DataScience Workbook / 09. Project Management / 3. Resource Management / 3.4 Documentation Improvement Tools / 3.4.2 Tools for Research Documentation


In the evolving research, maintaining meticulous and organized documentation of a project is pivotal for reproducibility, clarity, and collaboration. This tutorial aims to introduce you to a variety of tools that can streamline your research process and lead a project to the success. From note-taking and collaborative writing to data visualization and version control, we’ll delve deep into each tool’s functionalities, offering hands-on examples and tips to optimize your documentation efforts.

Unlocking the power of documentation

Documentation is a multifaceted pillar that supports more than just code — it’s integral to the entire spectrum of research activities. A well-documented project sheds light on the intricacies of the research process, paving the way for success. It amplifies clarity, ensures repeatability, and garners increased credibility for the research undertaken. Beyond its immediate benefits, documentation acts as a reservoir of knowledge, allowing researchers to effortlessly revisit previous works, retrieve pivotal methodologies, and draw insights for subsequent projects. This archival quality not only conserves precious time but also acts as a catalyst for elevating productivity and innovation in future endeavors.

Tools for Research Documentation

Tools for research documentation play an essential role in streamlining and organizing the vast array of information generated during research project. These tools encompass note-taking applications, collaborative writing platforms, reference managers, and data visualization software, among others. By facilitating precise documentation, they enhance the clarity, reproducibility, and dissemination of research findings. Moreover, they act as repositories, allowing researchers to effortlessly revisit past projects, thus fostering continuous learning and improvement. In essence, these tools are indispensable for modern researchers, aiming to maximize productivity and the impact of your work.

Digital Laboratory Notebooks

Digital Laboratory Notebooks (DLNs) provide an innovative solution for researchers to chronicle their experiments, observations, and findings in a digital format. They replace traditional paper lab notebooks, offering features like data integrity assurance, traceability, compliance with research standards, and enhanced collaboration. By integrating with various lab equipment and software, DLNs simplify and elevate the process of research documentation, making data transfer and management easier.

Digital Laboratory Notebooks (DLNs) have revolutionized the way scientists and researchers document their experimental processes and results. The adoption of these platforms ensures enhanced reproducibility, compliance with research standards, and seamless collaboration among research teams. DLNs provide tailored solutions that cater to various scientific disciplines.

Open-source tools:

tool description
ELabFTW eLabFTW is an open-source electronic lab notebook (ELN) and laboratory information management system (LIMS). It’s made by researchers, for researchers, and aims to be flexible and user-friendly. FREE
OpenBIS OpenBIS is an open-source software framework for constructing user-friendly, scalable, and powerful information systems for data and metadata acquired in the life sciences. FREE
SciNote SciNote offers practical solutions for researchers with features like electronic lab notebook functionalities, task management, and team collaboration. While SciNote offers premium versions, it does have a free version that can be quite useful for individual researchers or smaller teams.
Jupyter Notebooks While not a traditional ELN, Jupyter Notebooks are popular among researchers, especially in computational fields, for blending code, output, and documentation in a seamless manner. FREE
If you're part of an academic institution or are comfortable with setting up and maintaining software, hosting an open-source tool on institutional servers or cloud services might be a viable option. However, always ensure data privacy, regular backups, and compliance with any institutional guidelines when doing so.

Commercial tools:

tool description
Labguru Labguru is favored among life science researchers for its intuitive interface and specialized features. They provide packages for academia and industry
Benchling Benchling is extensively used in molecular biology and genetic engineering fields, given its adeptness at handling DNA sequences and related data. Initially offered a free version for academics, but with limited features.
LabArchives LabArchives offers versatility, catering to a wide array of scientific domains from physics to chemistry, ensuring structured and searchable documentation of research activities. Has both a free version and professional versions; the free version is quite limited.
feature ELabFTW OpenBIS SciNote Jupyter Notebooks Labguru Benchling LabArchives
Platform Type Open-source/Cloud-based Open-source/Cloud-based Open-source Open-source/Cloud-based Cloud-based Cloud-based Cloud & On-Premises  
Target Audience Academia & Research Academia & Research Life Sciences Computational Fields Academia & Industry Academia & Industry Academia & Industry
Molecular Biology Tools Basic Basic Advanced Not Specific Basic Advanced (DNA/RNA sequencing) Basic
Collaboration Tools Yes Yes Yes Yes Yes Yes Yes
Integration with Lab Instruments Limited Limited Yes Limited Yes Yes Yes
Data Storage Limit Varies by Hosting Varies by Hosting/Plan Varies by Hosting Depends on Hosting Varies by Plan Varies (Unlimited for Academics) Varies by Plan
Customizable Workflows & Templates Yes Yes Limited Not Specific Yes Yes Limited
API & Integration with Other Software Yes Yes Yes No (but has version control) Yes Yes Yes

Note-taking Tools

Note-taking tools, such as Evernote, Notion, and Microsoft OneNote, are versatile software solutions tailored to seamlessly capture, organize, and store a wide range of information. All of them offer free versions with basic features, but they also have premium tiers with additional functionalities. For open-source alternatives, consider tools like Joplin, Zim, and Standard Notes. They cater to diverse needs, from jotting down lecture insights to brainstorming sessions, supporting multiple formats like text, images, and voice. Equipped with organizational features like tags and notebooks, they’re indispensable for scientists aiming to methodically document their thoughts and findings.

