Women in computing: a journey into bioinformatics with Erin Baggs
For many in the bioinformatics world, learning to code is a leap into the unknown. What’s it like doing a bioinformatics PhD?
For many in the bioinformatics world, coding is a leap into the unknown. This was the case for Erin Baggs, who has learned from scratch how to apply computational science to biology while doing her PhD with Ksenia Krasileva. She gives us an insight into what life is like for a PhD student, and how to negotiate the intrepid plunge into the choppy sea of coding.
What does computing mean to you?
I really enjoy it, there is a lot of diversity and freedom on what you can work on, what is great is that you can approach problems in different ways but both can be correct. I find it really interesting to discuss an approach with others and see how they may have thought about the problem completely differently.
Although overall I love it, some days can feel like banging your head against a brick wall in search of where you have used something that conflicts with the programming logic or a spelling error, all too often my spelling errors are additional spaces but this in the past has taken me over an hour to find.
Did you ever think that you’d end up coding for a living??
Nope, I didn’t really understand what coding was and thought it was mainly used to play and create computer games, crime and intelligence services.
What was the PhD interview like?
It was stressful beforehand due to only having a few minutes to prepare due to a logistical miscommunication with the interview scheduler. Despite this the interview was ok, the panel of scientists from the research park were really friendly when they introduced themselves first and they seemed to be willing me to respond well.
It was nice to talk with others who seemed so excited and interested in the science I had done previously and what I wanted to do in the future. They did not ask me very much in the way of technical details but more seemed interested in my enthusiasm for science and willingness to learn.
How long did it take you to get to grips with coding? Was it easy to pick up?
It is definitely easy to pick up as it is quite intuitive as commands often have a logical name. For me there were three key factors that allowed me to feel more confident:
1. Practice. It takes time for the coding to become comfortable to the point you do not really think about how to translate simple processes you want to turn into code in your head prior to starting.
2. Taking the time to learn the logic behind coding. This is really useful to understand as it is often transferable between the different coding languages (e.g. perl, python, C...). Additionally it means you understand why you write things in certain ways and helps you to make sense of why your code may be flagged as a mistake or if it is doing something you did not intend it to.
3. Knowing how to phrase google searches about code. This may sound naive and silly but the bioinformatics community is really friendly and for nearly any problem you have you can find a cheat sheet or answer online already.
Erin learnt from scratch how to apply computational science to biology.
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What’s your PhD all about?
I am studying disease resistance in plants provided by a group of similar genes known as NLRs. They provide innate immunity in plants and are similarly diverse to animal MHC genes.
We are trying to use our understanding of plant evolution as a focal tool in our study of these genes. By identifying genes that are conserved over long periods of evolutionary time we can infer that these genes may be important, hence their retention.
We can also look for anomalies, such as species which have a different number of NLRs compared to species that have shared a common ancestor recently. One case we are particularly interested in is maize which has far fewer NLRs than other cereal grasses despite their close relationship.
How a-maize-ing is maize?
It is very interesting that it is resistant to so many diseases yet it has so few of the genes we normally expect to provide protection. We have been wondering if the genes it does have are really good compared to other grasses or it has developed another aspect of disease protection that enables maize to stay healthy.
Sweetcorn in tuna mayonnaise sandwiches: yes or no?
Yes, no question it tastes good and is one of your 5 a day. What more could you want?
[Ed. Pete strongly disagrees! Capers all the way.]
You’re moving to California soon, how’s your surfing? Will you even be able to concentrate on a PhD with all that sunshine?
My surfing is wobbly but I am looking forward to having a go, although I am not sure I will be so enthusiastic after I inevitably headbutt the board.
The sunshine will be glorious after this awful winter and I am super excited to meet all the people at Berkeley as the few I met when I stopped by earlier in the year were all really friendly. I am also really excited to hear about new projects as it always makes me feel really inspired for how I could use new techniques on my work. They have lots of CRISPR studies happening at the moment which seem to be leading to some rapid, exciting discoveries. I think I will be really enjoy both soaking up the sun and the science.
Do you reckon the machines will take over the world?
I think computer based technology is already and in the future will provide even greater tools to help us make every day life easier. I cannot wait to have a self-drive Tesla although I may have to come up with some creative plans in order to afford it.
What’s the most sucky thing about coding? Have you ever wanted to throw your computer out of the window?
Not out the window but down the stairs though that was more due to my clumsiness than any disdain for coding. It is definitely really annoying when you can’t work out what you are doing wrong and it holds up your plans for a long time, then when you find the mistake it is so small it seems crazy that it caused you so many problems. This is definitely super annoying when you start but as you practice you are able to proofread your code better as you begin to notice yourself making the same mistakes.
What tips do you have for anyone who might be interested in taking on a PhD, especially one in bioinformatics?
- Meet your supervisor (or the post-doc you are likely to be working with most) beforehand and check that you feel you can understand how they explain topics that are unfamiliar to you.
- Try to establish if you will have people you can turn to for advice at first, as initially I think this can really help speed up learning bioinformatics.
- Do not be scared of bioinformatics if you have not studied it previously, you do not need any background in IT just a willingness to learn.
You went from never having been a coder to doing a PhD in bioinformatics: is it safe to say that computing isn’t as scary as you might think?
Definitely not scary, you just need to have a go and not be too hard on yourself if you make mistakes as everyone does.