Thursday, March 21, 2019

Getting into the habit... A PhD student’s perspective on data management

Today's post is a guest post by Annemarie Hildegard Eckes. Annemarie is a PhD student in Biogeography at the department of Geography in Cambridge, working with all sorts of data and formats: Climate data in .netcdf, and .txt format. Tree growth dynamics data in .excel spreadsheets. Tree ring anatomical data as images, and later as .txt -files. Her project involves the development of a computer model that simulates how a tree stem grows in width, in response to the environment (temperature, precipitation etc..). The ultimate aim is for the final model to be used in the vegetation model HYBRID, developed by Andrew Friend, to help in projections on how vegetation will behave under climate change in the future.
All this data needed to be described and managed well, for example: who gave it to me? What did I do to it? How to make sure I don’t lose it? How do I version control and document the scripts that use the data and the model that I compare the data against? How will I make sure the data and scripts during my PhD will be shared with the community and what standards should I adhere to, to make reusability really easy? Annemarie didn’t feel that she had enough expertise in this, but wanted to do it right from the start. Before she started her PhD she worked with a database for crop data. That’s when she really learned how poorly documented and poorly organised research data can slow down a research project immensely and she did not want to make the same mistake which she has seen experienced researchers make. Her previous experience and motivation to acquire good habits right from the start got hervery interested in RDM and made me an advocate for it as Cambridge and JISC data champion.

A PhD project is a significant period in a researcher’s life. During the project, we generally must develop our own research question and methodology, generate data and publish our results in papers and as a final thesis. Such a project is meant to teach us how to conduct research. This is the crucial time in which we as early career researchers should pick up the right habits for our future as successful scientists.

Research Data Management (RDM) is an important day-to-day activity for Scientists. Research output, collaborations and productivity depend on it. No surprise, then, that the documentation of a project’s RDM has become a requirement for many grant applications. By writing a Data Management Plan as part of the PhD proposal, we students are not only confronted with the whole data lifecycle of our research data before it is even generated, but we also gain experience in how such a plan is written. Early career researchers such as us PhD students should not underestimate the importance of skills in RDM, which in my opinion are nowadays pretty essential for a good scientific career.

I think “data management” in its most basic form starts with managing your email inbox. To me, it often is simply the act of keeping all information that I deal with in order. We all do it more or less all the time. The tricky bit is how to deal with what we call research data the best way. As we may be new to the research subject of our PhD, we may not know how best to collect, document and manage the data we are dealing with.

PhD students and RDM training
The point of a PhD is to learn how to conduct research and RDM is part of that process. But sometimes it may be important to learn about good practices right from the beginning, rather than getting into bad habits that cause problems later in your research.

I think that training in RDM for us PhD students is useful for two reasons, firstly to learn the right habits and secondly to enhance productivity throughout the duration of the PhD.

Figure 1 RDM-smileys: In talks I give about research data management, I like to use these smileys in my presentations. The first row at the beginning and the second row at the end of the talk. The principle behind these smileys is based on a presentation by the Cambridge office for Scholarly communication.

I conducted a survey and interviews at our department, asking fellow PhD students about their data management practices, the data types they collected and their training needs. Participants at the end of their PhD indicated that they generally felt prepared to conduct data management in their coming research career, while they also say that they would have benefited from training at the beginning of their PhD. In one interview, this came out especially, with one interviewee stating that “the lack of training in research data management slowed me down”. This shows that while we PhD students have ourselves learned more on the aspects of data management during our PhD, early training would have made us more productive - and certainly more happy ( see figure 1)! Please check this blog entry where I discuss some of the survey results.

PhD students and the data tree training platform
An online platform that provides training on RDM for PhD students is in my opinion a much needed resource! I think that at the beginning of my PhD, I would have been happy if Data Tree had existed to provide me with a good overview of RDM.

As an online course it is accessible to all PhD students at any time. And with some of us having crazy schedules and weird working and sleeping habits, doing such training in our own time might help us remain flexible. It’s my experience that people do not spend the time to come to talks or workshops. While my survey showed clearly that PhD students do think RDM is important, the turnout to stand-alone talks, workshops and other events I have organised has been rather low. I hope that such a continuously accessible platform would decrease the barrier to learning more about RDM.

While time and timing might be a barrier to learning about and performing RDM, I wonder whether the main reason PhD for students not attending training courses is the lack of priority. For many busy PhD students, RDM never seems to be a priority- and neither does RDM training. Therefore, PhD students will probably need to be encouraged in some ways to make use of this online platform. One option could be that Universities make this online course count in their PhD training logs.

