Thursday, September 29, 2016

I am Seán Mac Fhearraigh and This is How I Work

Today I am interviewing Seán Mac Fhearraigh, PhD in the "How I Work" series. Seán was a PhD student at University College Dublin & a post-doc a Cambridge University where he studied mechanisms of cell division. Currently Seán run’s an ELISA assay company where you can find some great information on ELISA assay protocols and ELISA kits.

Current Job: co-founder of
Current Location: Dublin, Ireland
Current mobile device: iPhone 6s
Current computer: Dell

Can you briefly explain your current situation and research to us?

Recently I've started a biotech company selling ELISA assays and cell tools, before that I was a PhD and Post-Doc for over 6 years. I carried out a PhD in regulation of cell death during mitosis and carried on to a post-doc at Cambridge University looking at regulation of microtubule attachment.

Now I am setting up a Biotech company, I'm a marketer, website developer, sales rep and designer all in one. However, my PhD really helped me with the logical brain to promote these skills and the approach to learning new skills.

What tools, apps and software are essential to your workflow?
Wordpress - we're building the whole site on this platform. If you're starting off a website, it's a great place to start. More recently we've started to use to outsource some of the tech work we can't do. If you're a student and are having problems with data, excel, or programming, this could be a great resource to find someone to cheaply help you.

What does your workspace setup look like?
So at the moment it's a mix between the office and home. Since I am in charge of the website and development, I try and stay away from the distractions of the lab and focus on working on the site. During my PhD I wrote up my thesis at home. I found doing a mix of both can really help. Finding two spots to work that keep you motivated is better than one.

What is your best advice for productive academic work?
I'm a big believer in starting work early, 9 am if you can. This sets up the day with the right focus.

I also think exercise is a great motivator for work and can help you work through your problems without staring at a screen and provide a great hormonal boost to keep you motivated. It also reduces your stress levels.

How do you keep an overview of projects and tasks?

I try and keep it simple and do one thing at a time. Recently met with a colleague who provided an example of how multitasking can really slow down your work rather than speed it up. Since then I have been one task at a time.

Besides phone and computer, do you use other technological tools in work and daily life?
Fortunately, not, giving yourself some device-free time is a better tool than any.

Which skill makes you stand out as an academic?

I wasn't a great academic, but I did read a lot of papers - probably more papers than I should have. I think this helped me a lot with thinking about the problems I had. It also helped me keep up to date with competing labs and techniques that I could be working on. A great example of that was my boss in Cambridge, she was a great reader and journal clubs were a real insight into her detailed knowledge of the area. No wonder she had Science and Nature papers.

What do you listen to when you work?

I do listen to a lot of podcasts when travelling, but nothing at work. At the moment I'm a big Gary Vaynerchuk fan, he is great at providing motivation for people in all sectors and I can resonate to what he says as a scientists. i.e work hard and you’ll get there.

What are you currently reading? How do you find time for reading?

At the moment I'm reading “A random walk down Wall street”, it’s about the stock market, but gives a great insight to markets, which has a lot of parallels in the scientific world. People concentrating too much on one idea, resulting in people losing originality, which can be detrimental to the market and in this case scientific ideas.

I think it’s important to read: bus, train, lunch break I try and have a book with me.

Are you more of an introvert or extrovert? How does this influence your working habits?
I am ENTJ according to Briggs-Myers test, which means I'm an extrovert - wouldn't have thought so, but the test says I am. I think it helps when I meet new customers and scientists at conferences. I always like asking people about their work so being an extrovert removes some of the shyness when walking over to introduce myself.

What's your sleep routine like?
8 hours every night. Can't live without them.

What's your work routine like?
At the moment, 9 – 5 pm, then 8 till late. If I get time at the weekends a few hours too.

What's the best advice you ever received?
My favourite quote is “He who says he can and he who says he cannot are both usually right!” I found it in a youtube video under “why do we fail”, best line I've ever heard.

Tuesday, September 27, 2016

Tips for using Mendeley referencing

Today's guest post is a contribution from Seán Mac Fhearraigh, PhD. Seán was a PhD student at University College Dublin & a post-doc a Cambridge University where he studied mechanisms of cell division. Currently Seán run’s an ELISA assay company where you can find some great information on ELISA assay protocols and ELISA kits.

As an experimental biochemist embedded in a largely computational research group I was lucky enough to be exposed to some clever software tools that simplify everyday tasks such as primer design, DNA sequencing, homology modelling, and viewing protein structures. However, I noticed my peers were still performing many tedious tasks by hand, or using some really terrible software. The best example of this was reference management, although there are programs to collate and present your references, some can be troublesome. However, there is a better way for writing your PhD thesis. Mendeley is a free reference management tool that integrates seamlessly with MS Word, and Open Office. The developers of Mendeley have an excellent website with easy to follow tutorials on the main features, see, but nothing beats the experiences of someone who uses it on a daily basis.

