionize the way you work.

  • Plus: $8 per month paid yearly
  • Business: $15 per month paid yearly
  • Enterprise: Custom price


#14. Quillbot: Best for Paraphrasing and Improving Writing Clarity

Credits: Quillbot, Essential Software for Researchers,

  • Assists with paraphrasing and enhancing writing clarity
  • Offers various writing modes to cater to different styles and tones
  • Supports the construction of coherent and concise sentences

Quillbot is your personal wordsmith, adept at paraphrasing your text and enhancing its clarity. Its variety of writing modes cater to different styles and tones, and it can help in crafting concise and coherent sentences, making it an invaluable assistant in your research writing process.

Quillbot is your digital co-author. It helps in expressing your research findings in a clear and engaging manner, thereby improving your writing’s readability and impact. This is an essential companion in the quest to make your research more accessible and understandable. 

Here are other academic writing tools you may need.

  • Premium: $9.95 monthly


#15. Jasper AI: Best for AI-Powered Writing Assistance

Credits: Elegant Themes, Essential Software for Researchers,

  • Provides AI-driven assistance to enhance your writing quality
  • Suggests improvements for clarity, coherence, and grammar
  • Supports various writing styles and contexts, including academic research

Ever dreamt of having a personal writing mentor, constantly at your beck and call, simplifying the intricacies of academic writing for you? Welcome Jasper AI into your world – an exemplary writing companion that surpasses the functionalities of a typical digital assistant. 

This state-of-the-art tool propels your writing to a higher level. Gone are the days of laboring over endless edits and revisions. With Jasper AI, your writing process is streamlined, facilitating the creation of clear, compelling, and high-quality research work.

Here is a deep Jasper AI Review. Read it to learn more about how you can use Jasper

  • Creator: $49 monthly
  • Teams: $125 monthly
  • Business: Custom price


#16. GanttPRO: Best for Project Scheduling and Time Management

Credits: CloudWards, Essential Software for Researchers,

  • Offers robust tools for project scheduling and time management
  • Provides a visual representation of your project timeline
  • Supports team collaboration and task assignment

GanttPRO illuminates your project path with its visually appealing timeline representation. It becomes your dependable ally in planning tasks, monitoring progress, and optimizing your time management strategies. 

No longer do you have to wrestle with disorderly schedules and haphazard task allocations. GanttPRO simplifies the chaos and brings order to your project management landscape.

GanttPRO is not just a tool that assists in project scheduling; it’s your personal steward of time. This tool does more than just manage your project; it ensures your research endeavor is a resounding success.

  • Basic: $7.99 monthly
  • PRO: $12.99 monthly
  • Business: $19.99 monthly


#17. Scholarcy: Best for Quick Summarization of Academic Papers

Credits: Scholarcy, Essential Software for Researchers,

  • An efficient tool for extracting quick summaries from academic papers
  • Supports in-depth understanding by highlighting key points
  • Provides a reference list for further exploration

Scholarcy is your dedicated summarizer, rapidly transforming complex academic papers into digestible summaries. This amazing tool supports your understanding and equips you with a reference list for further research.

Scholarcy is your academic digest. It ensures you efficiently comprehend complex research papers, and ultimately, saves your precious time.

  • $9.99 monthly


#18. R Discovery: Best for Statistical Analysis and Data Visualization

Credits: APKCombo, Essential Software for Researchers,

  • A potent tool for comprehensive statistical analysis
  • Offers a robust platform for data visualization
  • Supports reproducible research with code sharing and reusability

R Discovery provides a platform for comprehensive statistical analysis. It also facilitates data visualization. This supports you in presenting your research findings convincingly.

Overall, R Discovery is your statistician, your illustrator, and your collaborator. It aids you in understanding data, presenting it effectively, and maintaining research integrity. This way, it contributes significantly to your research quality.


#19. Scopus: Best for Comprehensive Literature Search and Citation Tracking

Credits: Scopus, Essential Software for Researchers,

  • An extensive database for literature search across various fields
  • Supports citation tracking for managing your bibliographies
  • Offers analytical tools to assess the impact of research

Scopus is your academic searchlight, illuminating a vast landscape of scholarly literature. With its extensive database, citation tracking, and analytical tools, it aids you in finding relevant research, managing your references, and assessing your work’s impact.

Scopus is your scholarly sleuth and your research analyst. It equips you with the tools you need to conduct impactful research.

  • Paid ranges from $500 to $1000


#20. Journal Finder: Best for Identifying the Right Journals for Publishing Your Research

Credits: LibGuides, Essential Software for Researchers,

  • A dedicated platform for pinpointing suitable journals for research publication
  • Analyzes research abstract and keywords to suggest optimal matches
  • Helps researchers avoid unnecessary rejections and hasten publication process

Journal Finder serves as your publishing compass, steering you towards the right journals to publish your research. This tool saves you from the guesswork, maximizing the chances of your work reaching the right audience.

With Journal Finder, you’re not merely seeking publication – you’re targeting impact. By leading you to the most suitable journals, it increases the visibility and influence of your research.


#21. Global Journal Database: Best for Accessing Information about Various Journals

Credits: Researcher Life, Essential Software for Researchers,

  • A comprehensive database of various academic journals
  • Provides detailed information about the journals including impact factor
  • Assists researchers in finding the right publication platform

Global Journal Database is your encyclopedic companion in the quest for the right publication platform. It provides you with detailed information about various journals, helping you make informed decisions about where to submit your research for publication.

The Global Journal Database does not just offer information—it provides clarity. This tool empowers you to choose the best platform for your research, maximizing its impact.


#22. Citation Gecko: Best for Literature Review and Citation Network Exploration

Credits: Citation Gecko, Essential Software for Researchers,

  • A specialized tool for exploring citation networks
  • Aids in the literature review process by identifying key papers and authors
  • Supports academic networking by linking researchers with similar interests

Citation Gecko is your guide in the maze of academic citations. It helps you identify key papers and authors in your field. This way, the tool supports your literature review process, and fostering academic networking.

Citation Gecko is not just a citation tool—it’s your academic navigator. It not only aids in your literature review but also fosters academic networking, broadening the horizons of your research.


#23. OpenRefine: Best for Cleaning and Transforming Messy Data

Credits: OpenRefine, Essential Software for Researchers,

  • A powerful tool for cleaning up and transforming data into a usable format
  • Facilitates the exploration of large data sets with ease
  • Allows for batch editing and scripting for advanced data manipulation

OpenRefine is your personal data janitor, turning messy and inconsistent data into a clean, usable format. It gives you the power to explore, tidy up and transform large datasets, thus providing a robust foundation for your data analysis.

OpenRefine is not just a data cleaning tool—it’s your foundation for reliable data analysis. It provides you with clean, consistent data, which is vital for accurate results and insights in your research.


#24. MATLAB: Best for Complex Mathematical Calculations and Data Analysis

Credits: MATLAB, Essential Software for Researchers,

  • Offers an advanced platform for complex mathematical calculations
  • Supports high-level data analysis, visualization, and algorithm development
  • Provides an integrated environment for multidisciplinary research

MATLAB is your math whiz, providing a platform for handling complex mathematical calculations and data analysis. It offers a comprehensive environment for calculations, algorithm development and visualization. This makes MATLAB a one-stop shop for researchers in quantitative fields.

Overall, MATLAB is more than a calculator—it’s a complete computational environment. It allows you to perform complex calculations, analyze data, and visualize your results.

  • Premium: $860 yearly or $2150 for the perpetual license


#25. Amazon Drive: Best for Storing and Sharing Research Files

Credits: Amazon Drive, Essential Software for Researchers,

  • A reliable solution for storing and sharing research files
  • Ensures data safety with secure cloud storage
  • Supports collaboration by allowing file sharing among research team members

Amazon Drive is your digital locker, providing a secure home for your precious research files. Its cloud storage solutions ensure data safety and allow you to share files with your research team, promoting collaboration and efficiency.

Amazon Drive is a storage tool and a guardian of your research. It provides secure storage and facilitates collaboration, making sure your research work remains safe, organized, and accessible, wherever you are.

  • Ranges from $6.99 per month to $11.99 per month


#26. Best for Transcription of Interviews and Meetings

Credits: Business Wire, Essential Software for Researchers,

  • Efficiently transcribes audio content from interviews and meetings
  • Supports multiple languages and speakers
  • Provides keyword search in transcriptions for easy data navigation is your personal scribe, tirelessly transcribing your interviews and meetings into clear, accessible text. It recognizes multiple languages and speakers, and allows keyword search in transcriptions. This makes your data more manageable and the research process more effective. does more than transcription—it simplifies your qualitative data analysis. By transforming audio into searchable text, it saves time and enhances data accuracy, which can significantly boost the quality of your research.

  • Basic: Free
  • Pro: $8.33 per month paid yearly
  • Business: $20 per month paid yearly


#27. LabView: Best for Data Acquisition and Instrument Control in Lab Environments

Credits: LabView, Essential Software for Researchers,

  • Offers a platform for data acquisition and instrument control
  • Facilitates lab automation by integrating hardware and software
  • Allows real-time visualization of data for immediate analysis

LabView is your laboratory maestro, orchestrating a smooth interplay between data acquisition and instrument control. Its robust integration of hardware and software allows for lab automation, while real-time data visualization ensures immediate analysis, saving you valuable time and energy.

LabView is not just a lab tool—it’s a catalyst for efficiency and precision. By facilitating data acquisition, instrument control, and real-time analysis, it turns your lab into a hub of productivity, taking your research a notch higher.

  • Starts from $493 to $2771


#28. SAS: Best for Advanced Statistical Analysis and Predictive Modeling

Credits: SAS Institute, Essential Software for Researchers,

  • Provides a platform for advanced statistical analysis and predictive modeling
  • Supports data management and decision-making processes
  • Offers visualization capabilities for better data understanding

SAS is your statistical powerhouse, offering advanced statistical analysis and predictive modeling capabilities. Its data management, decision-making support, and visualization tools make it a comprehensive solution for researchers looking to derive deep insights from their data.

SAS is more than a statistical tool—it’s a comprehensive solution for data-driven research. By enabling advanced analysis, predictive modeling, and data visualization, it empowers you to make the most of your data, thereby enhancing the quality and impact of your research.

  • Paid ranges from $1000 to $5000


#29. BioRender: Best for Creating Scientific Figures and Illustrations

Credits: BioRender, Essential Software for Researchers,

  • Facilitates the creation of high-quality scientific figures and illustrations
  • Offers a vast library of pre-made templates and icons
  • Enables sharing and collaboration with peers and colleagues

BioRender is your personal scientific illustrator, providing a platform to create high-quality figures and illustrations. With a large library of templates and icons at your disposal, and collaborative capabilities, it empowers you to communicate your research visually.

BioRender is not just a graphics tool—it’s a bridge between your research and your audience. It aids in communicating your findings more effectively, amplifying the impact of your work.

  • Individual: $35 monthly
  • Lab: $99 monthly
  • Institution: Custom price


#30. Slack: Best for Team Communication and Collaboration

Credits: Slack, Essential Software for Researchers,

  • Enables smooth team communication and collaboration
  • Allows for organized discussions through channels and threads
  • Integrates with other productivity tools for a cohesive work experience

Slack is your team’s digital huddle, fostering effective communication and collaboration. Its organization of discussions into channels and threads, along with integration capabilities with other productivity tools, ensures a seamless, efficient research process.

Slack isn’t just a communication tool—it’s your team’s virtual meeting room. By enabling efficient communication and collaboration, it brings your research team closer, improving productivity and fostering a cohesive research process.

  • Pro: $7.25 per month
  • Business: $12.50 per month


#31. RStudio: Best for Statistical Computing and Graphics in R

Credits: Posit, Essential Software for Researchers,

  • Offers a dedicated environment for statistical computing in R
  • Facilitates the creation of high-quality graphics for data visualization
  • Supports the use of markdown for creating reproducible reports

RStudio is your personal statistician, providing a comprehensive environment for R, a popular language for statistical computing. 

