Simon Waldman https://www.simonwaldman.me.uk Fri, 27 Jul 2018 08:12:24 +0000 en-US hourly 1 Academic reading : My updated workflow https://www.simonwaldman.me.uk/2018/07/academic-reading-my-updated-workflow/ Fri, 27 Jul 2018 08:12:24 +0000 https://www.simonwaldman.me.uk/?p=556 When I started my PhD, one of the short-term goals that I set myself was to figure out how to efficiently read and annotate papers on a tablet – it’s much nicer than doing so on an upright screen, and more convenient and less paper-intensive than printing things out and then recording notes. I developed a nice workflow, and blogged about it elsewhere…

Since then things have changed a little due to software updates so, following a recent question on twitter as to how I do things, I thought I’d update the post and put it here.

To follow this method, you will need:

  • Zotero – an open source reference management system. It’s similar to the better-known Mendeley, but a little less polished, and a lot less owned by Elsevier (with the associated potential for future lock-in).
  • The Zotero Connector for your chosen browser. Firefox, Chrome and Safari are supported.
  • Zotfile – an addon for Zotero.
  • An Android tablet (I use a Nexus 9, but anything will do so long as it’s big enough to read a journal article on)
  • A PDF reader and annotator for the tablet which complies with the standards for such things – not all do, and if they don’t then you’ll have trouble. I use EzPDF.
  • Dropbox on the PC. A similar product (OneDrive, Google Drive, etc) could probably be used instead, but I have’t tried.
  • Dropsync on Android, which keeps a given folder in sync between Dropbox and your tablet. I think the free version will do. Dropbox’s own Android client will not work for this any more, because the way that it passes a PDF to a PDF reading app doesn’t allow for annotations to be saved and passed back again.

I’m not going to explain how to set it all up – it’s mostly fairly self-explanatory. Here’s how I use it:

Step 1: Grabbing new articles

When the Zotero Connector is installed, and Zotero is running in the background, sites such as Google Scholar and ScienceDirect have an extra icon in the address bar. Clicking that icon saves the paper you’re looking at as a reference, and often manages to grab the PDF too. Sometimes you have to help out with the PDF, depending on how obtuse the publishers’ paywalls are being that day. These days Zotero is remarkably good at automatically extracting all of the article’s metadata, but it’s wise to check as it sometimes needs help – especially on items that are (for instance) reports published by commercial bodies and not part of established academic literature.

Immediately after importing a PDF into Zotero I normally mark it with an “_unread” tag. I have a saved search set up to show me everything with that tag.

Step 2: Sending an article to the tablet

With Zotfile properly configured, simply right-clicking on a reference and selecting “Send to tablet” causes a copy to be put in a designated folder on Dropbox. Within an hour (configurable), Dropsync will copy this to the tablet.

Step 3: Reading and annotating

On the tablet, I open the PDF in EzPDF. I read through it, inserting sticky notes or highlighting as I go. I don’t use the more advanced annotation features, because they don’t convert properly later. They don’t really add anything anyway.

Step 4: Back on the PC

After waiting long enough to be sure that Dropsync has synced (or doing so manually), I right-click on the reference in Zotero, select “Get from tablet”, and it’s grabbed back from Dropbox. Annotations are automagically extracted and put into a searchable Note. This includes text in the PDF that has been highlighted.
At this point I usually skim through these annotations, while the paper is still reasonably fresh in my mind, and write another note with a brief summary.

When writing

Zotero has good support for managing one’s citations and bibliography in Word, through a Word add-in. It can also export BiBTeX, although this has a few wrinkles that usually lead to a bit of manual editing.

 

There we go. I hope that’s helpful to folk, but please ask questions if anything is unclear!

