- Personal Research Workflow
- Article Example Page
- Mediawiki for Scientists
- Kieran Healy's Writing and Presenting Social Science
- Matthew Butterick’s Practical Typography
Digital Research Tools
- A tutorial
- Academic writing with Markdown
- Markdown for academia
- Using Markdown like an academic
- Marxx - a markdown web app for science
- Scholarly Markdown and the art of academic writing - GIT repository
- Sustainable Authorship
- Using markdown + pandoc to write my biology PhD thesis
- Plain Text, Papers, Pandoc
- Slidify: Modern, simple presentations written in R Markdown
- Working With Multi-file Markdown Documents
Research with Mediawiki
- Mediawiki citations, references, and bibliography management
- Academic Phrasebank, University of Manchester
- Advice from University of Toronto
- Doctoral Writing SIG
- Explorations of Style
- Grad Hacker
- Research Voodoo
- The Research Whisperer
- Thesis Whisperer
- Git for Computer Scientists
- Git for Scientists: A Tutorial
- GitHub Help
- GitHub for Writers
- Pro Git Book
- Understanding Git Conceptually
- Learn Version Control with Git
Using Gists in Mediawiki
- <name>Example model</name>
Example: With GistHub extension
Feeding of Scientific Data 
Workflow management systems
- Taverna An open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.
- Wings A semantic workflow system that assists scientists with the design of computational experiments.
- Kepler Software designed to help scientists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines.
- VisTrails An open-source scientific workflow and provenance management system that supports data exploration and visualization.
Source code repositories
- Git A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
- Mercurial A free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
- Github A web-based hosting service for software development projects that use the Git revision control system, including many open source projects.
- BitBucket A web-based hosting service for projects that use either the Mercurial or Git revision control systems.
Systems to package, access, and execute data and code
- iPython Notebooks A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document.
- ROpenSci A suite of packages that allow access to data repositories through the R statistical programming environment.
- Authorea A collaborative online word processor for scholarly papers that allows the writing of web-native, living, dynamic, "executable" articles which include text, mathematical notation, images, and data. It currently support inclusion and rendering of d3.js and iPython notebooks.
- Dexy A multi-purpose project automation tool for working with documents via a command-line interface.
Data repositories (domain-agnostic)
- Dataverse A repository for research data that takes care of long term preservation and good archival practices, while researchers can share, keep control of and get recognition for their data.
- FigShare A repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.
- Zenodo A repository service that enables researchers, scientists, projects and institutions to share and showcase multidisciplinary research results (data and publications) that are not part of existing institutional or subject-based repositories.
- Dryad A repository that aims to make data archiving as simple and as rewarding as possible through a suite of services not necessarily provided by publishers or institutional websites.
Directories of research data repositories
- DataBib Databib is a tool for helping people identify and locate online repositories of research data. Users and bibliographers create and curate records that describe data repositories that users can search.
- re3data.org Re3data is a global registry of research data repositories from different academic disciplines for researchers, funding bodies, publishers and scholarly institutions.
- Open Aire
- Data repositories, Open Access Directory A list of repositories and databases for open data.
Software tools to run your own document repository
- Invenio Invenio is a free software suite enabling you to run your own digital library or document repository on the web. Invenio is an ideal solution to run document repositories of moderate to large sizes (several millions of records). Invenio is co-developed by CERN, DESY, EPFL, FNAL, and SLAC.
- Eprints EPrints is one of the easiest and fastest way to set up small to medium sized repositories of open access research literature, scientific data, theses, reports and multimedia. Developed at the University of Southampton, UK.
- DSpace DSpace is a turnkey institutional repository application developed by the Duraspace organization.
- Open Source Initiative, Licenses Open source licenses are licenses that comply with the Open Source Definition: they allow software to be freely used, modified, and shared. These include Apache, BSD, GNU (GPL), MIT, and Mozilla Public License.
- Privacy Tools for Sharing Research Data A Harvard-based collaborative and multidisciplinary effort to help enable the collection, analysis, and sharing of personal data for research in social science and other fields while providing privacy for individual subjects.
ACM Reference Format
- Authors Year. Title. Journal name, Volume (Issue), Pages.
- Arasu, A., Cho, J., Garcia-Molina, H., Paepcke, A., and Raghavan, S. 2001. Searching the web. ACM Trans. Internet Technol. 1, 1 (Aug.), 2-43.
ARTICLE IN AN EDITED BOOK
- Authors Year. Title, in Title of edited book, Name of editors ed. Publisher, City of Publication, Pages.
- Fischer, G. and Nakakoji, K. 1994. Amplifying designers' creativity with domain oriented design environments. in Artificial Intelligence and Creativity: An Interdisciplinary Approach, Dartnall, T. ed. Kluwer Academic Publishers, Dordrecht, 343-364.
- Authors Year. Book Title. Publisher, City of Publication.
- Fogg, B.J. 2003. Persuasive Technology: Using Computers to Change What We Think and Do. Morgan Kaufmann Publishers, Boston.
PAPER IN CONFERENCE PROCEEDINGS
- Authors Year. Title, in Title of conference, (Location of Conference, Year), Publisher, Pages.
- Leclercq, P. and Heylighen, A. 5,8 Analogies per hour: A designer's view on analogical reasoning. in 7th International Conference on Artificial Intelligence in Design, (Cambridge, UK, 2002), Kluwer Academic Publishers, 285-303.
- Latex Math Tutorial
- TEX Commands available in MathJax
- ShareLatex Guide
- SAGE Math
- ShareLatex Info
- TikZ Libraries
- Text based document generation
- AsciiDoc quick reference
- Getting started with Atlas
- Render AsciiDoc documents
- AsciiDoc writer's guide
- AsciiDoc plugins
- ChemDoodle and Macs in Chemistry
- Pandoc - A universal document converter
- pandoc document.md -o document.pdf
- pandoc document.md -o document.pdf --bibloiography citations.bib
- pandoc document.md -o document.pdf --bibliography cite.bib --csl style.csl
- pandoc -H margins.sty --bibliography Git_ms.bib --csl plos.csl Git_manuscript.md -o Git_manuscript.pdf
- pandoc document.md -o document.pdf -H margins.sty
- Styles: https://github.com/citation-style-language/styles
- Online Markdown editor
- Prose.io - For editing markdown directly in the GitHub repo
- Scrivener Toolbox + Another experience
- How to ditch Word
Alfred and Me
- Creative Applications, Processing Category
- Nature of Code
- Open Processing
- Processing 2
- XML in Processing
- Enthought Python Distribution (EPD)
- Python Documentation
- IPython Documentation
- SymPy Documentation
- Jupyter Notebook
- Efficient R Programming, Colin Gillespie and Robin Lovelace, 2017.
- R for Data Science, Garrett Grolemund and Hadley Wickham, 2016.
- Advanced R Programming
- Digital History Methods in R
- Goodman, A. et al. Appendix of 10 Simple Rules for the Care and Feeding of Scientific Data