This tool aids in creating high-quality graphics and supports markdown for reproducible reports, making it an essential tool for researchers dealing with statistical analysis.

RStudio isn’t just a programming tool—it’s your guide in the world of statistical computing. It aids in data analysis, visualization, and reproducibility, ensuring your research findings are accurate, compelling, and repeatable.


Academic research isn’t just about the pursuit of knowledge; it’s about leveraging the right tools to streamline that pursuit. As we’ve explored, these essential research software applications aren’t merely aids. 

They’re game-changers. They’re here to tackle challenges head-on, from organizing sources to research data analysis, and transform them into opportunities for growth and learning. 

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organizing research papers software

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Become a Writer Today

12 Best Software for Organizing Research (2024)

Discover our guide with the best software for organizing research; get on top of your academic papers, writing projects, and more with these top research organization assistants.

Whether researching for an academic paper, independent study or writing project, having an organization system is essential for managing your data. The right software can help to save time, promote teamwork and increase productivity, no matter the type of project.

Often, when starting a new writing project, like writing a historical fiction piece, I’ll use writing software to collate all of my data. Organizing my research on a digital platform lets me visualize all the information and quickly find facts and figures. Check out our writing tips for your next project.

Research organization tools are excellent for academic writing and helpful for students getting their heads around how to structure data correctly. Let’s check out why you should organize your research and the best software to do it with.

Why Organize Research Data?

Key features of research software, 2. mendeley, 3. evernote, academic writing and editing solutions, 4. grammarly, 5. hemingway editor, 6. prowritingaid, collaborative research platforms, 7. google docs, 8. authorea, 9. microsoft teams, data extraction and analysis tools, 10. octoparse, 11. contentmine, 12. tableau, what is an excellent way to organize research information, how does research organization software improve the quality of academic work.

  • It saves time. Instead of searching for information, you can focus on analyzing it.
  • Better collaboration. With software, teamwork becomes more straightforward, no matter where your team members are.
  • Improved work quality. Software ensures your data is well-organized and easy to access, enhancing the accuracy of your results.
  • Time Management: Software can automate repetitive tasks, helping researchers be more efficient.
  • Collaboration: Working together is essential in research. Software tools make it easy to communicate and ensure everyone is on the same page.
  • Quality: Software helps maintain high-quality work by organizing data and providing easy access.


Zotero is a personal research assistant who collects and organizes your research data on one platform. Not only does Zotero sort and organize your data, but it also assists with citations, which can be one of the research’s trickiest parts.

Zotero is ideal for academic writing, where you will need to create a bibliography. With an intuitive interface and helpful tools, Zotero can help you create seamless academic documents without having to tidy up your research sections.


Imagine having a virtual library at your fingertips, with all your research sources meticulously organized, including your pdf files and web pages – that’s the power of Mendeley ! Mendeley is a reference manager suited well to academic writing.

Mendeley makes writing papers less daunting, from facilitating collaboration to offering annotation and data extraction features. Despite some limitations, such as limited customization options, Mendeley shines as a tool that simplifies library management for researchers.


Evernote is a go-to note-taking software and an excellent research organization assistant. Evernote has a user-friendly interface that’s easy to navigate. With synchronization capabilities and intuitive tools, you can quickly jot down ideas and organize your research notes. A free version of the software is available; although it’s limited, it’s an excellent solution for students on a budget.

Academic writing is an art. It demands precision, clarity, and comprehensive knowledge of the subject matter. But even the most experienced writers need help to ensure their work is up to par.


Grammarly is like a personal English tutor, constantly guiding your writing towards precision and clarity. Grammarly is ideal for organizing your research because it can help create concise notes and format citations, and its new AI, GrammarlyGO, can even help generate text. 

Although it’s not the best for presenting your research data, it’s a secure online platform where you can save your research and citations for easy access from anywhere. Check out our guide on how to organize in-text citations .

Hemingway Editor

Writing is about communicating ideas clearly and simply. Hemingway Editor is designed to help you create clear and concise research notes. This tool is helpful for academic students looking to condense and clarify their research notes, particularly after conducting qualitative research like interviews.

The Hemingway Editor acts as a writing coach, pointing out long-winded sentences, unnecessary words, and complex phrases. It helps you simplify your writing, ensuring your ideas are communicated effectively. 


ProWritingAid is an all-in-one writing assistant that offers comprehensive writing assistance. It can analyze text for clarity, grammar, style and structure, ensuring that the information derived from your research is clear.

Effectively communicating your research findings is essential for academic success. To create a valuable research document, refine your research and organize it within ProWritingAid. Although this software doesn’t directly organize research, it’s a great way to enhance the quality of your content.

Research is often a team effort. And in today’s digital age, collaboration isn’t bound by geographical boundaries. Collaborative research platforms bridge the gap, providing a virtual space for researchers to work together. What is academic writing? Check out our guide to find out.

organizing research papers software

GoogleDocs is ideal for collaborative research organizations. Teams can collaborate on one document that updates in real time, providing a secure and functional space for collaboration. Using GoogleDocs, team members can add research data, tables, charts or statistical data, which the team can then work on.

As well as the functionality of the data presenting tools, GoogleDocs lets users view previous versions of the document. This essential feature ensures that no data is lost permanently and can be retrieved in the case of an accident.


Authorea is specifically designed for researchers. This software is a collaborative writing tool that allows authors to make real-time changes. Authorea stands out as a research organization tool because it has features like creating scientific notations, figures and data visualizations. As well as this, Authorea integrates with bibliographic tools, allowing users to create reference pages and bibliographies easily. This tool is most suited to students and academics.

Microsoft Teams

Communication is key in Research. From discussing ideas to sharing findings, efficient communication ensures everyone is on the same page. Microsoft Teams provides a centralized platform for research communication, bridging the gap between team members.

Microsoft Teams is like a virtual office, providing a space for discussions, meetings, and information sharing. Features like document collaboration, video conferencing, and team chats ensure seamless and efficient communication. While it may initially seem overwhelming, Microsoft Teams is a robust platform that can significantly enhance research communication.

Data is the lifeblood of Research. But collecting and analyzing all the data can be a daunting task. Thankfully, there are tools to make this process easier. Data extraction and analysis tools simplify the process, allowing researchers to focus on what matters – the Research.


Octoparse simplifies this process of extracting data from websites. It’s like having a personal data miner digging through the vast internet landscape to find the necessary data.

With Octoparse, you can automate the web scraping process, saving time and effort. It’s like using a metal detector to find that elusive needle in the haystack. While web scraping may seem complex, Octoparse makes it accessible to everyone, regardless of their technical skills.

Academic papers, including research and scientific papers, are a goldmine of information. However, extracting this information can take time and effort. ContentMine is like a virtual miner, digging through academic papers to extract valuable information.

With ContentMine, you can automate extracting data from academic papers. It’s like having a speed reader who can quickly scan through documents and extract the information you need. While text mining may seem daunting, ContentMine makes it accessible and efficient.


Tableau is a powerful tool for data visualization that can help bring your research data to life! Using Tableau, you can make your data easy to understand for all audiences. It’s like having a personal graphics designer who can transform raw data into a visually pleasing infographic. While data visualization may seem complex, Tableau makes it easy and accessible to everyone.

FAQs About Best Software for Organizing Research

Organize research information by tracking search processes using a research log or spreadsheet and use citation managers to create bibliographies. Additionally, it utilizes coloring and tagging techniques to assign meaning to data during the synthesis process.

Research organization software helps maintain the integrity and quality of academic work by providing a structured approach to data storage and accessibility. This ensures that information is readily available, reducing errors that arise from misplaced or misinterpreted data. 

Looking for more? Check out our round-up of the best essay writing apps !

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15 Best Free Web Tools to Organize Your Research

How to stay organized when researching and writing papers

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Organizing research is important not only for your own sanity, but because when it comes time to unfold the data and put it to use, you want the process to go as smoothly as possible. This is where research organizers come in.

There are lots of free web-based organizers that you can use for any purpose. Maybe you're collecting interviews for a news story, digging up newspaper archives for a history project, or writing a research paper over a science topic. Research organizers are also helpful for staying productive and preparing for tests.

Regardless of the topic, when you have multiple sources of information and lots to comb through later, optimizing your workflow with a dedicated organizer is essential.

Patrick Tomasso / Unsplash

Many of these tools provide unique features, so you might decide to use multiple resources simultaneously in whatever way suits your particular needs.

Research and Study

You need a place to gather the information you're finding. To avoid a cluttered space when collecting and organizing data, you can use a tool dedicated to research.

  • Pocket : Save web pages to your online account to reference them again later. It's much tidier than bookmarks, and it can all be retrieved from the web or the Pocket mobile app .
  • Mendeley : Organize papers and references, and generate citations and bibliographies.
  • Quizlet : Learn vocabulary with these free online flashcards .
  • Wikipedia : Find information on millions of different topics.
  • Quora : This is a question and answer website where you can ask the community for help with any question.
  • SparkNotes : Free online study guides on a wide variety of subjects, anything from famous literary works of the past century to the present day. 
  • Zotero : Collect, manage, and cite your research sources. Lets you organize data into collections and search through them by adding tags to every source. This is a computer program, but there's a browser extension that helps you send data to it.
  • Google Scholar : A simple way to search for scholarly literature on any subject.
  • Diigo : Collect, share, and interact with information from anywhere on the web. It's all accessible through the browser extension and saved to your online account.
  • GoConqr : Create flashcards, mind maps, notes, quizzes, and more to bridge the gap between your research and studying.

Writing Tools

Writing is the other half of a research paper, so you need somewhere useful to go to jot down notes, record information you might use in the final paper, create drafts, track sources, and finalize the paper.

  • Web Page Sticky Notes : For Chrome users, this tool lets you place sticky notes on any web page as you do your research. There are tons of settings you can customize, they're backed up to your Google Drive account, and they're visible not only on each page you created them on but also on a single page from the extension's settings.
  • Google Docs or Word Online : These are online word processors where you can write the entire research paper, organize lists, paste URLs, store off-hand notes, and more.
  • Google Keep : This note-taking app and website catalogs notes within labels that make sense for your research. Access them from the web on any computer or from your mobile device. It supports collaborations, custom colors, images, drawings, and reminders.
  • Yahoo Notepad : If you use Yahoo Mail , the notes area of your account is a great place to store text-based snippets for easy recall when you need them.
  • Notion : Workflows, notes, and more, in a space where you can collaborate with others.

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30 Tools and Resources for Academic Research


Merriam-Webster defines “research” as “careful or diligent search; studious inquiry or examination; the collecting of information about a particular subject”. It’s not easy to conduct academic research, so here we round up 30 tools that will facilitate your research in managing, indexing, and web scraping .

Looking for data resources for your research? Find it in  70 Amazing Free Data Resources you should know, covering government, crime, health, finances, social media, journalism, real estate, etc.

top 30 tools for academic research

10 Research Management Tools

1. marginnote.

License: Commercial

MarginNote is a powerful reading tool for learners. Whether you are a student, a teacher, a researcher, a lawyer, or someone with a curious mind to learn, MarginNote can help you quickly organize, study and manage large volumes of PDFs and EPUBs. All-in-one learning app enables you to highlight PDF and EPUB, take notes, create the mind map, review flashcards, and saves you from switching endlessly between different Apps. It is available on Mac, iPad, and iPhone.

License: Free

Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research. It is available for Mac, Windows, and Linux. It supports managing bibliographic data and related research materials (such as PDF files). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes, and bibliographies, as well as integration with the word processors Microsoft Word and LibreOffice Writer.