Essentially, Mendeley is iTunes for your research papers. It allows for easy uploading, storage, and retrieval of your papers from multiple computers, in multiple formats. In addition, it automatically generates a copy of all your documents on a cloud, thanks to the free 500Mb of storage space they provide for every user. After using this software for over two years the main features I think people will be interested in are as follows:

Creating your library is straightforward. I found the best way was to simply select the Watch Folder option from the add files menu in the main toolbar, and browse to the folder which contains your documents of interest. They can be pdf or word documents. Mendeley will now proceed to add each document to the library, scanning each for useful details such the title, the authors, the journal it was published in. In addition, any documents subsequently added to the folder will now automatically be visible in Mendeley. The documents do not need to be labelled logically for Mendeley to populate the metadata for each article. This is akin to letting iTunes fetch the details of a particular track for you, so that you have the correct album art, singer, album name etc. However, Mendeley does not always get this right, so some manual manipulation many be required to clean up the data. I consider this a small price to pay considering the benefits granted by the rest of the functions. Once your documents are imported, I suggest using the synchronization functionality: this uploads everything to the cloud storage they provide, allowing you to access it from any computer with an internet connection.

Once you have imported your documents the first thing you'll notice is that double clicking on any one of the articles brings you to a full version of the document. This is fully searchable via the toolbar on the top right. It might not seem like a major feature, but when you're trying to remember where you came across the evidence for that statement in your thesis it's an extremely valuable and time saving feature. In addition, your whole library is searchable, so you can search for authors names, or journal name, or just individual terms you are interested in. It's happened to me before that I couldn't remember the author, but I could remember a particular term used with the article, a few keystrokes quickly narrows down the list of possible suspects. It's worth noting, the more effort you put into having the correct details for each article the better the results of any search will be. If you're slightly OCD like me, you'll actually get enjoyment out of making sure everything is correct and welcome the distraction from writing your thesis.

How much you use this feature depends on how collaborative your research group is, and how many other people you can convince to use Mendeley. Essentially it allows you to select any number of journal articles from your library and send them to any other Mendeley user that you have invited to join Mendeley. It's actually much quicker than email, and the document is automatically integrated to your existing library, including any notes, and annotation made by the previous owner. The recipient does not have to have a subscription to the online publisher of that article, so it's an excellent way to share papers among less privileged colleagues.

This is perhaps one of my favorite features. Frequently, I will be reading an article which cites some other articles I’d like to read. Tracking down references can be extremely time-consuming depending on the way the references are cited. However, by far the easiest way is to go to the URL of the article you are currently reading, and hope that there are hyperlinks to the articles referenced in that paper. This still means entering the details of the current paper in Google Scholar, or PubMed, and getting to the right location. Mendeley bypasses all of that by providing the URL of the source article you are reading. You simply click on the link and you are on the correct webpage for that article, from there you can go straight to the reference section of the look for hyperlinks. It's a very fast and effective way to navigate from source to source with no typing involved.

A relatively minor, but useful feature of Mendeley is that individual documents can be have sticky notes attached to them, essentially a collapsible text box which you can place anywhere. Generally useful for making quick notes of questions or thoughts as you read the paper. It's also possible to make more detailed notes in the toolbar on the right hand side, this is a better option in my opinion, since these notes are searchable, so you can actually pick out a paper based on the contents of the notes you made as you were reading it.

Thursday, September 22, 2016

PhD Defenses around the world: Tinkering at a defense in Delft

Today, I am sharing with you a translation that I made of a post by Rolf Hut. Rolf is a scientist at Delft University of Technology. He solves his problems using a MacGyver attitude, builds measurement devices using scavanged parts from consumer-electronics, connects existing online data sources to answer relevant scientific questions and encourages his students to learn by discovering, building and doing. He is a public speaker on science and technology. He writes a monthly column in the Dutch national newspaper "De Volkskrant". He hosts workshops for audiences ranging from festival-goers to primary school kids. His workshops show, hands-on, that technology is fun and that technology is for everyone, not only for beta-nerds. He calls himself, most of all, endlessly curious.

You can read the original post in Dutch here.

My mom looks at a LEGO-sumo-wrestling robot with frustration, asking out loud: "And why is he now turning in the wrong direction?" Meanwhile, my friends are strengthening a miniature version of a dyke with hairspray, and my colleagues are admiring plasma sparks from a grape in a microwave.

