#(Collaborative) Scientific Writing and Reproducible Research

Mathias C. Walter, M.Sc.
Bioinformatican Technische Universität München

Abstract

Concepts

Word, Markdown, LaTeX, Wiki, Dropbox, Version Control System (VCS) like GitHub.

Dropbox

• Notifybox provides Check-in / Check-out of MS Office documents and logs user interactions with files (Windows-only).

Reference Management

Not all tools can import several references at once (e.g. from the search results of a PubMed search), which would be a big time saver. Mendeley and Zotero allow you to do this.

Editors

Online Editors

• Prose is linked with GitHub.
• Dillinger can be linked with GitHub and Dropbox.

Editor Applications (offline)

• Gonzo is lightweight desktop markdown editor built using Adobe Air, AS3, and Flex 4.5.
• MarkdownPad
• WriteMonkey

Tools

• GitHub for Windows GitHub for Non-Programmers and Windows users! ;-)
• SparkleShare File sync ala DropBox but using a git server as backend.

Links

• How to ditch Word
• Mastering Markdown: 30 Resources, Apps and Tutorials to Get You Started
• Writing papers using R Markdown
• stypi_ An online realtime collaboration editor
• SpanDeX LaTeX based online collaboration writing platform
• smb_git git: A powerful tool to facilitate greater reproducibility and transparency in science.