3. RefWorks

RefWorks is a web-based commercial reference management software package. Users’ reference databases are stored online, allowing them to be accessed and updated from any computer with an internet connection. Institutional licenses allow universities to subscribe to RefWorks on behalf of all their students, faculty, and staff. Individual licenses are also available. The software enables linking from a user’s RefWorks account to electronic editions of journals to which the institution’s library subscribes.

EndNote is the industry standard software tool for publishing and managing bibliographies, citations, and references on the Windows and Macintosh desktop. EndNote X9 is the reference management software that not only frees you from the tedious work of manually collecting and curating your research materials and formatting bibliographies, but also gives you greater ease and control in coordinating with your colleagues.

5. Mendeley

Mendeley Desktop is free academic software (Windows, Mac, Linux) for organizing and sharing research papers and generating bibliographies with 1GB of free online storage to automatically back up and synchronize your library across desktop, web, and mobile.

6. Readcube

ReadCube is a desktop and browser-based program for managing, annotating, and accessing academic research articles. It can sync your entire library including notes, lists, annotations, and even highlights across all of your devices including your desktop (Mac/PC), mobile devices (iOS/Android/Kindle), or even through the Web.

Qiqqa is a free research and reference manager. Its free version supports supercharged PDF management, annotation reports, expedition, Ad-supported, and 2GB free online storage.

Docear offers a single-section user interface that allows the most comprehensive organization of your literature; a literature suite concept that combines several tools in a single application (pdf management, reference management, mind mapping, …); A recommender system that helps you to discover new literature: Docear recommends papers which are free, in full-text, instantly to download, and tailored to your information needs.

9. Paperpile

Paperpile is a web-based commercial reference management software, with a special emphasis on integration with Google Docs and Google Scholar. Parts of Paperpile are implemented as a Google Chrome browser extension

JabRef is an open-source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef is a desktop application that runs on the Java VM (version 8), and works equally well on Windows, Linux, and Mac OS X. Entries can be searched in external databases and BibTeX entries can be fetched from there. Example sources include arXiv, CiteseerX, Google Scholar, Medline, GVK, IEEEXplore, and Springer.

10 Reference/Index Resources

1. google scholar.

Google Scholar is a freely accessible web search engine that indexes the full text or metadata of scholarly literature across an array of publishing formats and disciplines. It includes most peer-reviewed online academic journals and books, conference papers, theses and dissertations, preprints, abstracts, technical reports, and other scholarly literature, including court opinions and patents. You can extract these academic data easily by scraping Google Scholar search results .

arXiv (pronounced “archive”) is a repository of electronic preprints (known as e-prints) approved for publication after moderation, that consists of scientific papers in the fields of mathematics, physics, astronomy, electrical engineering, computer science, quantitative biology, statistics, and quantitative finance, which can be accessed online. In many fields of mathematics and physics, almost all scientific papers are self-archived on the arXiv repository.

3. Springer

Springer Science+Business Media or Springer, part of Springer Nature, has published more than 2,900 journals and 290,000 books, which covers science, humanities, technical and medical, etc.

4. Hyper Articles en Ligne

Hyper Articles en Ligne (HAL) is an open archive where authors can deposit scholarly documents from all academic fields, run by the Centre pour la Communication Scientifique direct, which is part of the French National Centre for Scientific Research. An uploaded document does not need to have been published or even to be intended for publication. It may be posted to HAL as long as its scientific content justifies it.

MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care. MEDLINE also covers much of the literature in biology and biochemistry, as well as fields such as molecular evolution.

Compiled by the United States National Library of Medicine (NLM), MEDLINE is freely available on the Internet and searchable via PubMed and NLM’s National Center for Biotechnology Information’s Entrez system.

6. ResearchGate

ResearchGate is a social networking site for scientists and researchers[3] to share papers, ask and answer questions, and find collaborators.[4] According to a study by Nature and an article in Times Higher Education, it is the largest academic social network in terms of active users.

7. CiteSeerx

Owner: Pennsylvania State University

CiteSeerx ( CiteSeer ) is a public search engine and digital library for scientific and academic papers, primarily in the fields of computer and information science. Many consider it to be the first academic paper search engine and the first automated citation indexing system. CiteSeer holds a United States patent # 6289342, titled “Autonomous citation indexing and literature browsing using citation context”.

Owner: Elsevier

Scopus is the world’s largest abstract and citation database of peer-reviewed research literature. With over 22,000 titles from more than 5,000 international publishers. You can use this free author lookup to search for any author; or, use the Author Feedback Wizard to verify your Scopus Author Profile.

9. Emerald Group Publishing

Emerald Publishing was founded in 1967, and now manages a portfolio of nearly 300 journals, more than 2,500 books, and over 1,500 teaching cases, covering the fields of management, business, education, library studies, health care, and engineering.

10. Web of Science

Owner: Clarivate Analytics (United States)

Web of Science (previously known as Web of Knowledge) is an online subscription-based scientific citation indexing service originally produced by the Institute for Scientific Information (ISI)

5 Information Survey Tools

1. google forms.

Google Forms is a simple option for you if you already have a Google account. It supports menu search, a shuffle of questions for randomized order, limiting responses to once per person, custom themes, automatically generating answer suggestions when creating forms, and an “Upload file” option for users answering to share content through.

Moreover, the response can be synced in Google Drive, and users can request file uploads from individuals outside their respective companies, with the storage cap initially set at 1 GB.

2. Survey Monkey

Survey Monkey is quite a well-known name in the field but is also costing. It is a great choice for you if you want an easy user interface for basic surveys, as its free plan supports unlimited surveys, however, each survey is limited to 10 questions.

3. Survey Gizmo

SurveyGizmo can be customized to meet a wide range of data-collection demands. The free version has up to 25 question types, letting you write a survey that caters to specific needs. It also offers nearly 100 different question types that can all be customized to the user’s liking.

4. PollDaddy

PollDaddy is online survey software that allows users to embed surveys on their website or invite respondents via email. Its free version supports unlimited polls, 19 types of questions, and even adding images, videos, and content from YouTube, Flickr, Google Maps, and more.

5. LimeSurvey

LimeSurvey is an open-source survey software as a professional SaaS solution or as a self-hosted Community Edition. LimeSurvey’s professional free version provides 25 responses/month with an unlimited number of surveys, unlimited administrators, and 10 MB of upload storage.

5 Web Data Collection Tools

1. octoparse.

Octoparse is the most easy-to-use web scraping tool for people without a prior tech background. It is widely used among online sellers, marketers, researchers, and data analysts. With its intuitive interface, you can scrape web data within points and clicks. It also provides ready-to-use web scraping templates to extract data from Amazon, eBay, Twitter, BestBuy, etc. If you are looking for a one-stop data solution, Octoparse also provides a  web data service . Or you can simply follow the Octoparse user guide to scrape website data easily for free.

Its free version offers unlimited pages per crawl, 10 crawlers, and up to 10,000 records per export. If the data collected is over 10,000, then you can pay $5.9 to export all the data. If you need to track the dynamic data in real time, you may want to use Octoparse’s premium feature: scheduled cloud extraction. Read its customer stories to get an idea of how web scraping enhances businesses.

2. Parsehub

Parsehub is another non-programmer-friendly desktop software for web scraping, which is available to various systems such as Windows, Mac OS X, and Linux. Its free version offers 200 pages per crawl, 5 public projects, and 14 days for data retention.

3. Docparser

Docparser converts PDF documents into structured and easy-to-handle data, which allows you to extract specific data fields from PDFs and scanned documents, convert PDF to text, PDF to JSON, PDF to XML, convert PDF tables into CSV or Excel, etc. Its starting price is $19, which includes 100 parsing credits.

Scrapy is an open-source and collaborative framework for extracting the data you need from websites. In a fast, simple, yet extensible way.

Feedity automagically extracts relevant content & data from public web pages to create auto-updating RSS feeds. Instantly convert online news, articles, discussion forums, reviews, jobs, events, products, blogs, press releases, social media posts, or any other Web content into subscribable or publishable notifications. The starter version offers 20 feeds and 6 hours update interval, with a cost of $9 per month.


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organizing research papers software

Proactive Grad

How to Organize Research Papers: A Cheat Sheet for Graduate Students

Aruna Kumarasiri

  • August 8, 2022

how to organize research papers cover

It is crucial to organize research papers so that the literature survey process goes smoothly once the data has been gathered and analyzed. This is where a research organizer is useful.

It may be helpful to plan the structure of your writing before you start writing: organizing your ideas before you begin to write will help you decide what to write and how to write it.

It can be challenging to keep your research organized when writing an essay. The truth is, there’s no one “ best ” way to get organized, and there’s no one answer. Whatever system you choose, make sure it works for your learning style and writing habits.

As a graduate student, learning how to organize research papers is therefore essential.

This blog post will cover the basics of organizing research papers and the tools I use to organize my research. 

Before you start

The importance of organizing research papers.

No matter how good your paper management system is, even if you keep all your literature in places that are easy to find, you won’t be able to “create” anything unless you haven’t thought about organizing what you get from them.

The goal of the research is to publish your own work to society for the benefit of everyone in the field and, ultimately, humanity.

In your final year of your PhD, when you see all the papers you’ve stored over the years, imagine the frustration you might experience if you hadn’t gathered the information from those papers in a way that allows you to “create” something with i.

This is why organizing research papers is important when starting your research.

Research with your final product in mind

It is very important to have a clear idea of what your research’s outcome will be to collect the information you really need.

If you don’t yet have all your information, consider what “subheadings” or chunks you could write about.

Write a concept map if you need help identifying your topic chunks. As an introduction to concept mapping, it involves writing down a term or idea and then brainstorming other ideas within it.

To gather information like this, you can use a mind map.

When you find useful information.

Come up with a proper file management system.

Sort your literature with a file management system. There’s no need to come up with a very narrow filing system at this point. Try sorting your research into broader areas of your field. When you’re more familiar with your own research, you’ll be able to narrow down your filing system.

Start with these methods:

Don’t waste your time on stuff that’s interesting but not useful :  

In your own research, what’s the most important part of a particular paper? You won’t have to pay attention to other sections of that paper if you find that section first. 

What is the argument behind your research? Make notes on that information, and then throw everything else away.

Create multiple folders :

Create a file containing related topics if you’re using a computer. Bind the related articles together if you like to print out papers. In other words, keep related things together!

Color code your research papers:   

To organize notes and articles, assign different colors to each sub-topic and use highlighters, tabs, or font colors.

Organize your literature chronologically: 

Even in a short period of time, you might have missed overarching themes or arguments if you hadn’t read them previously. It’s best to organize your research papers chronologically.

If you want to do all this at once, I suggest using a reference manager like Zotero or Mendeley (more on reference managers later).

File renaming 

Make sure you rename your files on your computer according to your own renaming strategy. Taking this step will save you time and confusion as your research progresses.

My usual way of naming a pdf is to use the first author’s last name, followed by the first ten letters of the title and then the year of publication. As an example, For the paper “ Temperature-Dependent Infrared Refractive Index of Polymers from a Calibrated Attenuated Total Reflection Infrared Measurement ” by Azam et al., I renamed the file as “ Azam_Temperature-Dependent_2022.pdf “.

One thing to notice is that I don’t do this manually for all the papers I download. That wouldn’t be as productive, and I’d probably give up after some time renaming every single file. In my reference manager of choice (Zotero), I use a plugin called Zotfile to do this automatically. Zotfile automatically renames files and puts them in the folder I specify every time I add a new paper.

Organizing your research articles by the last names of the lead authors will simplify your citation and referencing process since you have to cite the names of the researchers everywhere. The articles will also be easier to find because they’ll be lined up alphabetically by any researcher’s name you can remember.

Use keywords wisely

Keywords are the most important part of sorting. It’s easy to forget to move a paper to a specific file sometimes because you’re overwhelmed. But you can tag a paper in seconds. 

When organizing research papers, don’t forget to develop a better keyword system, especially if you use a reference manager.