The best moments of the day of my PhD defense were not your regular "hora est" or the commencement ceremony. I must say: I enjoyed defending my thesis, the speech of Prof. van Giesen*, the many congratulations and gifts and great party. But the icing on the cake were the workshops for friends and family.

graduation speech

After my defense and reception, Olivier Hoes, Felienne Hermans and John Cohn gave an entire afternoon of workshops to give my friends and family and idea of the fun parts of my work. In the water lab, Olivier instructed two groups to build a small dike, strengthened with hairspray or gel. Then, he let water flow over the dike, and the dike that remained standing longest was the winner. Fun competition, but also an important observation: breaches start at the polder side of the dike! Felienne arranged a few LEGO-mindstorm robots through the firstlegoleague. She invited all to improve a sumo-robot. Interesting to see that some immediately turned to the software, whereas others to the hardware. John Cohn gave a "Do Try This At Home" presentation in which you showed that you can put steel-wool in the microwave, can make a catapult with pvc, hairspray and a grill-lighter, or a "Harry Potter flame" with boric acid and white spirit.

strengthening a dike with hairspray

In all acknowledgments of dissertations I read that friends and family are essential to finishing the PhD. Therefore, I would like to ask every PhD candidate to give back to their friends and family on the day of their defense, and organize an activity for them, to show them what you worked on for the last 4 years, to show them how fun science is. But above all: to give your friends and family a great day.

dike collapse

PS: My workshops took place in lecture rooms and labs that were vacant at the time. Olivier, Felienne and John participated at no charge because they enjoy showing people more about their work. Except for some groceries, organizing these workshops cost me mostly time and barely no money. The cost for university is at most an opportunity cost, because colleagues participated while they could have been doing "real"** work.

PPS: In encouraging these activities, in my opinion, universities can play an important role on the institutional level. Not by making it part of the policy, not by developing a form for the request for approval to give a workshop - but by sending an email to all employees that says: "these kind of workshops are fun and good for the image of the university. If it fits within your tasks, go and give a hand. "Real"** work has the priority, but if it suits you, we think it is OK if you participate in these workshops." In other words: universities can help by creating a culture in which these initiatives are encouraged, not punished.

PPPS John Cohn wrote a short blog post about this topic too.

*nice hat!
** research and teaching

electrocution of a dill pickle

Tuesday, September 20, 2016

PhD Defenses around the world: a defense in Japan

Today, I am hosting the narrative of Ayumi Koso in the "Defenses around the world" series. Ayumi is a press officer at the Division for Strategic Public Relations, University of Tokyo and is an editor of UTokyo Research a bilingual English-Japanese website that showcases the University’s diverse research. She received her PhD in neurolinguistics in Japan. Ayumi has experience practicing science communication at Japanese research institutions and funding agencies. She researches media release models that maximize the effect of university research communication in Japan.

My viva experience was in Japan. Before moving on to science communication, I completed my graduate studies at the Tokyo Metropolitan University in neurolinguistics, a field that investigates how our brains are wired to learn and process language.

There are two main ways to earn a PhD in Japan; one is to complete a 3-year graduate course earning credits and completing a thesis (“katei hakase” or degree PhD), and the other is to prove that you have the qualifications to receive a PhD by handing in a thesis and having it evaluated (“ronbun hakase” or thesis PhD). The first route is more common and taken by most doctoral students in universities, while the second route is designed for researchers who have a full time job at companies and public research institutions. While the second route does not require any credits, the thesis requirements are extremely stringent.

Like the majority of people, I took the common route and did a 3-year graduate course. At my university, in order to reach the viva, there were certain requirements I had to fulfill.

First, I had to earn certain number of credits by taking courses offered in our department. Then I had to deliver a proposal that contained the first few chapters and a detailed outline of  my thesis, and progress of my research. There was a committee to evaluate my proposal and by the time I passed the review, I was approaching the third year of my studies.

Because I was on a  Japan Society for the Promotion of Science (JSPS) fellowship for the three years at graduate school, I had to think of an alternative way to sustain myself after my fellowship. I hadn’t quite finished my thesis yet, but luckily I was offered a science communication position at a research institution starting in April (the academic year in Japan starts in April!), so I decided to leave school in March, which was exactly the end of my third year. By then, I had a draft of my thesis, which was almost ready to be handed in for my viva.

For the next couple of months I worked full-time Mondays to Fridays, polished my draft, handed it in and created slides for my viva on the weekends. Looking back it was quite a tough time getting used to a new job, switching back and forth between science communication and research.