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Publication, of a sort… a corrigendum. https://www.simonwaldman.me.uk/2018/07/publication-of-a-sort-corrigendum/ Thu, 26 Jul 2018 07:50:08 +0000 https://www.simonwaldman.me.uk/?p=550 Everybody in academia receives email spam, much of it from China, inviting us to conferences that, if they exist, we probably don’t want to go to. One ignores it, and hits “delete”. Late last year I was about to do that when I realised that on this occasion, it was a genuine email from a Chinese PhD student who was using some code that I had published, and asking for help with it. Great!

I couldn’t immediately understand why the code wasn’t working for this student, so I asked him to send his files to me… and I found a bug in my code. With a growing sense of dread, I realised that this bug would have affected results that were already published. I notified my co-authors on the paper and in haste, on evenings and weekends (because this was not my full-time job at the time), I corrected the code, reran a hydrodyanamic model, redid the analysis… and found to my relief that the overall conclusions of the paper were not affected and so there would be no need for a retraction. It did, however, feel as though the record should be corrected, so I got in touch with the editor, and… long story short, a “corrigendum” to the original paper appeared online today. For those without a subscription to Ocean & Coastal Management, I’m also hosting it here for now.

I was already an advocate for good software development practices in science, in order to reduce the liklihood of exactly this sort of thing, and now my feeling on this matter is strengthened…

If you have been using my code for inserting tidal turbines into Delft3D you should make sure that you are using the current version, which had this error fixed in December 2017.

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Corrections accepted! https://www.simonwaldman.me.uk/2018/07/corrections-accepted/ Thu, 26 Jul 2018 07:35:05 +0000 https://www.simonwaldman.me.uk/?p=542 When I had my viva I reflected that although it was an important milestone, it didn’t feel very climactic because it was simply a gate passed beyond which there was more work to do.

A few weeks ago I finally got word back from my internal examiner that my thesis corrections had been accepted. This felt far more joyful and climatic, because this was an agreement that from an academic perspective, I had passed and would receive a PhD; the only remaining hurdles were bureaucratic ones.

A week later I printed four copies of the thesis and organised an overnight trip to Edinburgh to get them bound and handed in. I got a receipt, and I clutched on to it like the special document that it was. This was what I was waiting for – the point at which I could fully relax. Well, before worrying about the next job 😉

 

Two pictures. On the left, a cardboard box with "Simon's Thesis" scrawled on the top in marker. On the right, four hard bound theses - black books with gold lettering.

Before and after. Photos: Author.

 

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Relocation, relocation, relocation https://www.simonwaldman.me.uk/2018/05/relocation-relocation-relocation/ https://www.simonwaldman.me.uk/2018/05/relocation-relocation-relocation/#comments Sat, 05 May 2018 20:53:32 +0000 https://www.simonwaldman.me.uk/?p=530 Photograph of an art installation consisting of two very high piles of brightly coloured luggage.

Photo: Susanne Nilsson, Flickr user infomastern. Licensed CC BY-SA 2.0.

I’m about half way through a one year contract, so of course much of my headspace is occupied with wondering what comes next. (I’d rather it was occupied with great research, or any number of other things. This is one of many problems with the early-career norm of short-term contracts, but that’s another topic.)

As I look around at job adverts, naturally they are all over the world, and also varying in length. Recently I found myself looking at a short one in the US and thinking “I’m not sure I want to relocate intercontinentally for just a year”. My initial thinking was that I’d consider it more seriously for two or three years, but a one-year contract wasn’t worth the upheaval.

Then my officemate pointed out that I had jumped at the opportunity to live in Japan for two months, which is much shorter. I replied that I hadn’t actually “moved” there, it was simply a visit. But where does one draw the line? In my head, two or more years is definitely moving to a place, while two months is definitely a visit. Could a year be considered from either angle?

Possibly it’s less about duration than other things. In Japan I lived out of a suitcase, but I don’t think it really comes down to how many belongings one takes with. Perhaps it has more to do with whether one is getting paid in the other country, dealing with bank accounts, setting up local healthcare provision, househunting, etc.

Food for thought, and in the meantime I’m not ruling anything out.