My reference manager, for instance, allows me to view all the keywords I have assigned in the main window, making life much easier.

Create annotations

When reading literature, it is very important to create your own annotations, as discussed in the blog post series, “ Bulletproof literature management system “.

This is the fourth post of the four-part blog series:  The Bulletproof Literature Management System . Follow the links below to read the other posts in the series:

  • How to How to find Research Papers
  • How to Manage Research Papers
  • How to Read Research Papers
  • How to Organize Research Papers (You are here)

The best thing to do is to summarize each section of the article/book you are reading that interests you. Don’t forget to include the key parts/arguments/quotes you liked.

Write your own notes

If you decide to read the whole paper, make sure you write your own summary. The reason is that 95% of the things you read will be forgotten after a certain period of time. When that happens, you may have to read the paper all over again if you do not take notes and write your own summary.

By writing your own summary, you will likely memorize the basic idea of the research paper. Additionally, you can link to other similar papers. In this way, you can benefit from the knowledge you gain from reading research papers.

After reading a paper, make sure to ask these questions:

  • Why is this source helpful for your essay?  
  • How does it support your thesis?  

Keep all the relevant information in one place so that you can refer to it when writing your own thesis.

Use an app like Obsidian to link your thinking if you keep all your files on a computer, making things much easier.

When you are ready to write

Write out of order .

Once you have all the necessary information, you can use your filing system, PDF renaming strategy, and keywords to draw the annotations and notes you need.

Now that you’re all set to write, don’t worry about writing the perfect paper or thesis right away.

Your introduction doesn’t have to come first.

If necessary, you can change your introduction at the end – sometimes, your essay takes a different direction. Nothing to worry about!

Write down ideas as they come to you

As you complete your research, many full-sentence paragraphs will come to your mind. Do not forget to write these down – even in your notes or annotations. Keep a notebook or your phone handy to jot down ideas as you get them. You can then find the information and revise it again to develop a better version if you’re working on the same project for a few days/weeks.

My toolbox to organize research papers

Stick with the free stuff.

Trying to be a productive grease monkey, I’ve tried many apps over the years. Here’s what I learned.

  • The simplest solution is always the best solution (the Occam razor principle always wins!).
  • The free solution is always the best (because they have the best communities to help you out and are more customizable).

As someone who used to believe that if something is free, you’re the product, I’ve learned that statement isn’t always true.

Ironically, open-source software tends to get better support than proprietary stuff. It’s better to have millions of enthusiasts working for free than ten paid support staff.

There are a lot of reviews out there, and EndNote usually comes out at the bottom. I used EndNote for five years – it worked fine, but other software improved faster. Now I use Zotero, which I like for its web integration. 

Obsidian, my note-taking app of choice, is also free software. Furthermore, you own your files; also, you’ve got a thriving community.

There are a lot of similarities between the software as they adopt each other’s features, and it’s just a matter of preference.

In any researcher’s toolbox, a reference manager is an essential tool.

A reference manager has two important features: the ability to get citation data into the app and the ability to use the citation data in your writing tool.

It should also work on Windows just as well as macOS or Linux, be free, and allow you to manage PDFs of papers or scanned book chapters.

Zotero , in my opinion, gives you all of this and more.

Zotero is one of the best free reference managers for collecting citation data. It includes a browser plugin that lets you save citation information on Google Scholar, journal pages, YouTube, Amazon, and many other websites, including news articles. It automatically downloads a PDF of the associated source when available for news articles, which is very convenient.

One of the things I really like about Zotero is that it has so many third-party plugins that we have almost complete control over how we use it.

With Zotero 6, you can also read and annotate PDFs, which is perfect for your needs.

My Research paper organizing workflow in Zotero :

  • Get References and PDF papers into Zotero : I use Zotero’s web plugin to import PDFs directly 
  • Filing and sorting : I save files from the web plugin into the file system I already have created in Zotero and assign tags as I do so.
  • File renaming : When I save the file, the Zotero plugin (Zotfile) automatically renames it and stores the pdf where I specified.
  • Extracting Annotations and taking notes : I use Zotero in the build pdf reader to take notes and annotate, and then I extract them and link them in Obsidian (next section).

You need to keep your notes organized and accessible once you’ve established a strong reading habit. For this purpose, I use Obsidian . I use Obsidian to manage everything related to my graduate studies, including notes, projects, and tasks. 

Using a plugin called mdnotes , Obsidian can also sync up with my reference manager of choice, Zotero. It automatically adds new papers to my Obsidian database whenever I add them to Zotero.

Obsidian may have a steep learning curve for those unfamiliar with bi-directional linking , but using similar software will make things much easier. Thus, you may be better off investing your time in devising a note-taking system that works for you.

You can also use a spreadsheet! Make a table with all the papers you read, whatever tool you choose. Include the paper’s status (e.g., whether you’ve read it) and any relevant projects. This is what mine looks like.

how to organize research papers

I keep all my notes on an associated page for each paper. In a spreadsheet, you can write your notes directly in the row or link to a Google document for each row. Zotero, for example, allows you to attach notes directly to reference files.

While it might seem like a lot of work, keeping a database of papers you’ve read helps with literature reviews, funding applications, and more. I can filter by keywords or relevant projects, so I don’t have to re-read anything.

The habit of reading papers and learning how to organize research papers has made me a better researcher. It takes me much less time to read now, and I use it to improve my experiments. I used this system a lot when putting together my PhD fellowship application and my candidacy exam. In the future, I will thank myself for having the foresight to take these steps today before starting to write my dissertation.

I am curious to know how others organize their research papers since there is no “ right ” way. Feel free to comment, and we will update the post with any interesting responses!

Images courtesy : Classified vector created by storyset –

Aruna Kumarasiri

Aruna Kumarasiri

Founder at Proactive Grad, Materials Engineer, Researcher, and turned author. In 2019, he started his professional carrier as a materials engineer with the continuation of his research studies. His exposure to both academic and industrial worlds has provided many opportunities for him to give back to young professionals.

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How to Organize Research: Notes, PDF Files, & Documents

Topics covered ✅.

  • How to organize research papers and PDF files
  • How to organize research projects
  • Organizing research notes
  • Organizing research notes software
  • Organizing research tools
  • Research organizer template
  • How to organize research material

If you are a busy college student, creator, or blogger your life can get really cluttered. But the messiness in our lives can extend much farther than just a dorm room or office. As active researchers, we can often struggle to organize research in the form of copious amounts of articles, journals, academic writings, thesis, rough drafts, etc.

It gets pretty exhausting.

But where do you even begin?

What's the best way to organize research?

We believe we have created the best recipe for organizing your research and you will never go back to your old ways.

1. Note-taking and Mind mapping – How to Hack Your Mind

First, start by organizing your notes into categories. You can do this on a sticky note or on a mind map.

Even though you may feel like a middle school kid using colorful sticky paper, sticky notes are proven to be one of the most effective ways to organize research.

You'll want to do some research before you begin writing.

Use sticky notes to organize the information you find, and write down any thoughts or ideas that come up as you read or listen.

Also, sticky notes are great if you want to jot down quick notes during a lecture or discussion with friends about the topic at hand.

You can write down important points and make connections between them on sticky notes.

An option similar to this is creating a mind map.

If you are a very visual learner, this style of research may appeal to you because you can visually see where you will be taking this research into categories and subcategories.

Plus it’s fun making them!

organizing research papers software

2. The Hard Part – Research & Writing

You should be familiar with the different types of sources that you can use when writing a research paper.

5 Examples of Sources

Here are a few examples of sources:

  • Primary sources (original documents like letters or speeches)
  • Secondary sources (articles, books, etc.)
  • Audio files (podcasts, interviews, etc.)
  • Online databases (Academic Search Complete, JSTOR, LexisNexis)
  • Tertiary sources (reviews of other people's research and analysis of your topics

organizing research papers software


When conducting research for your essay, be sure to use academic sources only!

Academic sources are those written by experts in their field who have been published in peer-reviewed journals or books and are therefore considered credible resources for learning more about any given topic.

Academic sources will always include citations at the end of each paragraph (or chapter) so that readers can easily identify where they can go if they'd like to learn more about the topic being discussed in each section of the text.

You can use secondary sources for information about your topic, but make sure that they are academically-reputable sources.

Primary sources are also great for finding information, but they provide only one side of the story and should be used with caution.

Overall, try to use a variety of sources as this will strengthen the argument you are defending.

We recommend putting a lot of emphasis on option five (tertiary sources) because it is something that we were not previously familiar with and we believe it should become more known as it is super helpful.

Tertiary sources are those that have been compiled by other people, such as academic journals and published books.

They can be great resources for getting more background information on a topic, but they aren't original works of scholarship—so be sure to cite them accordingly!

organizing research papers software

Quick Bibliographies

As you organize research, there’s no need to get bogged down in how you structure or create your bibliography.

For starters, here’s a simple list of tools for quick bibliographies:


3. Putting Your Thoughts On Paper

One of the hardest parts is the beginning of the writing process. You should always keep in mind your thesis statement when you write.

It's easy to get carried away with details and forget what you're trying to say—but if you can keep your thesis statement in mind, it will help you stay focused on the main point of your work.

The writing process is a great way to get started with your research because it helps you organize your thoughts before writing them down into sentences and paragraphs.

You'll be able to take notes faster because everything is already written down for you!

Moving on, an excellent strategy that works best for me is just word vomiting onto a page to get a basis of everything you want to say, and then after that is done, organize and clean up what was written.

This is especially useful if you have collected all the data and you just don't know how to put your thoughts into actual words.

organizing research papers software

Claim My Free Research Organizer Template

This free research organizer template comes pre-built with folders, subfolders, aesthetic formatting, and much more.

4. The Finishing Touches

If there is anything you should take away from this, it’s to use a reference manager.

Reference managers help ensure that all your citations are correct and up-to-date.

When choosing one, make sure it's compatible with whatever citation style is required by your instructor or institution.

Research doesn't have to be something that you dread or bores you out of your mind.

Being organized can make this process fun and exciting.

So now it's time to put on your thinking cap and get to work.

Notion user? You might also like...

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“This tool really helped me to create good bibtex references for my research papers”

Ali Mohammed-Djafari

Director of Research at LSS-CNRS, France

“Any researcher could use it! The paper recommendations are great for anyone and everyone”

Swansea University, Wales

“As a student just venturing into the world of lit reviews, this is a tool that is outstanding and helping me find deeper results for my work.”

Franklin Jeffers

South Oregon University, USA

“One of the 3 most promising tools that (1) do not solely rely on keywords, (2) does nice visualizations, (3) is easy to use”

Singapore Management University

“Incredibly useful tool to get to know more literature, and to gain insight in existing research”

KU Leuven, Belgium

“Seeing my literature list as a network enhances my thinking process!”

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“I can’t live without you anymore! I also recommend you to my students.”

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“This has helped me so much in researching the literature. Currently, I am beginning to investigate new fields and this has helped me hugely”

Aran Warren

Canterbury University, NZ

“It's nice to get a quick overview of related literature. Really easy to use, and it helps getting on top of the often complicated structures of referencing”

Christoph Ludwig

Technische Universität Dresden, Germany

“Litmaps is extremely helpful with my research. It helps me organize each one of my projects and see how they relate to each other, as well as to keep up to date on publications done in my field”

Daniel Fuller

Clarkson University, USA

“Litmaps is a game changer for finding novel literature... it has been invaluable for my productivity.... I also got my PhD student to use it and they also found it invaluable, finding several gaps they missed”

Varun Venkatesh

Austin Health, Australia

organizing research papers software

Our Course: Learn and Teach with Litmaps

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Organizing Papers and References without Losing your Mind

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In January, Ulrike Träger wrote a great PLOS ECR post describing how to stay on top of reading during graduate school. If you haven’t read it yet, go take a look, as it’s relevant for people at all career stages. As a follow up, here are a few tips on how to keep track of the papers you want to read without losing your mind.