Then came my viva day. It was on a hot sticky Saturday in August, just in the middle of the summer holidays here in Japan called “obon”.

For my viva, there were three reviewers; my supervisor, another professor from my department and an external reviewer who was an expert in neuroscience. The viva was open for anyone to attend, so my lab members and classmates also came.

In my university, the viva has three parts: presentation, Q&A and review. I had 40 minutes to talk through my thesis, highlighting the main findings and conclusions. Then I took questions from both the floor and my reviewers for another 40 minutes. After the Q&A, I received feedback about my research from the reviewers about how it could be improved and the overall impression they had. The viva was about 90 minutes in total. Incidentally, while I wrote my thesis in English, my viva was conducted in Japanese.

The results of my viva and the evaluation of my thesis were reported to my department’s faculty committee for final approval. It was in September that I received official confirmation from my supervisor that I had passed.

Finally, I had to deposit six hardcover copies of my thesis, one of which was for the Japanese National Diet Library, before the degree could be awarded.

Normally, if you finish your viva in time for the awarding ceremonies in March, the president awards you the degree in front of the class and you can celebrate with your classmates.

In my case, by the time everything was done it was around September in the middle of the academic year so the award ceremony (if you can call it that) was quite simple and informal. I took a day off of work to visit my university wearing a nice two piece suit. I was called into the dean’s office and he awarded me the degree and congratulated me for my efforts. In the evening my supervisor and lab members organized a dinner for me where they congratulated me on receiving my PhD!

While I missed the formal ceremonies and celebrations, I was glad that I had made it to the end.

Thursday, September 15, 2016

Shear and moment capacity of the Ruytenschildt Bridge

My colleagues and I wrote a paper for IABMAS 2016, which was presented by my student Karen Flores.

The abstract of the presentation on the shear and moment capacity of the Ruytenschildt Bridge is as follows:

In August 2014, the Ruytenschildt Bridge, a reinforced concrete solid slab bridge, in Friesland, the Netherlands was tested until failure. One of the goals of the experiment is to analyze the failure mode of the slab bridge under a tandem of 4 wheel loads and to compare the capacity of the full bridge structure to the predicted results, to have an idea of the residual strength of existing bridges. The methods used are experi-mental (testing of the bridge to failure in two of its five spans) and analytical. The analytical work involved predicting the bending moment capacity, the shear capacity and the punching capacity of the bridge. In both spans, the bridge failed in flexure. The total capacity during the experiment was significantly higher than pre-dicted. The results indicate that the traditional rating procedures for shear are very conservative when applied to slab bridges that benefit from transverse load redistribution.

You can find the slides here:

Karen also presented the paper of her BSc thesis project. The abstract of this paper is as follows:

An analysis and visual inspection is presented of the bridge “Quebrada de Tambura”. This study emphasizes on the visual inspection of the bridge, the elements taken into consideration for the assessment, and the relevant failure modes that can be identified throughout the process, leading to a recommendation for maintenance.
In addition, CSI Bridge software is used for the case study of the bridge “Quebrada de Tambura” located in the Imbabura province in Ecuador, and where possible, causes for the identified failure modes are included in the model, such as settlements.
Finally, the processed and analyzed information was used for the proposal for maintenance of the bridge, including the underpinning of piles and foundations, and the use of carbon fiber reinforcements (CFRP) in shear-critical beams as calculated by the Sika program.

Tuesday, September 13, 2016

Afschuifcapaciteit van betonnen plaatbruggen

A bit of Dutch today :)

I recently gave a presentation with an overview of the practical recommendations that resulted from my PhD Thesis. For those of you who speak Dutch, you can find the slides below:

Thursday, September 8, 2016

Using Eurocodes and AASHTO for assessing shear in slab bridges

We've recently published a paper in the Proceedings of the Institution of Civil Engineers - Bridge Engineering. You can find this paper online. The abstract is as follows:

Reinforced concrete short-span solid-slab bridges are used to compare Dutch and North American practices. As an assessment of existing solid-slab bridges in the Netherlands showed that the shear capacity is often governing, this paper provides a comparison between Aashto (American Association of State Highway and Transportation Officials) practice and a method based on the Eurocodes, and recommendations from experimental research for the shear capacity of slab bridges under live loads. The results from recent slab shear experiments conducted at Delft University of Technology indicate that slabs benefit from transverse force redistribution. For ten selected cases of straight solid-slab bridges, unity checks (the ratio between the design value of the applied shear force and the
design beam shear resistance) are calculated according to the Eurocode-based method and the Aashto method. The results show similar design shear forces but higher shear resistances in the North American practice, which is not surprising as the associated reliability index for Aashto is lower.