It will be interesting to see how the platform is taken up and what strategies are used to encourage us busy PhD students to do this online course. I wish this platform a good start, a lot of users and that it makes a significant contribution to PhD students’ success in RDM!

Tuesday, March 19, 2019

What's the first thing you do in the morning?

I recently ran a poll on Twitter to learn how we start our days in the office. I usually make my coffee (I have to hurry so much to get out of the door in the morning that I don't have time to drink coffee at home), then revise my ToDoist list for the day (which I make up-to-date the night before, infant permitting), check my priorities in my BulletJournal, check my GoogleCalendar, and then get to work - or procrastinate with social media (guilty as charged!).

Based on the results of the poll, it looks like my habit of getting coffee first is quite common.

You can find the poll and its wake here:

Thursday, March 14, 2019

PhD Defenses Around the World: a Defense in Portugal

Today, Dr. Miguel Abambres shares his experiences of the PhD defense. Miguel is a passionate Portuguese scientist, born in Lisbon in 1984 (Leo), and also a cat guy who loves traveling and teaching. He received his degree in Civil/Structural engineering in 2007 from IST (University of Lisbon) after spending the final semester of his undergrad at TU Delft. He received his PhD in 2014 from IST (University of Lisbon) on the topic of computational mechanics (novel FE formulation) applied to thin-walled carbon/stainless steel structural members. He did a post-doc at FCT (University of Coimbra, Portugal) in 2017-2018 on the development of an AI-based software for nonlinear regression problems in any field of knowledge. He also has 1,5 years of experience as a structural engineer in national and international firms, has spend 1,5 years as a under/postgrad professor (in Spanish) in Lima, Peru, and has worked 9,5 years as a scientist in several countries. His research interests include: Applied Computational Intelligence, Artificial Neural Networks, Civil Engineering, Structural Engineering, and Steel Structures. Besides Portugal, he has lived in Holland, Australia, Norway, Perú, Colombia and Brazil. This post was written in August 2018.

In my case it was a remarkable period, i loved it, but not anything i wasn´t expecting. The exception was a "little stress" in the final semester (don't forget a 0.5 mg XANAX pill in your pocket during moments like this LOL), when one night I realized I had to restart my last computer simulations because the results were not good - I got afraid not having time to apply for the 2013 Vinnakota Award, but thanks to God I managed and at the end I had the honor to receive my first, yet the only (apart from grants), research prize.

I got a 4 year PhD grant from the Portuguese Government, and in order to apply I had to write a research proposal with my supervisors. Around the 3rd year I realized we had proposed enough topics for 2 PhDs (LOL), but my supervisor soon told me that the research proposal didn´t have to be fully completed as long as there was a major innovation in my final PhD thesis. Talk to your "bosses" and make it clear from the beginning. Researching under stress and anxiety harms a lot your performance.

Concerning thesis writing, my strategy was to start writing the theoretical part since day 1.
I proposed a novel mathematical formulation. Every stage of it was first written in MS Word (in the "final" thesis format, including text - not just formulas), then coded in MATLAB. After 4 years of research (including 6 compulsory postgrad courses and 15 papers (10 to conferences)), the so desired final phase had come - 6 months to finish the 328 page thesis.

After delivering the manuscript, I waited 6 months for the public defense. In the meantime I prepared my .pptx and went for holidays with my best friend a few months before the D day. In that day it was a piece of cake ahahaha (seriously, no one in that room knows more about your work than yourself).
Be confident and do not rehearse too much your presentation. Speaking at several conferences before the defense might help increasing your confidence and decreasing your anxiety (don´t forget the XANAX "friend", just in case).

Tuesday, March 12, 2019

Moving towards more Open Access publishing?

Eleven countries in Europe formed cOAlition-S, with as its basic principle:
"After 1 January 2020 scientific publications on the results from research funded by public grants provided by national and European research councils and funding bodies, must be published in compliant Open Access Journals or on compliant Open Access Platforms.”

I wondered if researchers are planning to move more towards open access, and ran a poll on the topic.

Here are the poll and its wake:

Thursday, March 7, 2019

PhD Talk for AcademicTransfer: Avoid These 10 Mistakes During Your Ph.D.

This post is part of the series PhD Talk for AcademicTransfer: posts written for the Dutch academic career network AcademicTransfer, your go-to resource for all research positions in the Netherlands.

These posts are sponsored by AcademicTransfer, and tailored to those of you interested in pursuing a research position in the Netherlands.

If these posts raise your interest in working as a researcher in the Netherlands, even better - and feel free to fire away any questions you might have on this topic!

