Tuesday, 28 February 2017

Open Science: Open Source, Open Data, Open Access

Squeaking this in on the last day of February; hey look, it's an update!

This month has been extremely busy and stressful, but still fruitful. At the beginning of the month, I attended a symposium called "Publishing for Impact," which included a discussion about Open Access. From that symposium, I was left wanting a bit - open access is one part of open science. By only focusing or committing to publishing open access as the solution, it's akin to declaring that you will try out a healthy diet, but only by switching to low fat yogurt for dessert. It's not the whole picture.

Today was my turn for a GSS session (Genetics Seminar Series), our weekly department meeting where we present our findings and practice conference talks, etc. I decided to talk about how to open up a genome project such as my own. Starting with sample prep all the way to annotation and analysis, I also included peripheral activities such as dissemination of results. I didn't intend to make this an exhaustive list of programs, but rather to encourage thinking about ways to open up all aspects of research.

So, here is that presentation, along with talking points in the Notes section of each slide: 
(CC BY 4.0 license)

Enjoy :)

Monday, 2 January 2017

Happy 2017 - January Update

Well, 2016 is done and gone, with a lot of us saying, "tbh, worst year" (and maybe it wasn't, maybe it was us who were the worst, and even it it was the worst, this year could take it as well).

I ended the year at a nice chill party in Rotterdam with some good people and some hilarious firework moments that were no fault of my own. And kitties! Then it was back to work today.

These past few months have been super busy - I held off on vacation until September (my parents visited for a bit, it was great to see them but also a lot of effort), and then was quite ill for the last week. And since then, it's been like I'm always running to the next thing (work, volunteer stuff, my social life). There have been some delays in my project that were unavoidable. And I'll admit, I haven't been dealing with the pressure as well as I ought to have - it's made me pretty anxious and tired, and there's work on my plate that should have been dealt with by now. I didn't recognize it at first, but my old pal Procrastination has come back and now I'm swimming in it a bit.

Luckily, I've considered the period of New Years to be more beneficial than useless. Not the whole "writing the correct year" thing - that takes me about 3 or 4 months to master. But rather, allowing to time period where not everyone is back at the office and you have a sense of renewal - that's when I like to try a reset. Last year, it even worked (I quit smoking!). So with that, I'm going to do better to waste less time procrastinating (such as in the mornings when I look at my phone for 20 minutes instead of getting ready) and more time addressing my anxiety and TCOB - taking care of business.

And looking forward to the new year! Hopefully I'll have some data, I'll align some genomes, I'll go to conferences and present posters and give talks. And not worry so much about my progress compared to my peers, but rather make sure that my progress and my goals align, and that my expectations are achievable.

Otherwise, I'm looking forward to going to Switzerland in a couple of weeks for a BINGO network meeting, and a BINGO summer school to Vienna in May. And hopefully some work trips to Poland, Japan, and/or Malaysia (wooo!). We're planning a summer vacation to Iceland, and this year, I want to go back to Edmonton for Christmas. Throw in some city trips, and I'll be set.

I'm coming up on living in Utrecht for a year, which is pretty huge considering all the places I've lived over the past 5 years. I've been taking my sweet time settling in, and have been busy and ill, but now I feel like it's time to settle in to Utrecht and really get to know the city and keep building my community here. Furthermore, I want to spend more time with my awesome boyfriend, who's a super supportive and helpful man, and I love that we can both be each others support when it's needed <3 br="">

Which leads to this blog and what it's purpose is. For now, I'll keep it as a place for occasional updates and a space for my scientific writing, but I want to figure out what to do with my limited time instead of trying to do everyone at once like I've tried before. So. I'll try to make more posts that aren't science related if I'm feelin' it, since I've been on a bit of a hiatus from blogging, but I also want to use this space to work on some ideas and forms that I'm thinking about.

So, to 2017, and less procrastinating!

Tuesday, 16 August 2016

Post over at the PLOS Early Career Researcher (ECR) Blog

Hey all,

A little while back, I applied and was accepted to be a contributor to the PLOS Early Career Researcher (ECR) Blog. It's a great opportunity to refine my writing skills, speak to a larger audience, and really "science" it up. Don't worry, I enjoy writing here on my own and will continue to, the ECR Blog is merely a more specific place to be sharing my work as well.