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EIMR, and future wave resource https://www.simonwaldman.me.uk/2018/04/eimr-and-future-wave-resource/ https://www.simonwaldman.me.uk/2018/04/eimr-and-future-wave-resource/#comments Wed, 25 Apr 2018 22:20:14 +0000 https://www.simonwaldman.me.uk/?p=524 This week I am at a conference on Environmental Interactions of Marine Renewables (EIMR), in Orkney. It’s the kind of event that covers quite a broad area, and most of it isn’t in line with my “interests” in a narrow sense – but the breadth makes it really helpful for talking to a wide range of people, and hearing about a wide range of research.

The majority of the research here is about the effects that renewable energy extraction will have on the environment, which is certainly an important topic. A few, including my own poster, look at “environmental interactions” in the other direction, in my case asking “how will the wave power arriving at the west coast of Orkney change, as the planet warms in the future?”

It’s only a short, preliminary look at the problem, and it has a high level of uncertainty attached. However, it looks as though the change between now and 2100 will be small. That’s good news for wave energy developers.

  View poster

 

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Viva!!! https://www.simonwaldman.me.uk/2018/02/viva/ Fri, 02 Feb 2018 11:03:51 +0000 https://www.simonwaldman.me.uk/?p=510 Yesterday was my viva, or thesis defence for those used to that terminology. For those not familiar, in the UK system this means an oral exam of unknown length, in private, with the candidate and two examiners – one from my university, one from elsewhere. It’s nerve-wracking in the lead-up, and one hears plenty of horror stories as well as the (far more common) good tales.

Mine was fine 🙂 I wouldn’t say that I enjoyed it, as some people describe, but it went for three and a bit hours with only a few difficult moments. My examiners were rigorous yet kind, in that when they identified areas of theory that I was clearly a little hazy about they noted that and backed off, rather than continuing to push. They asked for reasonable changes, which will improve the thesis, and one can’t really ask for better than that!

Cartoon of a spider in a viva, using many arms to write in different places and respod to multiple questions at the same time. Caption: "having extra arms helps in a viva, but not as much as an extra brain would".

Comic by errantscience.com, licensed CC-BY-NC.

So the upshot is that I’ve passed, subject to corrections. This is a huge milestone, in that – so long as I do the corrections to the examiner’s satisfaction – I will be awarded the degree. It’s certainly the end of a lot of tension; an evening of relief.

Yet, in some ways it doesn’t feel climatic, and when people ask “how did it go?” it’s a little hard to answer – because the vast majority of candidates who get to this stage pass with corrections (their supervisors would advise them against submitting the thesis if they wouldn’t), and it was very likely that I would as well, and I did! There’s no real surprise, or even a lot of uncertainty, involved – the real question was how significant the corrections would be (mine are not trivial, but are managable). So I’m certainly relieved, and relaxed, compared to this time yesterday, but at the same time it doesn’t feel like I’ve finished, because I haven’t. It would perhaps be more accurate to say that I’ve passed a gate and moved on to the next stage, and there’s still work to be done (and bureaucratic hoops to jump through) before I can be finished and move on.

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Thoughts on publishing in The Conversation https://www.simonwaldman.me.uk/2018/01/thoughts-on-publishing-in-the-conversation/ https://www.simonwaldman.me.uk/2018/01/thoughts-on-publishing-in-the-conversation/#comments Sun, 14 Jan 2018 13:45:08 +0000 https://www.simonwaldman.me.uk/?p=494 Last week, as regular readers will know, I had a piece published in The Conversation. Hopefully it will help communicate some of my work to a wider, non-specialist audience, but the process was also interesting.

It’s the first time in many years – since returning to university for my masters – that I’ve tried to write something journalistic. I used to do such articles long ago for the trade press in my old industry, but I never felt very good at it; the writing seemed stilted to me. I wondered whether having trained myself in academic writing would make this more difficult – but to my surprise, the opposite was true.

Small child in a hoodie shouting.