Here’s a table summarizing the features and applications of the selected note-taking tools:

tool key features applications
Joplin open-source, end-to-end encryption, markdown support, web clipper, synchronization capabilities note-taking, to-do lists, web clipping, journaling
Zim open-source, wiki-style linking, rich text formatting, plugins, desktop integration personal wiki, note-taking, task management
Standard Notes open-source, end-to-end encryption, extensible with editors and themes, cross-platform secure note-taking, journaling, knowledge storage
Evernote web clipper, OCR on images, templates, tags, integrations with third-party apps note-taking, web clipping, project management, journaling
Notion blocks-based structure, templates, database capabilities, collaborative workspace note-taking, project & task management, knowledge base, collaborative docs
Microsoft OneNote free-form canvas, handwriting support, integration with Office suite, templates digital note-taking, sketching, team collaboration, meeting notes

Collaborative Writing Platforms

Collaborative writing platforms, like the open-source tool Etherpad and commercial solutions such as Google Docs and Microsoft Word Online, enable multiple users to co-author, edit, and review documents in real-time. These platforms, equipped with features like live editing, commenting, and version control, are essential in fostering teamwork and synchronicity in research projects. By simplifying collaborative efforts, they ensure the accuracy, consistency, and timely completion of research documentation.

The table should offer a clearer and more concise view of each tool, their features, applications, and the nature of their accessibility and pricing.

tool key features applications access
Etherpad real-time collaboration, lightweight, plugins collaborative writing, note-taking open-source, free, no account required
Google Docs real-time collaboration, commenting, integration with g suite, version history collaborative document writing, academic papers, reports free, account required
Microsoft Word Online real-time collaboration, integration with Office 365, templates collaborative document writing, academic papers, reports free with office 365 subscription, account required
Overleaf real-time LaTeX collaboration, error highlighting, publisher templates technical & academic papers, theses, LaTeX projects free & subscription tiers, account required
Authorea supports LaTeX and rich text, integration with data repositories, commenting scientific writing, academic papers, data visualization free & subscription tiers, account required
Papeeria LaTeX editing, real-time collaboration, version control LaTeX document creation, academic writing, theses free & subscription tiers, account required
GitBook collaborative writing, version control and Git integration, markdown support technical documentation, educational guides & tutorials, handbooks free & subscription tiers, account required, public & private visibility
If you're affiliated with an academic or research institution, Microsoft Word Online might be included in your institution's Office 365 subscription, making it free for you to use.

When drafting scientific papers, remember that many journals provide templates in either Microsoft Word or LaTeX formats; the latter can be conveniently edited using Overleaf.

Additionally, Google Docs, with its Paperpile plugin, offers a seamless experience for collaborative writing by simplifying the online search and management of citations.

Reference Managers

Reference managers, such as the popular and free-to-use Zotero and Mendeley, streamline the process of collecting, organizing, and citing academic materials. These tools, often equipped with browser plugins, simplify the creation of bibliographies and annotations. Reference managers, are essential in academic and research settings, simplifying citation management and bibliography creation, thereby ensuring accuracy and consistency in scholarly writing.

This table provides a quick glance at which word processors each reference manager can integrate with.

tool key features compatible word_processor
Zotero Zotero stands out for being both free and open-source, offering capabilities for easy source annotation, categorization, and consistent formatting. Its browser integration makes source capture straightforward, while its diverse citation styles cater to a myriad of academic requirements. Microsoft Word, LibreOffice, Google Docs
Mendeley Mendeley is renowned for its integrated academic social network and cloud-based approach, ensuring researchers not only manage references but also collaborate and discover new research. Its functionality extends to PDF annotations, public and private groups, and consistent citation styles. Microsoft Word, LibreOffice (linux)
EndNote EndNote is a widely-used commercial option, known for its comprehensive features and integration with various word processors and comprehensive reference management capabilities. Paired with its ability to search international databases and retrieve full-text articles, it offers robust organization, synchronization across devices, and versatile formatting options. Microsoft Word, Apple Pages, OpenOffice
Paperpile Paperpile shines with its deep integration into Google Workspace, especially Google Docs. Its straightforward and modern interface makes reference management, PDF annotations, and online citation search streamlined, catering specifically to the needs of collaborative researchers in the digital age. Google Docs, Microsoft Word (via plugin)
It's worth noting that while some integrations come built-in, others might require separate plugins or extensions to function properly. Always refer to the official documentation for specific integration details.

Data Visualization Tools

Data visualization tools adeptly convert intricate datasets into clear and interactive visuals, offering diverse representations like graphs, charts, and maps to aid in data interpretation and presentation. These tools bridge the gap between raw data and comprehensible insights, making communication more effective.

For detailed tutorials on Data Visualization Tools and methodologies, refer to section 08. Data Visualization, which includes topics such as Introduction to Scientific Graphic Design and Introduction to Scientific Graphing, providing hands-on examples with tools like Adobe Creative Cloud, Gnuplot (creating plots in the UNIX shell), Plotly-Dash (data processing & interactive plotting with Python), and RStudio (data processing & plotting with R).

Further Reading

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