Choose a reference manager. Sure, you can get by creating a poster or two without a reference manager, but it’s incredibly risky to cite references by hand for manuscripts and grant proposals. Choosing and using a reference manager is also a great way to track papers as you collect them, particularly because reference managers often have powerful search functions. There are many to choose from. Some are free, like Zotero and some versions of Mendeley . Others, like Papers and EndNote , are not, though some paid programs may be free through your institution. Spend some time researching which manager fits your needs, but don’t get bogged down, you can always switch later. Personally, I have transferred references from RefWorks to Zotero to Mendeley to EndNote over the past several years without much trouble.

Choose a place to keep unread papers. Whether it’s a physical folder on your desk or a virtual folder on your desktop, it’s important to have a designated place for unread papers. This folder is more than just a storage space, it should also be a reminder for you to review unread papers. It’s tempting to download papers and forget about them, falling prey to PDF alibi syndrome , wherein you fool yourself into thinking that by downloading a paper you’ve somehow read it. So, set aside some time every few weeks (on your calendar if you need to) to review papers. You won’t necessarily read each paper in detail, but you should complete a quick skim and take a few notes. Try to resist the urge to leave notes like “finish reading later.” However, if needed, consider using notes like “need to read again before citing” for papers that were skimmed particularly quickly.

Choose how to keep track of your notes. It’s a great idea to create a summary of each paper as you read it, but where do you keep this information? Some people write separate documents for each paper (e.g., using the Rhetorical Précis Format ), others write nothing at all, but tag papers (virtually or physically) with key words. The exact components of your system matter less than having a system. Right now, I keep a running document with a few sentences about each paper I read. I also note whether I read it on paper or as a PDF so that I can find notes taken on the paper itself later. If I’m doing a deep read on a specific topic, I might also start another document that has in-depth summaries. I usually keep notes in Word documents, but it’s also possible to store these notes in many reference managers.

Choose how to file read papers. Again, having a system probably matters more than which system you choose. Given the interdisciplinary nature of science, it can be complex to file by topic. Therefore, I find it easiest to file papers by last name of the first author and the publication year. It’s also useful to include a few words in the file name that summarize its content. This will help you differentiate between articles written by authors with similar last names. So, for example, using this method, you might label this blog post as Breland_2017_tracking refs. I keep articles I’ve read in a folder labeled “Articles” that includes a folder for each letter of the alphabet. Therefore, I’d file this blog post in the “B” folder for Breland.

TL;DR. The goal of creating a system to organize papers and references is to be able to easily access them later. If you follow the steps above, it’s relatively easy to keep track of and use what you’ve read – if you want to find a paper, you can search for a key word in your reference manager and/or in your running document of article summaries and then find a copy of the paper in the appropriate alphabetized folder. That said, there is no right way to organize references and I’m curious about how others manage their files. Chime in through the comments and we’ll update the post with any interesting answers!

Pat Thomson (2015) PDF alibi syndrome , Patter blog. Accessed 2/27/17.

Ulrike Träger (2017) Ten tips to stay on top of your reading during grad school , PLoS ECR Community Blog.

Sample Rhetorical Précis:

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[…] Organizing Papers And References Without Losing Your Mind – Jessica Breland […]

You have a great organizing skills! I appreciate your tips!

Fantastic tips! Thank you for sharing.

Great tips! It helps me a lot while I’m doing my final diploma project. Thank you.

This is great, very helpful. Nicely written and clearly organized [like your ref lib 😉 ] C

im at the start of my phd and already feeling that i have a lot of literature. i am taking your notes onboard and going to spend some time to organise my files asap. thanks

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Organizing Your Research: Citation Management Tools

Research management tools.

It is a best practice to use a personal content management  tool to organize your own reference material which could be articles, data sets, books, websites, images and more. These tools will save you time and allow you to work more efficiently.

Reference management software programs, web tools, and browser extensions allow you to organize your research, collect and cite sources, create bibliographies in a variety of styles, add your own notes and keywords to your citations. Many reference managers work with word processing software to format in-text citations and bibliographies for papers and theses, allow you to share references, and enable you to attach or link PDFs to a citation record.

  • NoodleTools NoodleTools helps you format citations in APA, MLA, and Chicago style. With the full version, you can create and organize your research notes, share and collaborate on research projects, compose and error check citations, and complete your list of works cited. MJC has NoodleTools available to all students, staff, and faculty for free. Includes CrossRef DOI lookup.
  • Mendeley Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research
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Free software applications for authors for writing a research paper

Himel mondal.

1 Department of Physiology, All India Institute of Medical Sciences, Deoghar, Jharkhand, India

Ayesha Juhi

Anupkumar d. dhanvijay, mohammed jaffer pinjar, shaikat mondal.

2 Department of Physiology, Raiganj Government Medical College and Hospital, Raiganj, West Bengal, India

Basic computer skills are essential for authors writing research papers as it has the potential to make the task easier for a researcher. This article provides a glimpse about the essential software programs for a novice author writing a research paper. These software applications help streamline the writing process, improve the quality of work, and ensure that papers are formatted correctly. It covers word processing software, grammar correction software, bibliography management software, paraphrasing tool, writing tools, and statistical software. All of the tools described are free to use. Hence, it would help researchers from resource-limited settings or busy physicians who get lesser time for research writing. We presume this review paper would help provide valuable insights and guidance for novice authors looking to write a high-quality research paper.


An author is one who “writes a book, article, play, etc.” A researcher is “someone whose job is to study a subject carefully, especially in order to discover new information or understand the subject better.” However, in a broad sense, a researcher is an author first. In a research cycle, a researcher needs to become an author from the very beginning of the research (preparation of proposal) to the end of the research (writing a paper for publication).[ 1 ]

Basic computer skills are essential for authors writing research papers because computers and technology have become a fundamental part of the research and writing process. As a new author writing a research paper, there are several essential software skills that can help you streamline the writing process, improve the quality of work, and ensure that the proposal or paper is formatted correctly.[ 2 ] However, these skills are rarely taught in our formal undergraduate or postgraduate course of study.

In this context, we discuss some of the basic software skills that may enhance the the quality of an research article in this article. This includes word processing software, grammar-checking software, paraphrasing tools, statistical software, writing tools, and keyword-searching tool.

Software applications

We describe some of the free software applications that may help authors during the preparation of a research paper. All the applications described are available either for computers or can be used online without paying any fees. Relevant websites where the tools are available are shown in Table 1 .

Software application (downloadable and online) with websites and their primary use for research purposes

WPS=Writer, Presentation and Spreadsheets, MeSH=Medical Subject Headings, DOI=Digital Object Identifier, JANE=Journal/Author Name Estimator, GPT=Generative Pre-training Transformer

Computer software applications

Apache OpenOffice is a free and open-source office software suite that includes a word processor (writer), spreadsheet, presentation software, and other tools. OpenOffice Writer is similar to Microsoft Word and can be used to write and format your research article.[ 3 ] This program is capable of saving the file into its own format (.odt) and also helps in saving the file in Microsoft Word document format (.doc). Hence, any text typed in this program can easily be opened with Microsoft Word. Along with typing an article, this program can help in making a flow chart (e.g. PRISMA flow chart for systemic review and meta-analysis) for research articles. Figure 1 shows the user interface of OpenOffice writer.

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g001.jpg

A portion of a story written on OpenOffice Writer showing the user interface

There is alternative office software called WPS (an acronym for Writer, Presentation, and Spreadsheets) office. Its personal basic version is free to use. However, the full version needs a subscription. Hence, researchers who are not comfortable with OpenOffice can use this software for writing their papers.

JAMOVI is open-source software for statistical analysis, which means that it is free to download and use. This can be particularly useful for researchers on a budget who do not have access to expensive commercial software. JAMOVI has a user-friendly interface that is easy to navigate, even for beginners. JAMOVI offers a wide range of statistical analyses, including t-tests, ANOVA, regression, and factor analysis. It is particularly well suited for researchers who need to conduct statistical analyses but are not familiar with the more complex features of traditional statistical software like Statistical Package for the Social Sciences (SPSS).[ 4 ] Figure 2 shows a part of the software when we conducted a Wilcoxon signed rank test (the nonparametric equivalent of paired t -test).

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g002.jpg

Part of the application JAMOVI when a Wilcoxon signed rank test was conducted

Those who are not interested to learn the basics of the JAMOVI can refer to the “online statistics” section of this article where we provided some websites that help in conducting basic statistical tests.

Zotero allows researchers to collect and organize references from a variety of sources, including library catalogs, websites, and databases. This can help researchers keep track of their sources and ensure that they have all the necessary information to cite them correctly. Zotero allows users to store full-text articles as PDFs, web pages, or other formats, along with their corresponding bibliographic information. This can make it easier to access articles and ensure that the information is all in one place. Zotero makes it easy to create bibliographies in a variety of formats, including APA, MLA, Chicago, and many others. This can save researchers time and reduce the likelihood of errors.[ 5 ]

However, those who are not willing to manage the references by Zotero can simply use the comment option in the word processing software to easily keep the reference with the text, and after the final draft, copy those references to add them to the manuscript file.

Google drive

Google Drive is a cloud-based storage and collaboration tool that can be very useful for researchers. Google Drive allows researchers to access their work from any device with an internet connection, making it easy to work on the go and collaborate with others from anywhere in the world. Google Drive makes it easy for researchers to collaborate with colleagues by sharing documents, spreadsheets, and presentations in real time. Multiple users can work on the same document simultaneously, and changes are saved automatically. Google Drive allows researchers to organize their research materials and data in one place, making it easy to find and access them when needed. By storing research materials and data on Google Drive, researchers can ensure that their work is backed up and secure, reducing the risk of data loss due to hardware failure or other issues.[ 6 ] The drive application can be downloaded and installed [ Table 1 ] on computers that would create a separate drive in the computer and keeping any files in this folder would be synchronized online and you can access it from any device connected to the Internet. However, it is to remember that an account is provided free with 15 GB of free cloud storage.

Online software applications

Grammarly is an online grammar-checking tool that can be very helpful for writers who want to improve the accuracy and clarity of their writing. It uses advanced algorithms and artificial intelligence to analyze text and identify errors in grammar, spelling, and punctuation. In addition to catching grammar and punctuation errors, Grammarly can also suggest vocabulary enhancements improve the style and tone of your writing. This can help you avoid common writing mistakes and create more engaging content. When Grammarly identifies an error in your writing, it explains the rule that you may have violated and suggests corrections that you can make. This can help you learn from your mistakes and avoid making similar errors in the future.[ 7 ] A guide on how to use Grammarly is available elsewhere in the article by Mondal and Mondal.[ 8 ] The premium version of the software provides further enhancement of the article. However, the basic free version helps a lot in correcting grammar that is skipped by common word processing software.

Quillbot is a paraphrasing tool that uses advanced algorithms and artificial intelligence to help researchers rephrase and reword their writing. It can be very helpful for researchers who need to paraphrase content for academic or professional purposes. Quillbot can help researchers save time by automatically rephrasing and rewording content. This can be particularly useful for researchers who need to paraphrase large amounts of text or who are working under tight deadlines. Quillbot can help researchers avoid text similarity (i.e. text plagiarism) by providing a way to paraphrase the content. This can be important for researchers who need to avoid plagiarism in their academic or professional work. Quillbot can be used on a variety of platforms, including web browsers, mobile devices, and desktop applications. This makes it easy to use Quillbot on the platform of your choice and to access your writing from multiple devices.[ 8 ] Figure 3 shows an example where a paragraph of text is being paraphrased.

