Hello, will there be a workshop in Europe in the near future about Qiime2?
I’ll be teaching a QIIME2 section at the Workshop on Genomics in the Czech Republic in January. I think enrollment is still open for that workshop but am not positive.
I had a look at the workshop. It is quite expensive (I am a student). Still I want check if I can manage to get there (application is still possible). I will check if there is maybe a different price for students. If you don’t mind, could you please give me a little guidance on the following thoughts. I would really appreciate if I can get some guidance from people who have experience in bioinformatics.
My background is physical therapy (Bachleor of health) but especially Psychology (B.Sc.). Currently, I am in a M.Sc. Behavioral Science program and I focus a lot on Psychobiology. I am aware of the fact that I need to learn a lot if I want to incorporate microbiome data into possible future research projects. I will have the possibility to gain my first experiences with this during my master program (Behavioral Science). Within the last year I worked myself on learning Python a lot. I have now a good basis in Python. We currently learn R in that Master and I will learn also some microbiome data analysis in R. However, since I found out about Scikit bio, I think this is where I want to invest in since I want to focus on Python whenever possible.
So my goal is to learn how to do solid data analysis in the field of Psychobiology. For example analyzing data in longitudinal studies that have microbiome data, genetics data and other outcome measures. I want to be valuable for research groups in this field so that they would want to work together with me on their projects to let e.g. me analyze their data or help them with study designs. I saw on Gregs page that there is a nice resource for scikit bio. I could try to invest into this and learn this as good as I can. I already followed the course he recommended on coursera 2 years ago but this course of course is only a very basic course…
My most important question is:
- will this be worth the effort? I mean, would this be something that is really needed and appreciated in the scientific community? Or will there be more than enough statisticians in 3-5 years that could do that just as well? I am very motivated and curious but I need to wisely invest into the right skills now. Because I am 30 now and I want to not waste any time!
I forgot to ask in my previous post:
Do you think that my background is sufficient to attend such a workshop?
My Python skills are intermediate and basic/beginner in R. I have attended a good basic course in probability theory out side of my studies and had statistics in the B.Sc. Psychology and of course also in this research master. However, we will for example only learn about mixed effects models next year. I have no experience with bioinformatics yet but will gain on my first experience with microbiome data analysis in R next week…
I think statisticians are always needed
The Workshop on Genomics has a microbiome component but not an emphasis. It is more intended for a general survey of different techniques within the genomics fields, different approaches for handling those data, with a lot of hands on with the tools. There is sometimes programming but generally not. However, we do get into some advanced bash.
I can weigh in on this too.
First of all, there will be a need for people with statistics and programming backgrounds in many areas of biomedical research for the foreseeable future. This definitely includes microbiome research, and I would expect psychobiology research as well. Biomedical research now requires “data science” skills that haven’t typically been included in biology undergraduate or graduate training, so there is a gap that needs to be filled.
As @wasade mentioned, workshops like the Workshop on Genomics are generally great for getting hand-on experience with different bioinformatics tools. That’s a great way to get started with the software being used in a specific field. I haven’t been involved with that specific workshop, but I’ve heard very good things. @wasade didn’t mention this one, which is in Germany in December and is being taught by he and @antgonza. That one will be microbiome focused.
If you’re looking for something that is more focused on basic data science skills, like programming, working on a Unix/Linux command line, etc, you might see what Software Carpentry or Data Carpentry is offering in your area. There are also some great books on these topics - see for example the Reading List in An Introduction to Applied Bioinformatics.
A great way to learn, in my opinion, would be to work through some of those basic data science resources while at the same time starting to work with the bioinformatics tools that you want to learn, such as QIIME 2. This will give you a way to apply the skills you’re learning as you’re learning them, which typically helps me to learn quickly. Then, once you know which specific bioinformatics tools you want to learn more about, invest in attending a workshop that covers those tools. Having a little experience with those tools, while typically not required for a workshop, will probably let you get more out of a workshop.
Given your interest in psychobiology and longitudinal studies, you might be interested in our FMT tutorial which is based on a longitudinal study of children with autism who are treated with fecal microbiota transplant. The tutorial is based on a subset of the full data set, but you could start with that and then move on to the full data set once you’re comfortable. You could, for example, set a goal to reproduce the results in Figure 3 of the original study with QIIME 2 and the q2-longitudinal plugin - I expect that you’d be pretty comfortable with QIIME 2 and the command line when you met that goal. (If you’re going to go this route, you should still follow the order described in the QIIME 2 Getting Started guide.)
Hope this helps! Good luck and have fun!
thank you so much for taking the time to answer. This post is very helpful. I now applied for the workshop in Germany. No matter if I may join this workshop or not, I will run through the FMT tutorial for myself at the weekend and am confident that I can replicate the outputs. I read that paper related to the FMT data a few weeks ago before I wrote an essay related to autism.
Thank you both for your input!
I couldnt agree more. I am a physician and I think data science skills are vital nowadays if you want to stay competitive. Not only that, you get to be part of the ongoing scientific discussion only when you understand it. Plus, It s exciting when you can do so much on your own and so fun to learn new things. But be warned: you will learn to do things quickly but you WILL forget if you dont practice. it s like learning a new language.
I recommend some basic courses / tutorials that you can find on the internet s.a.:
also coursera courses are pretty cool. (Data science specialisation i.e.)
I also personally took the course “programming for evolutionary biology” offered by Katja Nowick and Rui Faria. it’s long, and it s intense but you learn SOOOOO much! would definitely recommend it.
good luck with everything! have fun in Braunschweig. Also @gregcaporaso…come on, only one course in Germany?? please show us some love.
Just to be clear, we are always happy to consider teaching a workshop, basically, anywhere in the world. As you can imagine, this takes some time to coordinate but we normally make it work.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.