This post is primarily for new members of FLMetab and provides an orientation to the software tools and infrastructure we use in our day-to-day research. Please read through this short document, install and familiarize yourself with the necessary programs. Don’t hesitate to ask for help.
Welcome to the FutureLab Social Metabolism & Impacts (FL Metab) at the Potsdam Institute for Climate Impact Research. This page will guide you through the process of setting up the various bits of infrastructure we use in our daily research practice. The page only discusses topics that are related the FL Metab specifically. Please also take some time to go through the general PIK welcome page.
Nextcloud is an open source cloud service (like Dropbox, iCloud, etc.) hosted internally at PIK to conveniently share data with people inside and outside the Institute. Simply download the Nextcloud client for your operating system (on Ubuntu, you can also add this ppa). Note that Nextcloud has version control which means you can go back to previous version of documents if something goes wrong. Once installed, connect to https://cloud.pik-potsdam.de using your PIK username and password. Make sure someone (e.g. Paul) adds you to the FL_Metab folder and other folders that might be relevant to your work.
Nextcloud provides this additional functionality:
https://cloud.pik-potsdam.deElement is a free chat software we use for non-sensitive mostly internal discussion on projects. It is also the easiest way to get quick help on anything you are working one. We have a number of rooms, some organized by topic (e.g. coding or economics) and some by specific projects. Ask Paul to get added to the rooms you are interested in. We are currently testing Element on a public server and you will need to make an account. You only have to give an arbitrary username (optionally an email to recover your password), no further personal information.
Zotero is a reference manager to collect, organize, cite and share literature references. It works well with a number of text editing software (e.g. RMarkdown, LaTeX, OpenOffice, MSWord). FL Metab has a shared library where we collect all of our literature.
We mostly use zoom for video conferences but there are limited licenses available. You can contact Paul to set up a meeting room if you need one. Alternatively, everyone with a PIK account can organize meetings using DFNConf which is the video conferencing software of the German Research Network
Git is a web-based version control system. PIK runs its own GitLab instance. Please have a look at the gitlab page on the intranet and these slides by Ciaron Linstead for help geting set up. For help on how to use git, especially with R and RStudio, please have a look here.
R is the default programming language in our research group. We use the RStudio IDE and strive to adhere to the Tidyverse style guide.
More resources on R can be found here
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Pichler (2020, Dec. 26). FL Metab methods blog: Software & Infrastructure. Retrieved from http://www.pik-potsdam.de/~pichler/metab/blog/posts/2020-12-26-software-infrastructure/
BibTeX citation
@misc{pichler2020software,
author = {Pichler, Peter-Paul},
title = {FL Metab methods blog: Software & Infrastructure},
url = {http://www.pik-potsdam.de/~pichler/metab/blog/posts/2020-12-26-software-infrastructure/},
year = {2020}
}