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g003.jpg

A paragraph of text is paraphrased by QuillBot

MeSH on demand

MeSH on Demand is a website that provides a user-friendly interface to create Medical Subject Headings (MeSH) terms, which are widely used in the biomedical literature to facilitate the indexing and retrieval of articles. It can be very useful for researchers who need to identify appropriate MeSH terms for their research articles. It generates keywords and phrases related to the text provided by the user. This can be very helpful for researchers who are unfamiliar with the MeSH vocabulary and want to ensure that their articles are indexed correctly.[ 9 ] Figure 4 shows searching MeSH terms in a paragraph of text. After getting the MeSH terms, the author needs to decide which are the most relevant keywords for their manuscript and use those. The majority of the journal has a limitation on the number of keywords.

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g004.jpg

MeSH terms were searched from a paragraph of text on MeSH on Demand web application

In addition to searching MeSH terms in an article, the search result also includes relevant articles available in PubMed. Authors can check the list if they had missed any relevant literature.

DOI stands for Digital Object Identifier, which is a unique identifier assigned to a digital object such as a research article, data set, or other types of research output. It is widely used in the scholarly publishing industry and can be very useful for researchers. Researchers can always locate and access the digital object with DOI. It also helps researchers accurately cite their sources by providing a unique identifier that can be included in the reference list. This can help ensure that the citation is accurate and can be easily located by copy editors or readers.[ 10 ] In many journals, DOI is printed as a quick response code in the printed version of the journal so that any reader can scan it and get the article online. During writing an article, authors may save the DOI number along with the reference for a quick access of the article in future. However, authors always need to check the DOI before putting it along with references as sometimes, due to technical problems, the DOI does not work. In that case, they can save the URL of the article for accessing the paper later.

JANE stands for Journal/Author Name Estimator, which is a Web-based application designed to help researchers find relevant journals and authors for their research. JANE is a free service provided by the Biosemantics Group and funded by Netherlands Bioinformatics Centre, which makes it an accessible and cost-effective tool for researchers. JANE can help researchers find relevant journals for their research by analyzing the title and abstract of their paper and comparing it to the content of thousands of journals. This can save researchers time and effort in identifying appropriate journals to submit their work. JANE can also help researchers identify potential collaborators for their research by analyzing the authors of the papers in the relevant journals. This can help researchers find other experts in their field who are working on similar research topics.[ 11 ] From the list, authors can get email address of the authors and can use those for suggesting reviewers for the article, if the journal wants some suggested peer reviewer. In Figure 5 , three buttons are shown for finding “journals,” “authors,” and “articles.”

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g005.jpg

User interface of JANE where text can be pasted or typed and journals, authors, or articles can be searched by pressing buttons below

Online statistics

There are several online free websites that provide statistical tests for researchers. These online free websites can be helpful for researchers who need to conduct statistical tests but may not have access to specialized software or support. They provide a range of statistical tests and tools that are user-friendly and can be accessed from any device with an internet connection. Table 2 is showing some of the websites. Furthermore, detailed guidelines along with practice materials are available in articles by Mondal et al .[ 12 - 15 ]

Websites for statistical analysis

This is not a comprehensive list of online calculator

There is several artificial intelligence (AI)-based writing assistance software available. In recent times, an AI language model, ChatGPT is in discussion among academicians due to its human-like conversational and writing capability. It can be a useful tool for researchers in the process of writing a research paper. Researchers can use ChatGPT to generate ideas and inspiration for their research paper by inputting a topic or question related to their research. ChatGPT can then generate relevant sentences or paragraphs that can serve as a starting point for the paper. Researchers can use ChatGPT to help them write more clearly and effectively. This would particularly be helpful for non-native speakers of English. ChatGPT can provide suggestions for improving the wording, grammar, and structure of sentences, and can also provide synonyms or related words to improve the richness of the text. ChatGPT can be used to summarize long passages of text, making it useful for summarizing articles and research papers for review and analysis. ChatGPT can assist researchers in managing their citations and references by generating citations and reference lists in the appropriate format.[ 16 ] However, many a times, ChatGPT generates fictitious references for text which is not found on the internet. Google Bard is an alternative to ChatGPT which can also help in the tasks done by ChatGPT.

An example of conversation with ChatGPT is shown in Figure 6 where the ChatGPT was asked to explain importance of family medicine in India with three references.

An external file that holds a picture, illustration, etc.
Object name is JFMPC-12-1802-g006.jpg

A conversation with ChatGPT showing the input and output

Overall, having a basic understanding of these software tools can help new authors write more efficiently, effectively, and accurately, and create a professional-looking research paper.

There are several advantages of using technology for writing a research paper. Technology can greatly increase the efficiency of the research paper writing process, enabling researchers to complete tasks faster and more accurately. For example, ChatGPT can write a portion of the manuscript within seconds and QuillBot can help paraphrase text in a very short time. Technology can facilitate collaboration among researchers by enabling them to work together remotely and share information and feedback in real time. Digital tools can help researchers organize their research materials and notes more effectively, making it easier to keep track of important information and sources. In both domains, Google Drive is of great help.[ 17 , 18 ]

There are some disadvantages to using technology for research. Overreliance on technology can lead to a loss of critical thinking and writing skills, as well as a reduced ability to solve problems independently. The Internet and other digital tools can be a source of distraction and can hinder concentration and focus, potentially leading to lower-quality research and writing. While the Internet provides access to vast amounts of information, not all of it is reliable or accurate, which can lead to lower-quality research and writing. Not all researchers have access to the necessary technology and resources to complete their research effectively, which can create barriers to entry and hinder research progress.[ 19 , 20 ]

While we use the software applications for shaping our research paper, should we acknowledge them in the research paper as we mention humans who help us for similar task? Researchers mention the software package details, acknowledge any third party editing services, or copy editing by any human. However, they usually do not acknowledge the software. When it comes to word processing software, such as Microsoft Word or OpenOffice, it is not necessary to acknowledge them in a research paper. These tools are commonly used for writing and formatting documents, and their usage is expected. Regarding specific tools like Grammarly or ChatGPT, if substantial help was obtained, then acknowledging them would be appropriate. However, specific role to be mentioned for which the help was taken.[ 21 ] For example, refer to the acknowledgement part of this manuscript to have a glimpse on how we acknowledged ChatGPT for its help in this manuscript. Similar text can be added when help is taken from other tools.

Overall, technology can greatly benefit the research paper writing process, but researchers need to be aware of its limitations and potential drawbacks. By balancing the advantages and disadvantages of using technology, researchers can use it as a tool to enhance their research and writing while maintaining the integrity and quality of their work. Primary care physicians often engage in research activities; however, busy primary care physicians hardly get time for writing. Hence, these applications can assist them in organizing research data, writing manuscripts, and formatting citations and references.

This review paper has discussed the essential software programs that are highly recommended for novice authors writing a research paper. The software programs discussed include Open Office for typing a paper, Jamovi for statistical analysis, Zotero for reference management, Google drive for data storage and accessibility, Grammarly for checking grammar, QuillBot for paraphrasing, MeSH on demand for searching keywords and related articles, DOI for searching the literature, JANE for author search, various online websites for statistical analysis, and language-based AI for generating content for a research paper. Utilizing these essential software programs and maintaining a balanced approach to technology use, novice authors can produce higher-quality research papers and contribute to the advancement of their respective fields.

Financial support and sponsorship

Conflicts of interest.

There are no conflicts of interest.


We would like to acknowledge the use of ChatGPT (May 24 Version), an AI language model developed by OpenAI ( ), for assisting in the language editing of this research paper. ChatGPT helped improve the clarity and readability of the manuscript.

Ideas on Fire

Tools and Apps for Organizing Research Materials

by Cathy Hannabach | Oct 25, 2016

Tools and Apps for Organizing Research Materials - Close up of a computer motherboard

Popular culture often represents the stereotype of messy professor offices with giant piles of papers and books about to fall over, with the professors themselves struggling to find that one journal article or grade book they know must be in there somewhere.

Yet as Jessie Daniels and Polly Thistlethwaite point out in their book Being a Scholar in the Digital Era , most of the research materials and other stuff we accumulate these days is digital. Depending on our fields, that might mean any combination of articles, books, pdfs, videos, websites, images, audio files, emails, and documents.

Here are some key apps and tools for organizing research materials, teaching items, and all the other digital stuff we accumulate as scholars.

The art of organizing research materials

Digital resource management tools are your friend. A good digital resource management tool does a few things:

  • Captures resources as you come across them in your daily life
  • Organizes those resources into some semblance of order
  • Keeps resources from getting lost
  • And most importantly: Lets you find an object whenever and wherever you want it

To start setting up your digital resource management system, take a look at some tools that can help you start to organize all that digital stuff.

Browser bookmarks

You might already use these to bookmark websites you want to come back to later. In your web browser’s bookmarks settings, you can organize your bookmarks into nested folders and add tags for easy searching. This is a great way to group together websites for different projects, and search them later.

If you use bookmarks, make sure to back them up regularly when you back up your computer (if you don’t regularly back up your computer, this is a great time to start).

Evernote is awesome. It’s available for all your devices, and lets you capture, organize, and use all your research materials, as well as take note s on everything.

Evernote is a great way to keep track of your different projects . You can also use it to annotate pdfs, draft manuscripts, rearrange pieces of your writing, or make to-do lists.

Evernote is free.

DevonThink is a more robust version of Evernote, which can organize more file formats (video, audio, images, pdfs, documents, websites).

It also has a very cool artificial intelligence feature that can find conceptual connections between your research materials that you might not have noticed before.

DevonThink is not free, but it does have a free trial and educational discount.

Zotero is reference management software that lets you keep track of your academic sources (books, articles, websites, etc.).

Zotero also formats your references in the citation format of your choosing and can produce bibliographies for your scholarly projects. It integrates with Word and OpenOffice, allowing you to create citations as you write.

You can take notes on pdfs and sync across your devices. If you’re always thinking “I swear I have a pdf article about that somewhere…” or “What is the difference between APA and Chicago style again?”, Zotero can be a great solution.

Zotero is free.

Find what works for you

Here is a worksheet that helps you find the digital resource management tools that work for you.

You can use the worksheet to identify 3 resource management apps that you are curious about (there is a list of options in the activity worksheet, or you can find your own). You should play around with each one—read each app’s website, see what features and design it has, and maybe read a review or two.

Then you can use the worksheet table to evaluate each app, considering 4 main things:

What can it do? What can it not do? Are there any missing features that you could supplement with another tool?

What is the price? Does the price fit with your budget and needs? Is the price worth it for the value it delivers? Think about this realistically for your own life. Oftentimes a free app is the best option, but sometimes a paid app that frees up more of your time and energy than the free version can be worth it.

Do you like the app’s visual design? Would you want to look at it every day? This isn’t frivolous—if the design is going to bug you, you won’t use it. And the best project management tool in the world can’t help if you don’t use it.

How does it fit into your existing routines? Is it available for your devices and the way you want to engage with your projects? If you prefer to run everything on your phone, and an app only comes in a desktop or web version, maybe that’s not the best app for you. Or if you only intermittently have wi-fi access, maybe an app that only works with Internet access isn’t the best fit. Or if you hate bouncing between a ton of different apps, maybe the best app for you would be one that combines multiple functions (calendar, email, to-do lists, contacts, notes, etc.).

From these three, pick one to test out for the next 2–3 weeks. Sign up for an account (or if it is a paid app, try a free trial first), download the app, and add a few projects and tasks in there. I recommend choosing 2–3 projects to test out your app with, unless you absolutely know you want to stick with the app you chose. Try out the different features, see how the project management system fits into your daily routine, and evaluate how or if it helps you make progress toward your goals.

After 2 or 3 weeks, evaluate how the app has been working for you. If you discover that the app you chose isn’t working for you, swap out another one. Or maybe add an analog (physical, non-digital) one. The point is to try out digital resource management tools in your real life to see what works and what doesn’t.

Once you find the tools that work for you, you can start organizing all of your research materials, finding materials when you need them, and using all those materials to write your kick-ass interdisciplinary scholarship.

Author: <a href="" target="_self">Cathy Hannabach</a>

Author: Cathy Hannabach

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Long Paper ("ARW Requirement") Resources

  • Selecting a Topic
  • Preemption Checking
  • Planning and Organizing Your Research

Chat With A Librarian

If you need more information on this topic, please contact the reference desk:

by phone: 651-290-6424

via e-mail: [email protected]

Or, during regular work hours , you may chat with a Mitchell Hamline research librarian here.

Planning Your Research

A research plan is not appropriate for every research paper, but it will give you the elements of a plan that you can adapt to your project.

  • Sample Research Plan

Starting Your Research

Scholarly research often begins with a literature review of published articles from law reviews and journals. The MHSL collection includes all all major law reviews and journals  as well as many non-legal journals in a combination of online and print formats.

Law reviews are generally published by law schools and edited by students. They contain articles, essays and other commentaries on legal topics by professors, judges,attorneys and students. Law review articles often describe, from the writer's perspective, a current issue in the law, along with analysis of history and a proposal for change or resolution. They also contain extensive footnotes, with citations to primary and secondary authority related to the author's thesis.

You can find full text articles in HeinOnline (coverage goes back to first issue of most journals), Westlaw and Lexis Advance. You can find non-legal articles (for interdisciplinary topics) in the subscription databases found on the library homepage in the Databases A-Z list.

Organizational Tools

Once you find sources, you will need to keep them organized. Managing, organizing and citing references and sources can sometimes be a real challenge especially if you don't keep track of what and who you cite. There are many tools available to help you; ask your librarian or faculty advisor for advice on organizing research projects.

  • PowerNotes PowerNotes helps you gather and track your research, annotate your sources and add freestanding notes by topic or issue. The Library has an institutional account, so you can sign up for free with your Mitchell Hamline email address. Its many relevant features for law students include Bluebook compatibility.
  • Zotero Zotero collects all your research in a single, searchable interface. You can add PDFs, images, audio and video files, snapshots of web pages, and really anything else. Zotero automatically indexes the full-text content of your library, enabling you to find exactly what you're looking for with just a few keystrokes.
  • Mendeley Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.
  • Evernote Save notes, tasks, ideas, inspiration, images, or anything you find online. Syncs it all between your phone and computer, automatically.
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Expert Commentary

Organizing your research: A scientist’s tips for journalists

Maya Gosztyla, a Ph.D. candidate in the Biomedical Sciences Graduate Program at the University of California San Diego, provides an overview of literature mapping tools, RSS feeds, research management software and databases to help journalists organize their research.

A colorful pile of papers.

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Creative Commons License

This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License .

by Naseem S. Miller, The Journalist's Resource March 21, 2023

This <a target="_blank" href="">article</a> first appeared on <a target="_blank" href="">The Journalist's Resource</a> and is republished here under a Creative Commons license.<img src="" style="width:1em;height:1em;margin-left:10px;">

Journalists collect a lot of stuff while reporting, especially for big stories and projects: interviews, documents, research papers, articles. It can be overwhelming at times.

Academics too must collect a large number of documents. They use a variety of tools to organize their work, some of which journalists can also use to organize materials. 

During a panel at the 2023 Association of Health Care Journalists conference in St. Louis, Missouri, Maya Gosztyla , a Ph.D. candidate in the Biomedical Sciences Graduate Program at the University of California San Diego, shared her organizational approach as a scientist, which journalists can easily adopt. She’s the authors of 2022 Nature career columns, “ How to Find, Read and Organize Papers ” and “ How to Manage Your Time as a Researcher .”

Below is a list of tips and tools that Gosztyla shared during the panel.

1. Find related research with literature mapping tools.

When journalists report on a new study, it’s important to consider where that study fits into the larger body of research.

Pubmed and Google Scholar are go-to research platforms to find academic research . But they’re not the most efficient tools for finding research related to a specific academic study.

A better approach is using literature mapping tools , which show the connection between research papers.

“Imagine papers like nodes in a network,” Gosztyla said. “Each paper will cite other papers, and what you can do is make a giant map of all the papers in a specific subject area. And then you can see the hubs — what are the papers that everyone cites that you should probably read.”

Some of the popular literature mapping tools, which offer free versions, include ResearchRabbit, Inciteful, Connected Papers and Litmaps .

2. Stay on top of current research with RSS feeds.

Many journalists, especially those who write about academic research, subscribe to journal email lists. But that may not be the best option for organizing research.

“It kind of overwhelms your inbox after a while,” said Gosztyla.

Another common method is setting up keyword email alerts. Both Pubmed and Google Scholar let you set up email alerts for specific keywords. But that too can crowd your email inbox.

Gosztyla’s solution is using an RSS feed reader .

RSS stands for “really simple syndication.” An RSS feed reader — or RSS feed aggregator — gets all the new articles or studies published on a website and brings them together in a timeline that you can quickly scroll through.

Many websites have RSS feeds. Once you have a link for the RSS feed, you can then add it to a free or paid RSS feed reader.

Here’s a good explainer by Lifewire on how to find RSS feeds and add it to a reader.

Gosztyla spends a few minutes every morning scrolling through her RSS feed reader — her favorite is Feedly — to check for new published research in her field.

This August 2022 article from Wired lists some of the more popular RSS feed readers.

3. Use research management software to file your research.

10 things we wish we’d known earlier about research: Tips from The Journalist’s Resource

There are several free online tools that can help you store what you find during your research instead having dozens of open tabs on your browser.

A popular tool developed by and for journalists is DocumentCloud , where you can upload documents, search the text, annotate, extract data , redact and edit.

Another option, popular among academics, is Zotero . It’s a free, open-source reference management tool and can store and organize your research material, including PDF files.

You can use Zotero in a browser, but for a more powerful experience, download it and install the Zotero plugin for your browser. When you come across a study or article that you want to save, click the plugin. It will save the item to your desired Zotero folder. You can create many folders and subfolders, and also share folders. You can also highlight and annotate PDFs.

“If you’re not using a reference manager, I highly, highly recommend them,” said Gosztyla.

You can integrate Zotero to several apps and programs, including, Word, Google Docs and literature mapping tools like ResearchRabbit.

Some of the alternatives to Zotero include, Mendeley , EndNote , RefWorks and Sciwheel .    

4. Routinely read your research pile.

To stay on top of what you’re collecting, Gosztyla offered this advice:

Block out a time each week, like two hours on Fridays, to read. If you have a big pile, maybe devote a couple of days to reading.

And decide how you’re going to spend that reading time: are you going to devote it to do a deep dive, or just scan what you’ve collected, take notes and decide what to keep and what to toss.

“Maybe it’s your routine that every week you buy yourself a nice cup of coffee. You go to a certain cafe and you just read,” Gosztyla said. “So find a routine that you really look forward to and it’s something you want to do.”

5. Don’t forget to take notes while reading documents .

“Don’t ever read without highlighting or taking notes,” Gosztyla said. “Otherwise, you will forget it. I guarantee it.”

Write a small note, a blurb, on the material you read to remind you of its main takeaways and where it fits into your project. Do you need to email or interview the author with follow-up questions? Or read the authors’ previous work? Make a note of those.

In the next step, you’ll learn about organizing those notes.

6. You have collected. You have read. Now organize your work in a database.

Research management software can help you organize your documents, but it’s helpful to create a database of what you’ve collected, your tasks for each item, and maybe a summary and key points. You can use Google Sheets of Microsoft Excel to create your list.

If you want something other than a classic spreadsheet, you can try web applications like Notion.

Notion is a powerful program, which Gosztyla described as a “multi-use database tool.” Notion describes itself as an all-in-one workspace. You can use it to organize your research, manage projects and tasks, note-taking and even your daily journals. You can also integrate Notion with many other apps and tools.

It has a steep learning curve. Give yourself time to learn to use it before integrating it into your workflow. Notion has tutorials on YouTube and a wiki page . Gosztyla recommended Thomas Frank Explains YouTube tutorials. Frank is an author, YouTuber, and Notion expert.

Some alternatives to Notion include Airtable , Trello and Coda .

7. Go one step further with automation tools.

If you want to go a step further in your Notion journey, you can link a Zotero folder to Notion with a tool called Notero . Every time you add an item to your Zotero folder, it populates your Notion database.

Notion has many templates you can choose from. Or you can use Gosztyla’s template .

You can automate and integrate other apps too, to create a better workflow for your work. Some of the popular options are IFTTT — Short for If This Then That — which integrates apps, devices and services to create automated workflows, and Zapier , which connects web applications and allows users to create automated workflows.

Keep in mind, you don’t have to use all the tools listed above.

“Take the pieces that work for you and apply them to your life,” advised Gosztyla.

If you want to share a tool that’s helped you organize your research, you can reach me at [email protected] . You can reach Gosztyla on Twitter @MayaGosztyla .

About The Author

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Naseem S. Miller

Sacred Heart University Library

Organizing Academic Research Papers: Purpose of Guide

Purpose of guide.

  • Design Flaws to Avoid
  • Glossary of Research Terms
  • Narrowing a Topic Idea
  • Broadening a Topic Idea
  • Extending the Timeliness of a Topic Idea
  • Academic Writing Style
  • Choosing a Title
  • Making an Outline
  • Paragraph Development
  • Executive Summary
  • Background Information
  • The Research Problem/Question
  • Theoretical Framework
  • Citation Tracking
  • Content Alert Services
  • Evaluating Sources
  • Primary Sources
  • Secondary Sources
  • Tertiary Sources
  • What Is Scholarly vs. Popular?
  • Qualitative Methods
  • Quantitative Methods
  • Using Non-Textual Elements
  • Limitations of the Study
  • Common Grammar Mistakes
  • Avoiding Plagiarism
  • Footnotes or Endnotes?
  • Further Readings
  • Annotated Bibliography
  • Dealing with Nervousness
  • Using Visual Aids
  • Grading Someone Else's Paper
  • How to Manage Group Projects
  • Multiple Book Review Essay
  • Reviewing Collected Essays
  • About Informed Consent
  • Writing Field Notes
  • Writing a Policy Memo
  • Writing a Research Proposal
  • Acknowledgements

This guide is intended to help you organize and write a quality academic research paper. Also included are recommendations regarding how to manage specific course assignments. Note that, if you have specific questions about how to write a research paper, you should always seek advice from your professor before you begin. Specific requirements stated by your professor will always supersede instructions provided in these general guidelines.

Thanks to Dr. Robert V. Labaree of the Von KleinSmid Center Library for International and Public Affairs, University of Southern California Libraries , for sharing the content of this guide.

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Software for Research and Digital Notetaking

Most of us utilize a range of media when conducting research—we gather documents from online databases, as well as images, audio, and video files from the web. We review box after box of physical documents at the archives. We take notes from books as well as from journal articles we’ve downloaded as pdfs. Some of us conduct oral history interviews, by person or phone. It can be a challenge to keep so much diverse material organized, accessible, and easy to work with when you’re in the process of writing a major research paper or dissertation.

Fortunately, there are a wide array of digital tools for notetaking, generating citations, and organizing your research. Listed below are a few of the many available options:

A free, easy-to-use tool to help you collect, organize, cite, and share your research sources from your browser. Integrates with Word to generate bibliographies and citations quickly.

PhD dissertation writing software. Helps to retain, organize, and evaluate assertions, ideas, and concepts for your dissertation, prepares outline-structured notes and saves your time by eliminating tedious cut-and-paste work.

Scrivener is a powerful content-generation tool for writers that allows you to concentrate on composing and structuring long and difficult documents. Scrivener puts everything you need for structuring, writing and editing long documents at your fingertips. On the left of the window, the “binder” allows you to navigate between the different parts of your manuscript, your notes, and research materials, with ease. No more switching between multiple applications to refer to research files: keep all of your background material—images, PDF files, movies, web pages, sound files—right inside Scrivener.

