Take aways

[sr320]

What do you feel are two of the primary things you will take away from this course that would be useful in the future?

[skreling]

1. Sort of a joke, but also very much not - patience and determination are required for bioinformatics. I somehow thought that it would be a few commands and then you'd be good to go and you have this beautiful data; clearly that is not true.
2. There are myriad software choices and I find it difficult to choose which one, but turns out if you read enough you'll figure out the pros and cons to each pretty quickly and then its about figuring out what gives you the best and most accurate results
3. Working in command line is something I really hadn't done at all, so I think this was a good place to start and will allow me to build on it in the future. This class also exposed me to a lot of different types of software and different visualization tools that I will most definitely be using in the near future.

[jdduprey]

1. The ability to understand and use git+github, organize my work for the benefit of future me, and work collaboratively on many projects (not just bioinformatic ones) - has already been hugely helpful.

2. In the past I had done a little work in bash, jupyter lab, and R studio. But this class has really helped me see how they can all link together, when one will be more useful than another, and how they can interact. For example, having bash code blocks in jupytlab, running r + python scripts from the command line.

3. Working with quality control tools and pipelines has helped me better understand the structure of bioinformatic data, how junk data arises, and the sequencing/processing of genetic data before it gets to the bioinformatic process.

[aspencoyle]

1. When learning something new, do it systematically - don't just jump in! When first starting in the lab, I totally just jumped in without much of a mental framework for how each puzzle piece fit together (for instance, rather than trying to learn the basics of bash, I started with trying to do a specific task in bash). Having this class start at square one and build from there was extraordinarily helpful for me.

2. The importance of staying organized! I have a bit of a tendency to jump right in during data exploration, producing files first and then worrying about organizing them later. This works alright for smaller projects, but as I've learned, really doesn't work for larger projects. I've learned that by doing that organization upfront, it pays off in efficiency and reproducibility later.

[meganewing]

1. Don't be afraid to ask for help when you're stuck on something. I'm still working on this, but I've definitely started asking for help more compared to the beginning of the quarter. I'm super used to the "work alone" mantra that a lot of previous classes have drilled into me and was always worried it'd be burdensome to constantly ask for help. But this class has shown me that its actually more annoying when you don't ask for help because a problem that would take hours for me to figure out on my own can be solved in minutes if I just post a discussion.

2. Being persistent and patient when it comes to computers and learning new things. I'm very much the type of person who gets frustrated easily when I try something for the first time and I'm not instantly good at it, or can't fully understand a new topic I've learned right away. There was a point during the quarter (I think around week 5) where I just seemed to be hitting error after error and thought to myself "well.. how bad would it be if I did drop the class. Not like I need it to graduate" (which is a bit dramatic on my end). But I stepped away for a bit, asked for help (🙄 see above lol), and tried again. Eventually I got it. And earlier today I ran through the same steps I was struggling with back then and didn't even bat an eye.

There were tools that were super useful to learn too (fastqc, kallisto, git/github) but honestly I think these ^ are the lessons that will be most broadly applicable to me going forward, even if I don't end up doing anything with bioinformatics in the future (though I doubt that will be the case since we're living in the age of computers). I also 100% agree with Aidans take aways but didn't want to just repeat what he said :)

[Brybrio]

1. I spent multiple days before this class trying to make sense of how to process the salmon genetic data and it would have taken me much longer to complete the whole pipeline if I had not been introduced to the basic concepts and functionality of UNIX and related software that I skipped to jump into a project with some documentation. So I will attempt to thoroughly explore and understand the basics of programs and their purposes before using them on my data.
2. These analyses can be quite challenging... I keep hearing that everyone encounters big issues at some point during genetics work, and I would doubt that. But it happened to me already in labwork and now with my sequence data. I am currently having issues in what should be a fairly simple step of demultiplexing, so just learning to be prepared to face these challenges as they come along while working with bioinformatics.

[dippelmax]

1. Like a lot of other people, I think patience is the most important thing I have learned in this class. Even though I have just been auditing the class, have still been stressed by the difficulties evolved with coding. Learning to code, in this class and others, has been the largest academic struggle I have had throughout college because it doesn't seem to come naturally to me. I'm really glad I have kept coming to class throughout the semester. I'm in such a better position for graduate school because of what I have learned here.
2. Learning the basics of terminal, bash, github, jupyter lab and other programs will be incredibly helpful to me in the future. I am no longer limited to R studio which is an excellent position to be in. Not only do I have knowledge of basic commands, but the vocabulary to explain what is going wrong and what I do not know.

[laurel-nave-powers]

1. I think one of the most important things I learned in this class is how to organize and plan out your work. Learning and getting comfortable with GitHub and Jupyter Notebooks has taught me a lot about project organization and best practices. This will be very helpful for me going forward.
2. The other important thing I learned was how powerful working in the terminal can be. I always found it scary before this class, but now I feel comfortable and have a good appreciation for it. Generally, I am taking away an understanding of how challenging and time consuming even the seemingly simple tasks can be.