Johanna: Sebastian, you made a cheat sheet for linux bash commands and tricks. Did you know that I printed your cheat sheet, laminated it and use it regularly? How did you get the idea?
Sebastian: No, I didn't knew that and I’m very excited to learn that this cheat sheet is still used and considered helpful. How did I get the idea? Well, cheat sheets are quite common, at least from my experience, and in particular in computer science for all different kinds of aspects, techniques, and tricks. And having a brief and compact printout of the most important commands for the command line interface was something I hoped would be very helpful for the participants in our workshops. Also, this also underlines one of the goals we try to achieve in our courses, which is to enable people to help themselves rather than just asking right along.
Johanna: What makes the cheat sheet especially useful for computational biologists and bioinformaticians?
Sebastian: This is a difficult question to answer. First of all, anyone involved in bioinformatics should be familiar with any Linux shell - in this sense I wouldn't say that this cheat sheet is specifically tailored to computational biologists. The main motivation for me to design this cheat sheet was the fact that the publicly available cheat sheets on this subject were either too complex, too simple, or just didn't cover the parts I thought were more important to be used for our training activities. For example, in our annual de.NBI training course on metagenomics, participants need some prior knowledge of the command line, and if not, we recommend that they attend the upfront Linux introduction. Here, the participants will learn how to use simple commands like ls and cp, but also how to inspect the content of a FASTA file with grep & Co. And such a tailored cheat sheet helps immensely as a memory aid.
Johanna: Do you think it is important that scientists share their READMEs, cheat sheets and stuff like that?
Sebastian: Yes, of course, but with a slight caveat. First of all, any researcher should be transparent on what he or she is actually doing and how their main achievements, let it be a scientific outcome, a new algorithm, or a software tool, can be recreated, utilized or used. That would more or less cover the README part. For cheat sheets and shared information, which would all fit into some sort of advisory or introductory category, I think it is a bit more complicated. This clearly requires more effort and should be put in the right environment or perspective. What I mean is that you can’t have a sheet cheat on every possible topic and use it to solve almost every problem you might encounter without further investment. This is always just a starting point one can and should build upon.
Johanna: What is your most favorite “cheat” and why?
Sebastian: I have quite a few cheat sheets that literally plaster part of my office wall. But what I end up using the most isn’t actually a real cheat sheet but a printout of the confusion matrix of the corresponding wikipedia article because I always get confused about it.
Johanna: Where can we find your cheat sheet and did you also make other cheat sheets for bioinformaticians?
Sebastian: Well, this cheat sheet was created with cheatography, a web service that allows for a quite easy creation of such customized sheets while also making it public available to anyone. There you will also be able to find my one. This is by the way a quite nice resource to look up if you’re interested, I use some of theirs too. And no, I have not made any other one yet.