For the last few years, I've been consistently giving you my best advice. Today, I will give you a list of what not to do during your PhD years. Without me blabbering away with too much of an introduction, here are the 10 mistakes you should avoid when doing your PhD:

1. Start research without reading
When you start your PhD, you may be very eager to start working right away. While you may need to start working in the lab very soon after starting because of project deadlines, you need to start reading at the beginning as well to get a better understanding of what lies behind your observations in the laboratory. Your literature review is the basis of how you will phrase and tackle your research question. Pay due attention to the foundation of your work before you start building your research castle.

2. Stop reading after finishing the literature review
Once you finished your literature review, you may feel like you are "done" with the reading part of your research. Spoiler alert: you're never done reading. As a researchers, you need to keep up with the literature constantly. Set aside time on a weekly basis to read new papers, or to read classic/historical papers you missed when you did your literature review. Use this material to update your literature review until the final version of your dissertation is ready. And before your defense, delve into the literature again, so that you can show your committee members that your knowledge on your research topic is up-to-date and that you knwo their work very well too.

3. Avoid all "extra" work
You are not traveling to conferences and presenting your work because writing a conference paper is not a graduation requirement. You don't volunteer for extra work for committees within your university or of professional organizations. You reject all invitations to review papers. While I'm not an advocate for overloading you with work, you should consider opportunities carefully. For example, writing a conference paper can be a good first step before writing a journal paper. Presenting at conferences and other events helps you grow as a speaker, and replying questions during the Q&A prepares you for your defense.

4. Isolate yourself as a researcher
You don't talk about your research to the senior PhD students and post-docs. You don´t ask your supervisor for help when you feel stuck. You don´t listen to the input of the laboratory staff on your test setup. You are a complete solo player in your research. Unfortunately, research is a collaborative effort. Work in a team, and learn from those around you. Ask for help and advice - there's no shame in asking for help.

5. Isolate yourself socially
You eat lunch behind your computer. Your friends haven't seen you in months. At night, you watch Buzzfeed videos on your phone. Your mood levels are subarctic. Maybe you don´t even go to campus anymore but prefer to "work from home". Sounds familiar? Break out of your rut and make sure you rekindle your friendships and work relationships. Even better: set goals for your relationships with others, and add events to your planner (I learned this from Laura Vanderkam's 2018 book "Off the Clock" and now set goals for work, self, and relationships to balance these aspects of my life).

6. Procrastinate
OK, we all procrastinate. I love watching cat pictures on Twitter and reading random Wikipedia entries. But, when you can't get any work done because you are procrastinating more than anything else, you need to take action. You need to have a conversation with yourself about why you are not getting to your work. Is the task ahead seemingly too complex? Split it up into smaller, actionable items, and make lists and a planning. Do you have difficulties staying concentrated? Remove distractions and try the Pomodoro technique. Do you have something in your personal life that throws you off balance? Deal with it first and then get back to work.

7. Work without documenting your work
You want to work fast and don't want to get writing to slow you down - so you do all your calculations without documenting the references you used, the steps you followed, and the iterative changes your procedures went through. Big mistake. Document everything you do. If possible, ask for a computer with two screens: one screen for doing your calculations, and one screen in which you write down what you have been doing. Don't read without taking notes. Add a "version management" tab to your spreadsheets to log changes to your calculation sheets.

8. Work without a planning
You don't know where research will be leading you, so you don't need a planning. Maybe you work based on what comes into your email inbox. When you work like this, it's easy to lose track of your priorities. Make a list with your goals and priorities, and allocate your time accordingly. I'm a big advocate of setting milestones during the PhD, and planning at multiple levels (entire PhD trajectory, per year, per semester, per month, per week, and per day). I use a combination of lists in Todoist, planning and a weekly template in Google Calendar, and a Bullet Journal to write down my priorities and reflect on my progress.

9. Have the wrong motivation
Your goal in life is to become a professor so you need that PhD. Or, your goal in life is to make a lot of money, so you need the Dr. title. If you have the wrong motivation for doing your PhD, you will dread the journey. If you don't like what you're doing, then something is wrong. Try to find what motivates you to get to work every workday - will your research possibly have an impact on society? Whose lives will improve thanks to your work? How do you feel in the lab? If you really regret your decision, don't try to drag yourself through the next three or four years, but see if you can change project, topic, university, or even quit altogether if you learn that research is not for you.

10. Forget about self-care
You need to get through that PhD, whatever it takes. Well - it may take your health (physical and/or mental), and then you won't be able to finish maybe. So prioritize self-care, even when you feel you don't deserve it. Schedule time to unwind and do what energizes you. Take proper care of yourself by getting enough sleep, movement, and healthy food.

