Scientific Writing and Scholarly Publishing: Writing tools

Scientific writing can be done collaboratively using a number of tools that allow researchers to work synchronously, ensuring all team authors are seeing the most current edits. Here are some featured products:

• Authorea (Wiley) - a free online platform for researchers to create, edit, and share documents. Add tables and figures, live data, equations, and dynamic charts. Supports LaTeX for writing with mathematical formulas and includes a large library of writing templates.
• Google Docs - a free platform for creating and editing documents collaboratively. Includes education, report, and business templates. Integrates with the SciWheel reference manager (UCSF subscription) through a Google Docs add-on, as well as Paperpile (free trial) and Zotero (free).
• Manubot - a free, open source authoring platform built on a Git repository. Requires some coding. Authors write their manuscript in Markdown and convert it to .html, .pdf, or .doc file formats. Read more about Manubot. 
• Microsoft Word - the web (cloud) version of Word is available through Microsoft 365 to all with a UCSF email address. Allows collaborative editing within UCSF and document history. Integrations are available for several reference managers, including SciWheel (UCSF subscription), Zotero, Mendeley, and ReadCube Papers. 
• Overleaf (Digital Science) - an online LaTeX editor that includes thousands of writing templates. Free accounts are limited to one collaborator. Paid accounts include real-time track changes, document history, and integrations with Git, GitHub, Mendeley, and Zotero.

AI features, such as automated suggestions for keywords and related articles, are built into many content platforms. Generative AI tools (Gen AI)  use a machine learning model to create new content, such as text, images, and code, based on large amounts of data the model is trained on. 

AI training materials

• Generative AI Foundations series (Library, CLE) - video recordings of four workshops: What is machine learning? Large Language Models (including ChatGPT), Image generation technologies, and AI ethical considerations
• AI resources for educators and learners, compiled by the School of Medicine

Publishing and NIH guidelines for the use and disclosure of AI tools in authorship

Before using an AI tool for preparing your paper, note that the use of AI programs for creating text and images is restricted or prohibited by many journals and funders, and the use of any Gen AI for manuscript preparation should be disclosed. An AI tool does not meet the requirements for authorship.

• AI and defining the role of authors and contributors from the International Committee of Medical Journal Editors (ICMJE)
• Use of AI to conduct a study should be disclosed in the Methods section per ICMJE
• Authorship and AI tools position from the Committee on Publication Ethics (COPE)
• Example publisher policies on author use of Gen AI and AI-assisted technology: Elsevier | JAMA | Springer Nature
• NIH prohibits Gen AI tools for peer review of grant proposals, and allows them within limits for grant applications

Tips for using Gen AI responsibly

• Consider Gen AI as a writing and research assistant, and not as a tool for replacing your own writing.
• Always review Gen AI outputs for accuracy.
• Never share sensitive data outside of UCSF Versa or another person's unpublished manuscript or grant proposal with an AI tool.
• Avoid sharing your unfunded research ideas with an AI tool, since many of them train their models on user inputs. You may also opt your data out of training by AI and online programs you sign up with.
• Consider the environmental impact of AI tools and whether a less energy-intensive resource would suffice.

UCSF-provided

• Covidence - a systematic review, meta-analysis, and clinical guideline tool which uses some AI features. Covidence helps researchers screen references, extract data, and keep track of their work. Learn how to sign up through UCSF's subscription.
• Grammarly - reviews your writing in email, Word, Google Docs, Papers, and other programs and suggests spelling, grammar, punctuation, and tone improvements.
• Turnitin Similarity Self-Check - available through the UCSF Collaborative Learning Environment (CLE), this tool allows authors to compare their manuscript to published articles and UCSF papers for text that could be detected as plagiarism. See how to interpret a Similarity Check report.
• UCSF Versa - a protected environment for UCSF faculty, staff and learners to interact with Gen AI technologies. Includes Versa Chat (free) and Versa API (subsidized). Approved for UCSF protected P2, P3, and P4 data. See Versa FAQs on the UCSF wiki.

Selected additional programs
Commercial AI platforms offer free and paid (Pro) plans. Follow the guidelines outlined above and do not share sensitive data or another person's intellectual property (e.g. a publication manuscript or grant proposal).

• Claude (Anthropic) - text generation, summarization, content creation, coding, and problem-solving. Uses security features including account verification by phone/text. Opus model for writing and complex tasks comes with Pro. Mobile app and API available. See overview video and help documentation.
• Elicit (Ought) - a research assistant for researchers and academics, focusing on automating literature reviews. Uses Semantic Scholar as literature corpus. Unlimited summaries of 4 papers at once with free account or 8 papers with Pro account. Systematic review workflows come with Pro account. See video tutorial and overview article.
• Perplexity (Perplexity AI) - produces generative text based on user prompts. Source documents are cited and are based on live Internet searches. Users can limit sources to scholarly papers, upload documents for analysis, and create images (Pro account). See an introductory video.
• SciSpace (SciSpace LLC) - a research tool for searching and summarizing scholarly articles, writing, detecting AI writing, generating citations, and extracting data from publications. Exporting requires a premium account. See a video comparison of SciSpace and Elicit.
• Scite (Research Solutions, free trial) - conduct full text literature searches via an AI research assistant and see context for citations in the literature (Smart Citations and Citation Statements). Free browser extension helps analyze how a research article has been cited.