With that, I'm pleased to share my first post with you, which went up yesterday: 

(@sgerner on Flickr, CC by-SA 2.0)
 The Definitions They Are a-Changin': Lemarck, Inheritance, and Genomes

Go to the post, check it out, comment if you wish! Next week I head to Switzerland for a course, so I should have something to share in about two weeks. By the way, if you're interested in writing for the ECR blog and want to know more, see the About page on the ECR Blog for more details.

Thursday, 4 August 2016

It's Dangerous To Go Alone!

For something a little different, let's consider some resources for burgeoning researchers out there...

The beginning of a career in research is often described as an adventure – a journey of self-discovery, where the adventurer must face deeps valleys and ascend tall peaks for the pursuit of knowledge. And as a wise old man once said, it’s dangerous to go alone! So take this: a collection of gems to be found within the PLOS collections titled Ten Simple Rules. All of the articles found within the Ten Simple Rules collection are published within PLOS Computational Biology; if this isn’t your field, fear not! Most articles within the collection transcend field of interest, and are useful tools throughout your career. And, because it's PLOS, it's open access, and can be useful to those outside of institutions and non-researchers as well.

8 bit mysticism care of The Legend of Zelda (1986), pretend the sword is this post

My first encounter with the Ten Simple Rules collection was in 2014. I was writing my Master’s thesis and was trying to eke out useable figures that weren’t crowded or useless. A herald from beyond, Ten Simple Rules for Better Figures, clearly outlined all aspects of figure generation I had to consider. The basics were there – Rule 5: Do Not Trust The Defaults – as well as plenty of tips and resources that benefit beginners and experts alike. In the end, my own figures were stronger, and I also made sure to make them accessible and check for how the images looked for those with red/green colour-blindness, something I had never considered before and now won’t ever forget.
I survived my Master’s, and began to consider a PhD program. Luckily, there was Ten Simple Rules for Graduate Students to really affirm that I wanted to pursue a doctorate. Within my program, I wanted to undertake a large Wikipedia editing project, but didn’t know where to start – enter Ten Simple Rules for Editing Wikipedia. My most recent reads from the collection are all about data: Ten Simple Rules for the Care and Feeding of Scientific Data, and Ten Simple Rules for Effective Statistical Practice. Double whammy, but necessary to establish good practices before I get too far ahead into my research.

I could go on, but I think I’ve made my point. Instead, when going through the collection, you may start to wonder why these articles are needed. The goal of most of these articles is an attempt to bridge a gap in training or knowledge. This may be a gap that the authors may have experienced themselves, or challenges of peers that they witness. When members of the PLOS Ecology community were asked in an informal survey about the trade-offs between teaching and research, a rule of thumb emerged: “If they are asking for 3-4 classes per semester and research excellence, you’ll have to ask yourself where that extra time is going to come from.” The results are daunting, but take heed, there’s a Ten Simple Rules that may help you out early before it’s too late.

And for the ambitious among us, there’s a Ten Simple Rules to Win a Nobel Prize. 

This was an abandoned post for another blog I write for, but I really liked how it turned out and tried to re-purpose it. I hope it's useful to any researchers out there!

Tuesday, 14 June 2016

Presentation on biocontrol and my project

Just a quick update:

Today I gave a presentation to my peers in the Lab of Genetics here at Wageningen University, and I've posted the presentation on SlideShare:

It's part (re-) introduction to biocontrol and part project update from me. Check the Notes section of the SlideShare for the slide commentary!

Wednesday, 1 June 2016

A Tale of Two Conferences, Part II

In my previous post, I mentioned that I've attended two conferences for work recently, and I cover the first one, the 68th ISCP in Gent. Today I will talk about the second conference, InsightOut. This post is written in a more informal way, and gets a bit ranty in the end, but I hope it was useful. Definitely consider this one to be Kim's Opinion.

