## getting started See [Ten simple rules for scientists: Improving your writing productivity](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006379_ ## 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](https://github.com/MaloofLab/Mueller-Moule-PeerJ-2016) for a good example. These issues are discussed in more detail by [Ram, 2013](http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-7) ## 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](https://www.zotero.org/) and we maintain a [shared lab library](https://www.zotero.org/groups/maloof_lab) 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](http://ggplot2.org/). [Cowplot](https://cran.r-project.org/web/packages/cowplot/vignettes/introduction.html) 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](https://affinity.serif.com/en-us/designer/) and [Affinity Photo](https://affinity.serif.com/en-us/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"](https://tpc.msubmit.net/cgi-bin/main.plex?form_type=display_auth_instructions) described in Instruction for authors in the Plant Cell. ["Creating Colorblind-Friendly Figures" using R](http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/) looks useful for R user.