Tuesday, March 5, 2019

I am Miguel Abambres, and This is How I Work.

Today, I have the pleasure of interviewing Dr. Miguel Abambres. Miguel is a passionate Portuguese scientist, born in Lisbon in 1984 (Leo), and also a cat guy who loves traveling and teaching. He received his degree in Civil/Structural engineering in 2007 from IST (University of Lisbon) after spending the final semester of his undergrad at TU Delft. He received his PhD in 2014 from IST (University of Lisbon) on the topic of computational mechanics (novel FE formulation) applied to thin-walled carbon/stainless steel structural members. He did a post-doc at FCT (University of Coimbra, Portugal) in 2017-2018 on the development of an AI-based software for nonlinear regression problems in any field of knowledge. He also has 1,5 years of experience as a structural engineer in national and international firms, has spend 1,5 years as a under/postgrad professor (in Spanish) in Lima, Peru, and has worked 9,5 years as a scientist in several countries. His research interests include: Applied Computational Intelligence, Artificial Neural Networks, Civil Engineering, Structural Engineering, and Steel Structures. Besides Portugal, he has lived in Holland, Australia, Norway, Perú, Colombia and Brazil. This interview was conducted in August 2018.

Current Job: Pro bono scientist
Current Location: Lisbon, Portugal
Current mobile device: black Samsung Galaxy A3
Current computer: hp pavilion x360 convertible (laptop)

Can you briefly explain your current situation and research to us?
I'm in a sabbatical year since I finished my postdoc (Feb 20th, 2018), but actively looking for a faculty position since then (Europe, Canada or Latin America preferred). After finishing postdoc, in which I developed/validated an Artificial Neural Network software for functional approximation and classification problems in any field of knowledge, I’ve started looking for collaborations worldwide aiming to apply my software to real problems and propose novel analytical models to the scientific and technical communities (interested researchers are very welcome to get in touch @AbambresM and/or ResearchGate).

What tools, apps and software are essential to your workflow?

Windows-based laptop and desktop computer (running MATLAB simulations 24/7), Android-based cell phone, fast internet, MS office, MATLAB software, AnyDesk software/app.

What does your workspace setup look like?
I LOVE to work, so I might work anywhere as long as I have my laptop and a quiet/cozy place. My favorite office is in my place in Lisbon, where I work most of the time when i´m in town. At the moment I don´t have any institutional office (also, that´s not a requirement in my job seeking 😊 )

What is your best advice for productive academic work?
Work exclusively on what you love and with the people you like. Rest enough and have some workout every week.

How do you keep an overview of projects and tasks?
Checking email and the daily task list written on my phone’s calendar.

Besides phone and computer, do you use other technological tools in work and daily life?
A smart plug to schedule the time my home office fan is working when i´m abroad, in order to avoid computer overheating in hot days (air conditioning is much better, but mine cannot be accessed remotely)

Which skill makes you stand out as an academic?
Analytical, hard-worker, ambitious and passionate (all in one 😊)

What do you listen to when you work?
None, some American hiphop (50 cent, Ryan Leslie), TV news in the background, classical music

What are you currently reading? How do you find time for reading?
I don’t like reading….never did…only news in social media and job-related reading!

Are you more of an introvert or extrovert? How does this influence your working habits?
Introvert. I am more productive when alone, but sometimes it feels good working at relatively quiet public places (libraries, coffee shops)

What's your sleep routine like?
When i´m employed, I like starting the day quite early. I try to sleep at least 7 h every night (if I cant some night, I compensate in other night). I´m a night owl when i´m not employed (2-6 am).

What's your work routine like?
I don´t have a fixed routine. I work whenever i´m not doing basic tasks or hanging out. Every single day is a working day for me (as long as I work on what i´m passionate about).

What's the best advice you ever received?

Be happy, follow your dreams, follow your inner voice.

Thursday, February 28, 2019

Working hours in academia

I recently ran a poll on Twitter on how many hours academics work per week. As I've gone from 30(ish) hours per week for a year back to 40 hours - after always having worked 6 days a week for 8+ hours daily, I sometimes feel that I am not working enough, but I also realize that I don't have more hour that I can be in the office because of childcare constraints. I can try to put in some extra hours at night (or work on my blog at night, as I am doing now at 9pm on a Friday night), but I feel that I have to be super efficient at work and then still fall behind. I also feel guilty at times, because of the persistent myth that we all should be working 80 hours per week.

Long story short, I did a poll about working hours and very few of the respondents work more than 50 hours per week.

Here's the poll and its wake: