For an overview of course goals, grading, policies, and so on, please refer to the syllabus. Here, I will focus on practical information to help you orient to the course.
You can email me (Jelmer, main instructor) or Zach (TA) any time, and you should generally expect to get an answer within 24 hours, certainly on weekdays. We prefer to be referred to simply using our first names.
Jelmer and Zach both have biweekly office hours, see the course’s home page on the Carmen Canvas site for times. You can reserve a slot by going to the Calendar on Carmen Canvas, clicking “Find Appointment” (right-hand side), then selecting this course and clicking “Submit”, and finally, clicking on a time slot in the main Calendar window and clicking “Reserve”.
Each module is one week, and for all except two modules we will meet twice: There are two brief instructional breaks that each affect a module this course (no Zoom meetings on Tue, Feb 9, or on Thu, Apr 1). Therefore, those two modules are “half-modules” with half the material of regular modules.
Material for each module will generally be published on the preceding Friday.
This GitHub website has all material for the course including slide decks, exercises, assignments, information about readings, and so on.
The Carmen Canvas site has the syllabus, Zoom and contact information, a calendar with all due dates, grades, and course announcements.
The instructors will mainly be communicating with you using CarmenCanvas Announcements. Make sure that you are set up to receive a notification whenever an announcement is posted – see this page for more information. If you haven’t received a notification by the first week of the course, go back to check your settings and your email Spam folder.
We will be reading parts of the following two textbooks:
Allesina S, Wilmes M (2019). Computing Skills for Biologists. Princeton UP. Available online through the OSU library here; you can also find a PDF on the Carmen Canvas website for the course.
This book will be referred to as CSB for short, e.g. “CSB Ch. 1” refers to chapter 1 of this book.
Buffalo V (2015). Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. O’Reilly Media, Inc. Available online through the OSU library here; you can also find a PDF on the Carmen Canvas website for the course.
This book will be referred to as Buffalo for short, e.g. “Buffalo Ch. 3” refers to chapter 3 of this book.
In most modules, we will read and, in class, work through a chapter of CSB, our main book for the course. In four of the modules, our primary reading will be a chapter of Buffalo so we can learn about project management and Markdown (week 2) and cover the shell and shell scripting in greater detail (weeks 4-6).1
In week 7, we will read part of the OSC documentation, and in week 13, we will read two papers related to automated workflow management, a topic largely omitted in both books.
Because all of the software needed for this course is available at the Ohio Supercomputer Center (OSC), we will be working at OSC. The way this works is that we can access the software through our browser after logging in at https://ondemand.osc.edu. We have an OSC “classroom project” for the course, and you will be asked to sign up at OSC in a pre-course assignment.
Because we will work at OSC, you are not required to install anything for this course, and we can accommodate all operating systems. However, you may still want to install software to be able to work locally: this optional assignment covers local software installation.
I have created a Carmen Canvas “assignment” for everything that I would like you to do outside of synchronous zoom sessions, including readings, exercises, graded assignments, and creating accounts. All these assignments have due dates associated with them so you can easily see in the Carmen Canvas course calendar when you are expected or recommended to do them.
Here are the different types of homework (Canvas assignments), and when you are generally expected to do them:
Readings: There are readings for every week, and you are recommended to read before the first class of the week.
Exercises: Most weeks will have one or more exercises. These don’t have to be submitted, but you are strongly recommended to do them and we may ask about them in class. It’s generally recommended to do these exercises after the second day of class of the week.
Graded Assignments: Three graded assignments (10 points each) are due on Tuesday just before our Zoom meeting in weeks 4, 7, and 9, each covering material from the week prior. These assignments should be submitted through GitHub; you will learn how to do this during the course.
Final Project: Your final project is divided into 4 graded components: a proposal (week 11, 10 points), a draft (week 13, 10 points), a lightning presentation (week 15, 10 points), and the final submission (April 16th, 20 points). These components (except for the presentation) should also be submitted through GitHub.
Setup: Computer setup such as signing up for a GitHub account or installing software.
Surveys: There will be three brief surveys – pre-course, mid-course, and post-course.
Overall, the Zoom sessions will be highly hands-on, so you should be prepared to be engaged during class. We will spend most of the time doing “participatory live coding” (or “code-along”), in which the instructor demonstrates and you are expected to follow along in your own terminal or console. During participatory live-coding, there will also be regular questions for students and small exercises.
During participatory live coding, it will be beneficial to either have a (very) large monitor or two screens/monitors. This way, you can see what the instructor is doing and also do this yourself.
If you don’t have multiple monitors set up with a single device, you’re welcome to connect to the Zoom sessions with two devices; e.g., a laptop and a desktop, two laptops, etc. If you have neither a large screen nor multiple devices, you’ll have to decide if you will put the Zoom window and your own coding window side-by-side, or if you can effectively switch between windows. (The latter will work best by using Alt+Tab (Windows/Linux) or Command+Tab (Mac), and by having as few windows as possible open in your workspace.)
You may occasionally be asked to share your screen, so try to have a setup where this is possible. For example, if you watch the Zoom session on an iPad, but code on a computer, do also connect to the Zoom session with your computer so you can share your coding screen.
Please keep your camera turned on as much as possible. This will be very helpful for the instructor, and probably for your fellow students too, in creating an engaging environment that resembles an in-person class meeting as much as possible. If you prefer not to have your camera on or have bandwidth problems, a note to the instructors about this would be appreciated.
Please have your microphone on mute by default, but feel free to unmute yourself whenever you would like to say something.
Do I need any prior experience with scripting/programming or the tools that we will use?
No. That said, this will probably not be an “easy” course especially for those that have no prior experience with any programming language or any of the tools that we will be learning about. You should therefore try to make sure you can invest several hours per week outside of class meetings to be able to do all the readings and exercises.
Will I need a powerful computer?
No. We will not be working with large amounts of data in this course and most or all of our work can be done at OSC. Therefore, you will not need a particularly powerful computer, or a large amount of hard drive space. But if your computer is very slow or nearly out of storage space, please do contact me to make sure you will not run into problems.
Should I buy paper copies of the coursebooks?
While the coursebooks can be accessed online and I also provide PDFs (see above), I recommend that you do buy a paper copy of the CSB book if you’re able to do so. If you’re working with sequencing data, I would recommend that you also buy the Buffalo book.
We will not cover the second half of CSB, which deals with LaTeX, R, and relational databases.↩︎
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