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. The program automatically generate bibliographies, imports papers from other research software, helps you find papers based on what you are reading, and enables you to collaborate with other researchers online.


Powerful database software for organizing your research (available for Mac and PC). Take notes, import pdfs, images, videos, and audio files, cross-reference your documents, and more. FilemakerPro comes with built in templates for research notes, but it is completely customizable as well. Fully-searchable. Take advantage of a significant student discount by purchasing this software through the UVa bookstore.

Intuitive notetaking software that comes with Microsoft Office. OneNote is a digital notebook that provides a single place where you can gather all of your notes and information, with the added benefits of powerful search capabilities to find what you are looking for quickly, plus easy-to-use shared notebooks so you can manage information overload and work together with others more effectively. You can insert almost anything into a page, and create as many pages as you want in a notebook. Use to take notes and organize documents, images, websites and more in a user-friendly program with a great visual interface. (For PCs)

GrowlyBird Notes

The closest approximation to OneNote for the Mac--and it's free.Growly Notes lets you capture everything you’re interested in, all in one place. Pages can contain almost anything: formatted text, images, movies, audio clips, PDF files, tables, lists, web and file links, and drawings you create in Notes. There are no rules for where things have to go: put an image beside text or under it. Draw shapes on top of other notes. Put two snippets of text right next to each other. Click anywhere and start typing.

Omeka is a free, flexible, and open source web-publishing platform for the display of library, museum, archives, and scholarly collections and exhibitions. Its “five-minute setup” makes launching an online exhibition as easy as launching a blog.

A.nnotate is an online annotation, collaboration and indexing system for documents and images, supporting PDF and MS Office formats.

A reference manager for Mac and iOS users. Bookends can perform Internet searches to retrieve references and associated pdfs or web pages, or immediately find and import references for which you already have the pdf.

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9 Organizing Research: Taking and Keeping Effective Notes

Once you’ve located the right primary and secondary sources, it’s time to glean all the information you can from them. In this chapter, you’ll first get some tips on taking and organizing notes. The second part addresses how to approach the sort of intermediary assignments (such as book reviews) that are often part of a history course.

Honing your own strategy for organizing your primary and secondary research is a pathway to less stress and better paper success. Moreover, if you can find the method that helps you best organize your notes, these methods can be applied to research you do for any of your classes.

Before the personal computing revolution, most historians labored through archives and primary documents and wrote down their notes on index cards, and then found innovative ways to organize them for their purposes. When doing secondary research, historians often utilized (and many still do) pen and paper for taking notes on secondary sources. With the advent of digital photography and useful note-taking tools like OneNote, some of these older methods have been phased out – though some persist. And, most importantly, once you start using some of the newer techniques below, you may find that you are a little “old school,” and might opt to integrate some of the older techniques with newer technology.

Whether you choose to use a low-tech method of taking and organizing your notes or an app that will help you organize your research, here are a few pointers for good note-taking.

Principles of note-taking

  • If you are going low-tech, choose a method that prevents a loss of any notes. Perhaps use one spiral notebook, or an accordion folder, that will keep everything for your project in one space. If you end up taking notes away from your notebook or folder, replace them—or tape them onto blank pages if you are using a notebook—as soon as possible.
  • If you are going high-tech, pick one application and stick with it. Using a cloud-based app, including one that you can download to your smart phone, will allow you to keep adding to your notes even if you find yourself with time to take notes unexpectedly.
  • When taking notes, whether you’re using 3X5 note cards or using an app described below, write down the author and a shortened title for the publication, along with the page number on EVERY card. We can’t emphasize this point enough; writing down the bibliographic information the first time and repeatedly will save you loads of time later when you are writing your paper and must cite all key information.
  • Include keywords or “tags” that capture why you thought to take down this information in a consistent place on each note card (and when using the apps described below). If you are writing a paper about why Martin Luther King, Jr., became a successful Civil Rights movement leader, for example, you may have a few theories as you read his speeches or how those around him described his leadership. Those theories—religious beliefs, choice of lieutenants, understanding of Gandhi—might become the tags you put on each note card.
  • Note-taking applications can help organize tags for you, but if you are going low tech, a good idea is to put tags on the left side of a note card, and bibliographic info on the right side.

organizing research papers software

Organizing research- applications that can help

Using images in research.

  • If you are in an archive: make your first picture one that includes the formal collection name, the box number, the folder name and call numbe r and anything else that would help you relocate this information if you or someone else needed to. Do this BEFORE you start taking photos of what is in the folder.
  • If you are photographing a book or something you may need to return to the library: take a picture of all the front matter (the title page, the page behind the title with all the publication information, maybe even the table of contents).

Once you have recorded where you find it, resist the urge to rename these photographs. By renaming them, they may be re-ordered and you might forget where you found them. Instead, use tags for your own purposes, and carefully name and date the folder into which the photographs were automatically sorted. There is one free, open-source program, Tropy , which is designed to help organize photos taken in archives, as well as tag, annotate, and organize them. It was developed and is supported by the Roy Rosenzweig Center for History and New Media at George Mason University. It is free to download, and you can find it here: ; it is not, however, cloud-based, so you should back up your photos. In other cases, if an archive doesn’t allow photography (this is highly unlikely if you’ve made the trip to the archive), you might have a laptop on hand so that you can transcribe crucial documents.

Using note or project-organizing apps

When you have the time to sit down and begin taking notes on your primary sources, you can annotate your photos in Tropy. Alternatively, OneNote, which is cloud-based, can serve as a way to organize your research. OneNote allows you to create separate “Notebooks” for various projects, but this doesn’t preclude you from searching for terms or tags across projects if the need ever arises. Within each project you can start new tabs, say, for each different collection that you have documents from, or you can start new tabs for different themes that you are investigating. Just as in Tropy, as you go through taking notes on your documents you can create your own “tags” and place them wherever you want in the notes.

Another powerful, free tool to help organize research, especially secondary research though not exclusively, is Zotero found @ . Once downloaded, you can begin to save sources (and their URL) that you find on the internet to Zotero. You can create main folders for each major project that you have and then subfolders for various themes if you would like. Just like the other software mentioned, you can create notes and tags about each source, and Zotero can also be used to create bibliographies in the precise format that you will be using. Obviously, this function is super useful when doing a long-term, expansive project like a thesis or dissertation.

How History is Made: A Student’s Guide to Reading, Writing, and Thinking in the Discipline Copyright © 2022 by Stephanie Cole; Kimberly Breuer; Scott W. Palmer; and Brandon Blakeslee is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

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Donna Janell Bowman

Organizing a Mountain of Research

Posted September 20, 2020

organizing research papers software

Final fact-checking for King of the Tightrope: When the Great Blondin Ruled Niagara

11/10/22 ADDED NOTE TO PROVE THE VALUE OF ORGANIZED RESEARCH: In 2020, four years after Step Right Up published (even longer than that since I was in active research mode), I was contacted by a Hollywood producer who wanted to chat about the story. And this year, 2022, I have given two interviews to BBC about Doc and Jim. In both cases, I needed to refresh my memory and access my research, but I did not flail through random articles and notes. My binders were 100% organized, and my book bible (below) provided everything I needed in one place. 

One of my favorite things about writing nonfiction is research—part scavenger hunt and part archaeological dig into the past. But what’s the best way to organize the resulting mountain of research? It’s a question that always pops up in forums and writers’ groups. The truth is, there is no single right system. Much depends on the topic, the volume and type of materials, and most importantly, each person’s individual style.

Early in my writing career, I flailed my way through index cards, spiral notebooks, file boxes, endless manilla folders. The problem was that, when I needed to find a detail, fact, or quote, it was like searching for the proverbial needle in a haystack. So I pursued a more streamlined process—one that allowed easy access for my immersive writing style and comprehensive research style in a low-tech way. When it comes to my work, I want to be able to find what I’m looking for immediately. For some writers, software programs like Scrivener or Evernote are perfect tools for that goal and their own styles. For others, the spiral notebooks and index cards that make me a little dizzy, are ideal. To each her own! I experimented widely until I settled on a system that works for me. No doubt, my process will evolve over time, but here’s my current 4-step system:

#1— Research like the dickens—beyond the obvious sources

#2— Create digital file folders for thoughtfully-labeled, easily-sharable, digitized or scanned documents, interview transcriptions, etc.

#3— D-ring binders—the perfect adjustable container. * If the book is topical, I organize the binder by related sub-topics. * If the book is historical or biography, I organize chronologically, with necessary sub-topic categories, too. * I print the most reliable sources for the binder.

[rl_gallery id=”8948″]

#4 Create a Book Bible— * Open a Word document and turn on Navigation Pane or Document Map (usually under the Sidebar option) * Create category headings using a heading style, which automatically triggers the navigable sidebar, like a table of contents. Clicking on one of the headings jumps the cursor to that section of the document. No more scrolling. Nifty, huh? * Extract relevant quotes, details, information from the binder sources, books, and interviews, and type them under the appropriate headings, with citations. (Most often, a single source, like a book or newspaper article, has information that fits under multiple categories. For example, a single eyewitness account for King of the Tightrope can include rope information, Blondin’s background, Niagara details, and Blondin’s costume—all of which can be extracted for different category headings. This is especially important when there are conflicting details across sources. It’s much easier to scrutinize disparities when the accounts are in one place.

Creating a book bible is tedious and time-consuming, and the process makes me grouchy. But once completed, I feel empowered and confident. A single book bible (usually 50-100 pages for a picture book) contains the most relevant and important information for my book project in one Word document. When does it come in handy? When it’s time to craft a bibliography; when I need to share a source with my editor; when I’m knee-deep in revision or rewrites and need to quickly find information; if anyone questions the content in my nonfiction narratives. And just imagine how ready I’ll be if Hollywood comes knocking, or if an opportunity related to one of my books arises in the future, when the research is no longer fresh in my memory.

Could I write a nonfiction picture book without researching as deeply and as widely as I do? Probably. Could I wrangle the research without going the extra mile with my binders and my book bibles? Sure, but it would feel like wearing ill-fitting shoes. I know myself and my immersive writing and research style enough to know that condensing and containing information is what I need.

Writer friends, you do you. Whatever your style, however you roll, allow yourself time to flail around until you find what works best for your unique comfort level. In the meantime, I hope you’ll share your own suggestions in the comments.

Happy researching!

[rl_gallery id=”8935″] Above: Book bibles for Step Right Up (92-page document), Abraham Lincoln’s Dueling Words (54-page document), and King of the Tightrope (49-page document) Below: A Sample page from my King of the Tightrope book bible, with partial sidebar visible

organizing research papers software

7 Responses to “Organizing a Mountain of Research”

Donna, I’d love to hear more about your digital files. I keep folders and subfolders but think I could do better.

Also, for your print sources, do you scan each one which has relevant content?

I just shared this post as a resource and challenge in my nonfiction class. It’s so important to see a variety of ways to organize. Your Book Bibles are pretty amazing. I have not done that, but I can see how it would help in so many ways. Thank you!

Thanks for this sneak peek into your writing process! I always like to see how other writers go about their work. I also love doing research and discovering some unexpected nugget!

I’d like to try that Book bible – I’m sure there are soooooo many cool tools available like that Navigation Pane that I know nothing about. Thanks for sharing this!

I just set up the Navigation Pane with section & chapter heading styles for my WIP reference document. Subheadings will be next. Your tip started saving me time immediately–thank you!

Oh, I’m so glad, JoAnn! I hope you continue to find it helpful.

Donna, Thanks so much for sharing your process! It is very helpful. I tend to over research and end up with so much info, I become sidetracked with the narrow theme I know I have to stick to. All the best to you!

I hear ya, Sue. Nonfiction has unique challenges, and among the biggest is the research rabbit hole.

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