Director of FOM [Physics Organization], Christa Hooijer, welcoming everybody to the conference

On May 24th, I attended InsightOut, a conference for women in science - in the Netherlands ostensibly, as it was presented by NWO, the national science organization here. To be specific, according to the conference website, "Insight Out is an initiative of NWO Chemical Sciences and Physical Sciences, NWO Earth and Life Sciences and Foundation for Fundamental Research on Matter." The NWO and all of these organizations are undergoing a period of transition into one big organization to serve the sciences (so I've been told, science in the Netherlands is still a fairly new thing to me), and this conference is the first under this name, but not the first time a conference for women in science has been undertaken within the NWO.

If the ISCP was focused on one aspect of my scientific work, InsightOut focused on a major aspect of my life and career - being a woman in science and what that means. As pointed out by my colleague Marjon de Vos, one thing it means is that in a conference for women, you can feasibly use the men's washroom without causing anyone undue stress.

Before going into the conference, I wanted to be mindful about two things (so of course I tweeted it) - I had no idea what to expect, but that I was going to be paying attention and looking for some intersectional feminism to be at play here. If you weren't aware, I'm a feminist, and I promote intersectional feminism whenever I talk about feminism. Essentially, that means that we're not just talking about women's rights as though being a woman is all we all. We are also members of different socioeconomic classes, we are different races and from different backgrounds, we have different gender identities and sexualities (and these are separate), and we have different abilities in all semblance of the word. All of these differences, all of this diversity, it means that we face issues not just as monolithic women, but as different aspects of our identity that can compound. For more information, use Google. Or go to the Intersectional Feminism 101 tumblr. The main thing I want to get across though is that as a foreigner to this country that can still pass as Dutch, I want to make sure that I ask the question, "How does this issue relate to race/sexuality/ability/etc." Another question that also formed in my head later on that day (due to frustration) was "How does this apply to women who choose not to have a family."

Prof. Dr. Tamalika Banerjee gave the first opening talk about her experience in India and the different stages she experienced as being a woman in science.

So I was pleased that the first speaker was Prof. Dr. Tamalika Banerjee, a researcher at the University of Groningen who is a woman of colour as well as a from a non-EU country. Don't perceive this as tokenism - we need more diverse perspectives in this conversation, and Dr. Banerjee's talk was great. While Dr. Banerjee didn't talk about how her race played into her work outside of India, it was great to hear her perspective of being a woman in science, such as the double-edged sword of self-doubt and perceived tokenism. She was encouraged by a female teacher early on in her life, but was later discouraged by male supervisors. Luckily, she was able to persevere, and eventually got over that feeling of the female 'handicap'. Her biggest push was for fixing it early - disassemble the stereotypes in our culture about the masculine/feminine, especially in respecting diversity as a huge benefit instead of being the differences between us.

What we think about men VS What we think about women - Dr. Corina Brussaard presented quite a few of these as a comparison between herself and her partner, both scientists in similar circumstances, so why are the responses different? [the likely answer is, Because of systemic sexism and cultural expectations]

Following Dr. Banerjee was Prof. Dr. Corina Brussaard, a marine oceanographer and self-professed extrovert. She has first-hand experience of being perceived as 'bitchy' whereas her male counterparts are 'assertive', and while this frustrates her, her biggest piece of advice was to 'mirror' the response - make people question why they feel it's appropriate to say to a woman and not a man. I've seen similar advice regarding dealing with racist jokes - instead of laughing, act confused and ask for an explanation as to why it's funny, then wait for people to stumble over themselves in explaining (or witness unabashed prejudice). She was very lively and funny, and I really appreciated the energy that she brought into the discussion, as well as a lot of comparisons to her work. It will definitely work for individuals who are more outspoken or use d to a culture of speaking up, but for those of us who are timid, shy, introverted, or from a different culture, it may not be the most pragmatic advice (and that's where policies and the support of others is supposed to help). Still, very nice lecture.

Some of the audience questions we were able to ask via a really nifty interface (reliant on smartphones or SMS, but it worked).