Communication? (Photo: Flickr user mindaugasdanys, licensed CC-BY-2.0)

I did have to consciously avoid some of the usual turns of phrase from journal articles, and try to write more as people speak, but it was much smoother than past experience. I attribute this to three things: part of it is simply that I’ve had more writing experience now. Part will be because this was shorter, so I was concentrating on optimising rather than writing lots. The biggest part was probably the input of the editor.

Unlike the trade magazines that I’ve written for before, which simply use your text verbatim, The Conversation (hereafter TC) assigns a professional editor to each article, as a newspaper might do. However, wheras for a newspaper you’d submit your copy and then be at the editor’s mercy, for TC it’s a two-way process where the researcher gets final approval of everything, including pictures and the headline. We did go back and forth a couple of times where the editor made things a bit too hyperbolic, claiming things that weren’t supported by the study – but she was willing to roll them back when I explained, and she did wonders for improving the readability of the article for the public. It’s a good way of working.

TC provides analytics, and I spent some of last week glued to that page. So far, three days after it appeared, it’s had 1450 readers. This is gratifying, and vastly surpasses both the audience that anything of mine has had before, and the audience that the vast majority of journal articles ever get. For a while I had a response of “eek. So many people. What if it’s controversial, or wrong?”, and I had to remind myself that I do have confidence in my results, and so does a peer reviewer or two.

On Twitter I was gratified to see it retweeted by such accounts as @NERCscience and @BGSScotland, in addition to my own institution. Most of those reads were in the first two days, while it was at the top of the feeds and making its way around social media, and it’s leveled off now; it probably won’t ever get many more. 28% of readers were in the US, which surprised me, 26% in the UK, which didn’t, and 31% in Other, which I wish was broken down more. I hope that a lot of that is Japan, since the article is about the energy situation there.

A dog staring intently at a laptop screen

Readers. (Photo:
Jean Beaufort. Public domain (CC0))

TC also provides analytics that compare your reader numbers to articles published by others from your own institution, and I found myself feeling surprisingly competitive as I watched mine climb from the bottom to… well, quite near the bottom still. The high-flyers there are timely articles that tie in with a news story, or social science based ones that resonate with the zeitgeist and get picked up and republished by The Guardian. That’s fair enough. But having more readers than the articles by two of my former bosses is strangely gratifying!

This wasn’t a major time investment. It probably took two hours to write – which would be less with practice – and maybe an hour after that for editing and correspondence. When considered in the context of the number of hours that go into performing research and getting it into journals, it’s nothing – and it’s a nothing that brings the research to more than a thousand eyes. Good experience, would do again 🙂

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After the tsunami: how tidal energy could help Japan with its nuclear power problem https://www.simonwaldman.me.uk/2018/01/after-the-tsunami-how-tidal-energy-could-help-japan-with-its-nuclear-power-problem/ Wed, 10 Jan 2018 22:16:41 +0000 https://www.simonwaldman.me.uk/?p=469

This article originally appeared in The Conversation. It is licensed CC-BY-ND. Click here for original.

Japan was the third-largest producer of nuclear power in the world in 2011. Then, on March 11 of that year, an earthquake of magnitude 9 was followed by a catastrophic tsunami, resulting in the first nuclear disaster of the 21st century – at the Fukushima Daiichi power station. The country’s nuclear plants were shut down, and within a year Japan had become the world’s second biggest importer of fossil fuels.

Before the tsunami, nuclear power provided 25% of Japan’s electricity, and a strategic plan was in place to expand this to 50%. Japan has few fossil-fuel resources of its own, so most of the resulting shortfall in electricity was made up by burning imported coal, oil and gas – an unsustainable solution from both environmental and economic perspectives.

But on a group of islands to the west, tidal power may offer part of the solution to the country’s energy needs.

A renewable future

By 2030, the Japanese government plans once more for nuclear power to provide around 21% of the nation’s electricity – which is highly controversial – but also stipulates (see page 8) that 22-24% should be delivered by renewable energy sources. At a local scale, two prefectural governments, Fukushima and Nagano, have pledged that all of their electricity will come from renewables by 2050.

