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 http://www.mendeley.com/videos-tutorials/, 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.

Tuesday, September 6, 2016

PhD Defenses around the World: a Viva in New Zealand

Felicity Bright is a rehabilitation researcher and lecturer at AUT University in Auckland, New Zealand. Her professional background is in speech-language therapy. She recently defended her PhD, entitled “Reconceptualising engagement: A relational practice with people experiencing communication disability after stroke”. Felicity is currently working to disseminate findings. She is exploring how best to work with rehabilitation practitioners to implement the knowledge gained through her PhD, and is working on several projects to extend her doctoral research.

In New Zealand, it is common to do a viva as part of the PhD examination process. It is compulsory at most universities. At AUT University, the viva is attended by the convenor (a senior academic member of the university staff who oversees the process and ensures it follows regulations and is fair to the student), the three examiners, the student and their supervisor/s. The examiners may attend in person or via videoconference. The supervisors are there to support the student and may not participate in the viva.

My viva was scheduled in late March, four months after I submitted my PhD for examination. One week prior to the viva, my primary supervisor and I met the convenor to discuss the viva. At this time, I found out who my examiners were and received their reports. I had had several conversations with my supervisors and suggested names; the three examiners were all people we had discussed over the course of my study. The reports were de-identified, though it was possible to guess who wrote which report (and my guesses were correct!). I took a few days to read and digest the results. I discussed them with colleagues, and did several mock vivas with my supervisors.

However, five days prior to my viva, I broke my foot. I spent two nights in hospital and had surgery. While I was initially convinced I could do the viva as planned, it didn’t take long for me to realise that wasn’t going to be possible. I couldn’t sit for more than 20 minutes, let alone have a robust scholarly discussion about my research! The university postgraduate office was able to reschedule the viva for two weeks’ time. This extra time gave me some breathing space. After my mock vivas, I’d been highly anxious. That anxiety dissipated and I went into the viva feeling cautiously confident: confident in my knowledge and my contributions to knowledge, and confident in my ability to answer questions, even the tricky ones!

On the day of the viva, my supervisor and I arrived at the University Postgraduate Centre, where all vivas are held. The staff were welcoming and showed me into a waiting room which they’d set up for me, with extra chairs and pillows. I had a last minute change of convenor, so met her briefly before it started. While I waited, the postgrad staff were getting the videoconference organised. One examiner was in the country on holiday and was able to attend in person; the other two were on video. I was called in fairly quickly and re-introduced to everyone. I’d met all of my examiners at different times – aphasia rehabilitation research is a rather small world!
My convenor explained there would be four core themes they would focus the questions around, and I was invited to start the viva by providing an overview of my research. I spent about five minutes discussing the research, starting with the experiences which prompted my research, through to detailing the novel contributions my research made. I then spent the next hour or so responding to their questions. When the examiners submitted their reports, they provided a list of questions. These were not given to me, but the likely areas were evident in their written reports. The viva was did not take a transactional question-answer format. Instead, it was a discussion which occurred in response to questions about the research methodology, process and findings. The examiners also queried how the findings connected to other research in the field, and discussed areas for future research.
After an hour when the examiners had asked their questions, my supervisor and I left the room while they deliberated. When I was called back in, I was advised of the outcome. I passed with no amendments, bar correcting spelling errors. After this, the convenor left. After a brief chat with the examiners on videoconference, they signed off, but my supervisor and I kept chatting with on-site examiner for a while longer. This was a nice relaxed way to finish.

My viva was an enjoyable process
. The time passed so quickly. While I’d been a little nervous before arriving, as soon as I went into the examination room, I felt at ease. As I’ve heard others say, the viva is the only time you have the opportunity to discuss your research with three topic/methodology experts who have read your work and are interested in it. My examiners asked some challenging questions (tip: always have a sip of water before answering the question – it gives you some time to think). They were all interested and encouraging and made thoughtful suggestions for how I could extend my research further. My supervisor made notes throughout the viva, which meant the key questions and areas for further consideration are captured for me to reflect on further. The viva was a very positive experience, and I’m very pleased I had the opportunity to discuss and defend my work.

After the viva, there was champagne. My colleagues came, as did my second supervisor, and I was able to start to relax, before heading home to the onslaught of small children and the routine of everyday life. Later that week, I went through the thesis, fixed the spelling errors, had a last minute issue with Endnote (thank goodness for the patient university librarian), then submitted it to our online repository, printed copies for the university, myself and my supervisors, and wrote the synopsis for graduation in July.
UA-49678081-1