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Week 0 - Introduction

3-hours Zoom video-conference

Introduction of the Companions and Instructors (10 min)

Presentation of the IOC general workflow (Scheme) (15 min)

Presentation of the IOC tools (2 hours)

Zoom

We currently use the Zoom software for our video-conferences. They will be recorded and available off line in the psilo data server (see below)

Please, follow these guides lines for Zoom usage

  1. Use a local, desktop Zoom application instead of the online web application. You can download Zoom here
  2. Test your Zoom application once if you never used it. We will be happy to arrange a quick Zoom session a few days before the IOC if you feel that there may be an issue.
  3. Be sure that your internet connection is reasonably fast to allow the use of your camera. We much value visual interactions!
  4. Arrange a quiet local place for your Zoom weekly session. People talking around you are disturbing you as well as the other conference participants. If you cannot arrange to be alone in your office, please warn you colleagues well ahead the session that you will need peace.
  5. Use a headset with a built-in microphone. It's not a gimmick! There are now cheap headsets for video-conference that works well. Test your headset with your computer and Zoom well ahead the first IOC session.
  6. Prefer a Desktop (generally more powerful) to a Laptop computer.
  7. Use the largest screen you have (another reason not using a laptop). If you have two screens, even better, but then test zoom with your dual screen setup. We may have to leave open several windows and applications during the Zoom session.
  8. Be on time at the session!
  9. You are welcome to use the chat panel of Zoom to exchange links, code issues, etc., but Slack (see below) is likely better suited to this, especially because the Zoom chat is lost when the application is shutdown. Therefore, be sure to have you Slack board available during the Zoom sessions.

There are many other interesting functionalities with Zoom, which will be covered in the presentation.

Trello

One of our favorite tools is Trello. You will be invited to access to the trello board of the IOC. Not a lot to say about Trello. It is just a great tool to capture information, collaborate, and organize projects.

We hope that you will still use Trello for your own projects and purposes when the IOC is finished!

STARTbio

Our STARTbio web site is the hub where we connect all the training materials for IOCs. To access rapidly to your IOC-R, use this URL shortcut.

Here, you'll find all weekly lessons, exercises, instructions, etc.

Importantly, you, yes, you, are welcome to propose modifications or fixes to the STARTbio IOC web pages! Assuming that during this IOC you will become familiar with the use of GitHub, all you have to do is click on the pencil icon at the top of each page and propose your modifications in a branch of our GitHub startbio repository.

Slack

Slack is a workspace to exchange messages or files, follow conversations, communicate about issues and ideas.

If you haven't already done so, you will first need to open a Slack account by providing a username and password (you can also use authentication through Google or Apple).

If you have already a Slack account, you can connect to this account using this URL.

Attention!

If you have multiple login emails for your Slack account, it can become confusing if some of your workspaces are identified with one email and others with another email.

This might happen, for example, if you were invited to a Slack workspace with a different email than the one you initially used to create your first Slack workspace.

Get Slack app on your local computer

We really strongly recommend that you use a desktop version of the slack application on your computer(s).

Once installed, this desktop Slack application will connect to your Slack account(s) and import locally your workspace, including the workspace dedicated to this IOC

Apple Desktop Slack | Windows Desktop Slack

Last but not least, Slack is not an option for this IOC!

We will be extremely reluctant to communicate by email with you about this IOC.

Indeed, emails capture information very poorly, because very often the subject headings are poorly chosen (or not chosen at all...), conversations by email deal with heterogeneous subjects, the recipients of a series of messages vary over time, and other joyful things - the imagination of Internet users is limitless (and exhausting)...

Instead, use your IOC Slack.

GitHub

Git is a powerful versionning system. The software was implemented in web environments to create even more powerful system of continuous development and continuous integration.

This is the case of GitHub which we have chosen in ARTbio. GitLab is another option, which will not use here.

Disclosure

The learning curve of git and github is not steep for a biologist... which unfortunately means that you will have to make a substantial effort before understanding the benefit of GitHub and being able to manipulate it without discomfort. But if you make the necessary effort, rest assured that you won't regret it.

For a very good introductory journal to Git and GitHub, although a bit old, see this article

GitHub is also very good at teaching how to use it... You can go from there!

R and RStudio

We do not intend to redo yet another version of the introductory R tutorials: there are many of them, they are often excellent and deserve to be used!

Therefore, what is following is a rather classical plan to learn R and for each notion to be learned, we made not only one but multiple links to content built by other authors. This is the occasion here to thank them collectively for their efforts; detailed credits will be given in addition all along the following pages.

The most specific feature of the programming language R compared to other languages is its extensive and specialized support for statistical analysis, data manipulation, and visualization.

An overview of R and RStudio

Brief, but the essential is here or here. We will do the same, but at your own pace!

Do it yourself!

  • Familiarize yourself with RStudio, play with the different panels.
  • Create a new Rproject in RStudio, containing folders for your scripts, the input data and the output data.
  • Try to navigate between projects.

Thank you for your attention and see you next week 👏 👏 👏