Following these two talks was a panel on sexual harassment and intimidation in the workplace, and the panel was led by Prof. Dr. Frances Brazier, who I thought was amazing and wish I could work with her, while the panel was composed HR/Confidential Officers at universities or work for professional organizations for women --- the names of the panel members were not listed on the website and I didn't catch all of the names, apologies. Overall, the panel was related to sexual harassment on campus as well as reporting sexual harassment, but for me, the panel was at a disadvantage to answer some of the questions to anyone's satisfaction. I'm glad that Dr. Brazer held the panellists to their answers and was quick to call out disappointing answers.

After this was lunch, then a really helpful workshop on careers outside of academia presented by NaturalScience.Careers, and then before I knew it, it was time for the final lecture from engineer Gabby Kroes, who works in astronomical instrumentation and again talked about her own experiences as a woman in a male-dominated field (unfortunately no picture, but you can check out the #InsightOut hashtag on Twitter for more!).

And then the day was done! It was a mix of enthusiasm and frustration. I was surrounded by successful women who were intent on at least addressing issues within our field if not being the change that they want to see. Meanwhile, I became frustrated at some aspects of the tone of conference and attendees that I'd like to detail below.

Three things.

1)   Support other women
Women need to stick up for other women, especially those who are at a disadvantage or may not be aware of harassment or different treatment. I am a feminist who is fairly well read on issues of sexual harassment and gender bias in the STEM field, so none of these stories were a surprise to me. I was empathetic, listened, and now I want to know how I can stop this from happening to other women before it becomes an anecdote for them. The answer for that is to call out inappropriate behaviour, report to managers, support other women, and provide advice, and that was missing at times in these discussions.

2)   The effects of having children is definitely a conversation, but not the only conversation
How ironic is it that the only issue that we seem to be able to talk about is the unforgiving nature of academia/science to women for having children -- it's true, there is a lot of shit that women who choose to have a children via pregnancy put up with that others, especially men who do not get pregnant do not have to put up with, such as perceived loss of scientific output, time off, etc. But there are other reasons that you may need to take a career break. Depression, taking on dependents, family loss, injury, visa issues, etc. and if these happen outside of employment, they look like gaps in our career, and we can also be punished for that. And women who choose not to have children are not suddenly *saved* from gender-bias at the workplace.

3)   One woman can not and should not speak for all women
Positive discrimination re: grants for women, this conference, etc... There's nothing that frustrates me more than a woman in a position of authority/status/power saying that because she didn't need a grant or access program, they are unnecessary - she just worked hard and other women just need to work harder... Similarly, women who say that they've just been lucky to get to where they are alongside hard work. Listen, a lot of the times when people say they are lucky, they're not talking about winning a randomized situation. They're talking about being a priviledged position and either not realizing it or not acknowledging it. See everything on white feminism.

When it comes to dealing with gender inequality, it's a two-pronged approach. There are short term solutions, like the kind of programs I've mentioned, that are supposed to fix things in the short term - if you don't see any women at the top, how do you know that it's possible? You can't be what you can't see. Then there are long term solutions, where we try to dismantle problematic systems and educate the next generation. I feel like some people didn't get this memo, and prefer to think of the short term solutions as "positive discrimination" or "reverse sexist." And what I want to say to women who are a part of this problem, is to stop poisoning the well. Instead of talking about how you didn't need help, address your own privilege, support other women, and promote the programs for those who do need them.

*rant over*

For anyone asking, What about Men? I refer you to two articles from Bustle that sum it up:
6 Ways The Patriarchy Is Harmful To Men, Because Feminism Isn't Just For Women
10 Ways Men Can Be Feminist Allies, Because Yes, Feminism Is For Everybody

So yeah, what a do! I will definitely look forward to next year and will do my best to ensure that all of my female colleages attend if they're able.

Wednesday, 25 May 2016

A Tale of Two Conferences, Part I

This month, I had the opportunity to attend two conferences for work, and I'm going to fill you in on them, as well as what conferences can be like. These were both professional conferences for a specific scientific audience, but very different in their scope, execution, and most of all, swag.

[Okay, so the swag isn't that great - my dad is in corporate-level IT and his conference swag game is strong]

So I've already mislead you a bit; there was one symposium and one conference. As I learned last year when I went to the Artificial Light and Wildlife Symposium in 2014 - a symposium is for a specific issue or field, whereas a conference is likely larger and open for variation and different fields. But I digress. I attended the 68th International Symposium on Crop Protection in Gent, and the InsightOut, a conference for women in science in Ede. This post will be split into two parts (hence the title), with this first part on the ISCP.

