The Best Tools for Managing Academic Projects in 2025

Academic research projects are rarely solo ventures anymore. Whether you're supervising students, collaborating across universities, or coordinating with industry partners, managing the moving parts of a research project can be just as challenging as the science itself.

Thankfully, there’s been a rise in tools designed specifically to support academic workflows. In this post, we’ll highlight some of the best tools available today for managing academic projectsfrom planning and communication to writing and version control.

1. ResearchDock – A central workspace for academic teams

Best for: Research teams, supervisors, and academic collaborations

ResearchDock is a purpose-built platform for managing academic projects. Unlike generic project management tools, it includes features tailored to the research lifecycle:

Project Spaces: Organize projects by team, funding body, or research stream.
Manuscript Approval Tool: Upload drafts, automatically compare document versions, and consolidate feedback from co-authors in one place.
Task and Milestone Management: Assign tasks, set deadlines, and track progress with a clear overview.
**Paper suggestions: **Get suggestions of literature that are automatically inferred to be relevant to your work based on the context of your research
Central Hub: Keep reference libraries, meeting notes, and funding documents all in one hub.

Whether you’re managing a PhD supervision, multi-institution grant, or student cohort, ResearchDock brings the structure of project management without sacrificing the flexibility needed for academic work.

2. Notion – Flexible knowledge management

Best for: Personal research organization, literature reviews, lab wikis

Notion is a powerful, all-in-one workspace where you can create databases, notes, to-do lists, and more. Academics use it to track readings, manage research plans, or collaborate on lab handbooks.

Pros:

Beautiful interface
Highly customizable
Great for solo or small-team projects

Cons:

Lacks research-specific integrations (e.g., citation management, paper comparison, suggestions of relevant papers)

3. Overleaf – Collaborative LaTeX writing

Best for: Writing scientific papers, especially in STEM

Overleaf has become the default platform for collaborative LaTeX writing. Its version control, real-time editing, and journal templates make it ideal for co-authoring technical papers.

Pros:

Built-in journal templates
No LaTeX setup required
Version history and GitHub sync

Tip: You can use ResearchDock to manage the collaboration process (comments, approvals, version comparison) even if you're drafting the paper in Overleaf.

4. Zotero, Mendeley, and EndNote – Reference and citation management tools

Best for: Managing citations, building bibliographies, organizing academic literature

Every research project needs a solid system for handling references. Zotero, Mendeley, and EndNote are three of the most widely used tools—but they serve slightly different needs and preferences:

Zotero

Pros: Free and open-source, easy browser integration, strong community support, good tagging and note-taking features
Ideal for: Researchers who want flexibility and openness; integrates well with Word, LibreOffice, and Google Docs
Cons: Slightly less slick interface than commercial tools

Mendeley

Pros: Cloud-based, PDF annotation, collaboration features, integration with Elsevier journals
Ideal for: Users in STEM fields, especially those publishing in Elsevier journals
Cons: Owned by Elsevier, which may be a concern for open-access advocates; some features now behind a login or paywall

EndNote

Pros: Very powerful for large libraries, robust citation formatting, commonly used in institutional settings
Ideal for: Researchers in medical, legal, or life sciences fields with institutional licenses
Cons: Expensive for individuals, steeper learning curve

Bottom line:

Zotero is great for flexibility and openness.
Mendeley is good for integrated workflows and quick annotations.
EndNote excels in enterprise or highly formal publishing environments.

5. Slack or Microsoft Teams – Communication hubs

Best for: Keeping in touch with collaborators

If your team spans departments or institutions, a real-time communication tool is essential. Slack is widely used in academic startups and tech-oriented labs, while Teams is often used in universities.

Just be careful—too many messages can become noise. That's where structured tools like ResearchDock help keep communication focused around specific projects or documents.

6. Confluence – Structured knowledge management

Best for: Internal documentation, lab wikis, grant reporting

Confluence by Atlassian is a popular documentation tool used widely in corporate and technical teams. It lets you create structured pages, collaborate on internal documents, and build searchable knowledge bases.

Pros: Hierarchical organization, integration with Jira (for issue/task tracking), good versioning and templates
Cons: Feels overly formal or heavyweight for academic teams; lacks citation and reference support; more common in enterprise/engineering settings

While Confluence is powerful, many academics find it too rigid or complex for everyday use—especially when tools like Notion or ResearchDock offer more flexible, research-friendly interfaces.

Final Thoughts

There’s no one-size-fits-all solution for academic project management, but pairing the right tools together can save you hours each week and reduce the chaos of email chains and misplaced files.

If you're looking for a central platform built specifically with research teams in mind, ResearchDock is one of the best options to start with. It simplifies project collaboration, keeps manuscripts under control, and ensures nothing slips through the cracks.

Want to try ResearchDock? Sign up here.