Reproducibility

Reproducible analyses and results are critical. All particles published from the Maloof Lab should include: Access to raw data A Git hub repository that where a user can run code to reproduce all analyses and figures. See Mueller-Moule-PeerJ-2016 for a good example. These issues are discussed in more detail by Ram, 2013

Word Processing

Preferred editors are Google Docs and Word. A common workflow is to start in Google Docs so that we can do real-time collaborative writing and then transfer to Word for final formatting and citations.

Citation Management

Preferred citation management program is Zotero and we maintain a shared lab library of papers there. Ask Julin to add you as a member. Unfortunately there is not a clean way to use Zotero in Google Docs.

Getting started with Zotero

  • register Zotero (https://www.zotero.org/)
  • download standalone Zotero (https://www.zotero.org/)
  • tutorial https://www.youtube.com/watch?v=RuRF8zxkxIo#!
  • install extension (Zotero connecter) in your Google Chrome.
  • (option) install journal style (preference > Cite > click "Styles" tab > "Get additional style" > click "+" and select downloaded .csl file. > click install.

Images and Figures

It is recommended that data analysis figures be produced using ggplot2. Cowplot is useful for layout and formatting. If you need to do additional formatting, then save your plots as a PDF and edit using Adobe Illustrator (available on lab mac minis), or try Affinity Designer and Affinity Photo . Currently the lab does not have an Affinity license but if this would be helpful, let Julin know. Please follow "Preparing figures for color vision-deficient readers" described in Instruction for authors in the Plant Cell. "Creating Colorblind-Friendly Figures" using R looks useful for R user.