Most of the new renewable energy available in 2030 is likely to be solar and wind, along with existing hydropower, but some contribution from the tides is possible. To this end, a zone in the Goto Islands of Nagasaki Prefecture has been designated for tidal energy development, and a cluster of companies plans to install the first turbine in 2019. This project will be of the tidal stream type, where underwater turbines are placed in the free flow without any dam or barrage, similar to the MeyGen project in Scotland.

Installing a tidal stream turbine base at the MeyGen project off the coast of Caithness in northeast Scotland.
MeyGen/Atlantis Resources

When tidal turbines are placed in a channel, they remove energy from the flow. This causes it to slow, and represents a partial blockage of that channel. In turn, that means that the behaviour of the tides in an area after turbines are installed can be different to how it was before. Understanding and predicting this change is important for estimating both how much energy is available and the impacts of removing it; if there are too many turbines, the flow could slow too much and much less power would be generated.

Going with the flow

My recent work, in collaboration with researchers in Scotland and Japan, involved using a computer simulation of tidal flow around the Goto Islands to investigate the effects of installing large numbers of turbines.

We estimated that between 24 and 79 MW of power could be generated from the designated area. The reason for this range is because the number of turbines that are used will ultimately depend on economic considerations. The first few will offer the most benefit, while later ones will suffer from diminishing returns. Tens of megawatts represents a very small contribution to Japan’s overall electricity needs, but a very large chunk of the local demand in these islands.

A number of parallel channels run through the Goto archipelago, of which two are within the tidal energy zone. In situations like this, it is common to find that adding turbines to one channel simply causes the water to flow by a different route. That means that to harvest energy efficiently we need to collect it from all the channels at once – an expensive proposition for a new technology.

In the Goto Islands, all the channels run parallel but separate to each other, never merging or meeting, so they can each be exploited without affecting the others.
Elsevier, Author provided

However, our modelling shows (see sections 4 and 7.2) that the parallel channels in Goto do not behave this way; instead, they are independent of each other. The reason for this unusual behaviour lies in the geometry of the islands.

Partially blocking a channel causes water levels to rise a little behind the blockage. The interactions that we see elsewhere in the world are a result of this extra water “spilling” into other channels. In Goto, because all of the channels run separately from one end to the other without meeting or merging, and because their mouths are spaced well apart, there is no way for this “overspill” to occur. Consequently, any or all of the channels can be exploited without affecting the others, which should make the area more attractive for commercial development.

If the relatively small-scale development in Goto is a success, it could act as a proving ground and a springboard, leading to the use of tidal energy in other locations all over Japan. And for a country ambivalent about its return to dependence on nuclear power, additional contributions from renewable energy will be welcome.

The Conversation

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“My favourite tool” https://www.simonwaldman.me.uk/2018/01/my-favourite-tool/ Wed, 03 Jan 2018 00:07:45 +0000 https://www.simonwaldman.me.uk/?p=459

Software Carpentry are running a series of short blog posts where they ask their supporters what their favourite tools are. Most have been software, although a few people have gone for things like “asking for help”. QGIS probably isn’t my favourite tool, but my first few choices had already been mentioned by others…

This post originally appeared at https://software-carpentry.org/blog/2018/01/waldman-fave.html

QGIS (formerly Quantum GIS) is an open source Geographic Information System.

QGIS is capable of advanced analysis and cartography, but I don’t use it for that.

In my research in hydrodynamic modelling, I deal with a lot of spatial data – coastlines, bathymetry, and the like – and this will eventually be processed and plotted using R, MATLAB or Python.

But if I’ve received a file and simply want to take a quick look at it, or if I want to quickly compare two files that use different coordinate systems and see if things line up, most of the time I can throw the file at QGIS and it will show it to me with a few clicks. This approach lacks the reproducibility of a coded solution, but it’s an awful lot quicker for a throwaway visualisation.

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