Inner garden area of Universiteit Gent, where the 68th ISCP was held

Part I: The 68th International Symposium on Crop Protection 

The ISCP was last week in Belgium, which was great - I was able to visit my sister in Leuven at the same time, and as for the conference, it was very insightful into what crop protection/biocontrol conferences can be like for content, as well as the environment in Belgium. I arrived in Gent, ready to head to the university, and proceeded to take the wrong tram. So a great start to that day. But being a little bit late wasn't a huge problem, these things rarely start on time. There was quite a crowd with hundreds of attendees and seven parallel sessions in the morning and afternoon. Attendees were a mix of agriculture researchers, industry representatives, policy researchers, and ecologists/biologists like myself, both from companies and from universities. I stuck to my field of interest in the morning, Agricultural Entomology and Acarology (Entomology is the study of insects, whereas Acarology is the study of acarids such as like mites). Lots of mite talk, which was to be expected, as mites make up quite a bit of the research focus as well as economic focus of biological control.

I could give you a breakdown of every single presentation I saw but suffice it to say, it was fairly Belgium-centric (this makes sense, it's a Belgian conference despite being an International Symposium), with some presentations on projects being undertaken at Biobest (Belgian biocontrol company), and a really interesting study from Hilde Wustenberghs involving aspects of sociology re: Belgian tomato growers and use of pesticides (would they ever go pesticide-free? not likely, $$ plays a huge role), as well as more application-based studies such as flower strips for strawberries --- Again, I can't describe them all. And what I noticed was a there was a lack of genetic work in my session, as well as a lack of parasitoids. I spent some of my afternoon session in the nematode room as there were some genetic-based talks there. Therefore, I definitely foresee myself submitting an abstract for this conference next year with my own work, and I think it would have a great reception, so, something to plan for!

One of two poster sessions at the 68th ISCP
And if not a presentation, then a poster. Poster sessions are hard to explain to folks outside of research -- lectures and seminars make sense, but what are poster sessions and how are they useful? Essentially, they're part communication and part competition, and allow scientists to share information to large amounts of people without needing a stage and a microphone and a specific session at a conference to do so. The contents are likely to be an intro explaining a problem, the experiment they did, and the results, all in  a super short form with some graphs and pictures. They are posted in a separate room or area for people to view, mostly at a specific time or inbetween coffee breaks, and often there are prizes for best posters (selected either by a panel or by vote).
I've put some poster examples below to give you a sense, and for those familiar with scientific posters, you should be happy to know that portrait format is still in vogue!
"Cold hardiness of Drosophila suzukii (Diptera: Drosophilidae) in Belgium" from M. de Ro et al (ILVO, Merelbeke, Belgium)
"Landscape plant composition differentially influences aphid parasitoids in fruit orchards" from A. Alhmedi et al (pcfruit vzw, Sint-Truiden, Belgium)

"Effects of selected release methods on the establishment of predatory mirids in greenhouse tomatoes" from M. Nannini et al (Agris Sardegna, Cagliari, Italy)

"New records of biological control agents in Slovenia in the period 2012-2014" from S. Trdan et al (University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia)

"Effects of different foods and essential oils on bumblebees" from Y. Ulu et al (S├╝leyman Demirel University, Isparta, Turkey)

So overall, a nice conference, not so much networking as I was ill (and myself, I'm a bad networker but I was too sick to shake hands at this point), great catering an hosting from UGent, and I will try to go back next year with some data to present!

Oh, and my swag? There were pens and notepads and the usual, but the best piece was the lanyard, a secret swag item that I didn't figure out until days later at home:

Spoiler alert: it was mainly promotional material and an attendance list but STILL! #surpriseswag
If you're interested in some of the posters or talks I've presented here, click here for the full programme. My only complaint? No official hashtag, but luckily, I was able to retweet the majority of tweets from the Emphasis Project, as we were in the same morning session and they had their shit together and were on point re: Twitter.

Next week: A Tale of Two Conferences, Part II!