My first paper: one year on


Today marks one year since the publication of my first academic paper in the Orphanet Journal of Rare Diseases (OJRD), and with several other papers currently at various stages of completion, I thought I’d take a quick look to see how my first has fared over the last 12 months[1].


The paper was written while I worked for the TREAT-NMD Alliance, an international translational medicine research network connecting scientists, clinicians, patients and patient organisations, and the pharmaceutical industry in the neuromuscular field. In rare diseases, finding appropriately equipped clinical trial sites and patient populations is often tricky, and the Care and Trial Site Registry (CTSR) is of the resources TREAT-NMD provides to overcome these challenges. The paper gives an overview of the CTSR and analyses the data it held on Duchenne muscular dystrophy (DMD).

The journal

The OJRD is an open-access journal, with a current Impact Factor of 3.96[2], and with papers being free to download and re-host elsewhere. For that reason, the access data below is an underestimate: a Google Scholar search currently indexes “11 versions” hosted in various places, and only data on BioMed Central websites are tracked, despite being indexed in other bibliographic databases and the full-text being included on Springer Link.

Some data


The publisher itself provides basic metrics, and as of 22nd October 2014 the paper had been accessed 3183 times via PubMed Central and is therefore “Highly Accessed”. PubMed Central also includes the paper’s Altmetric score of 21, though one has to click through for full details and the score in context. Although the utility of Altmetric scores is debated, especially their ‘social media’ component, they allow comparison with other tracked articles. The paper is apparently the fifth-highest scoring article in the OJRD (98th percentile); is the top scoring article amongst those of similar age (± 6 weeks); and is in the top 5% of all 2,446,094 articles tracked by Altmetric. The article has also been cited in 2 other papers, both written by people with whom I previously worked.

So what does it all mean?

Well, it is nice to know that the paper has been accessed (and hopefully read)! More seriously, this points to the fact that the jury is still out on whether “accesses” or Altmetric scores are good indicators of the utility of an academic paper to others. Citations, rather than other metrics, are the main way in which academic prestige is accumulated, and so from this perspective the paper is not a particularly high flier! However, the subject matter of the paper also mitigates against this: it does not describe a new gene or other discovery, but a tool which may be of use to the neuromuscular field in conducting trials, so I would not necessarily expect a particularly high citation count.

geographicI suspect metrics are rather more useful, however, in terms of raising the profile of research and beginning to understand your readers. This is an ever present concern given the focus on “impact” by funding bodies such as Research Councils UK. In turn, this may have real-world effects: in the case of my paper, by raising awareness of the utility of the CTSR in clinical research, it may help with the planning and conduct of clinical trials.

Since I wrote the paper, the CTSR has expanded to included neurodegenerative diseases as well as neuromuscular diseases, and now has an integrated Phenosearch tool to allow “match-making” amongst registered researchers with undiagnosed patients – ultimately improving the knowledge in the rare disease field, and hopefully improving the treatment available to patients. For me, that is the most rewarding part of having published this paper.

  1. All values in this blog post will, by their nature, be out of date fairly soon…  ↩
  2. The actual value of Impact Factors is the source of much debate and criticism, much of which I agree with, but this is a much bigger discussion for another time…  ↩

Regular Expressions with RegExr

RegExr Screenshot

RegExr Screenshot (Sunil Rodger)

Regular expressions are incredibly useful when programming for pattern matching against strings, but they can be quite confusing when you’re first getting started with them. I’ve been using them intermittently for several years (scripting is not my day job) and certainly cannot claim to have mastered their use.

RegExr is a fantastic tool for checking that your regular expressions work as intended, or just playing with them to see what you can do. Although there are apps dedicated to this which are more fully-featured, such as Oyster for the Mac, RegExr is a very good starting point.

Underground Pasts


London Underground Train, 1973 at Oxford Circus by Graham Lees

Last year marked the 150th anniversary of the London Underground, and there were plenty of special events, commemorative gifts, celebratory ramblings and features to celebrate. In fact, such was the enthusiasm around the event, the general tendancy to complain about delayed trains, overcrowding and ticket prices on the Tube was (momentarily, at least) forgotten.

But which past are we referring to? Like anything else, there is always more than one narrative of the past to consider. For all the focus on the Tube itself, something I have always found fascinating about transportation networks is their relationship with the city they serve. On one level, there is the obvious symbiotic relationship between a network constructed to serve flows of people, and the people themselves who in turn respond to the existence and growth of the network. The development of Metroland in the 1930s is one historic example, but more recently the London Overground demonstrates how investment can also spur latent demand by offering new journey possibilities, frequent services and a safe environment.

King's Cross Station by Nick

King’s Cross Station by Nick

However, at a more fundamental level the experiences of people who use the network are brief moments like that shown in the image above, usually lost in time and forgotten (unless in the case of an exceptionally bad delay such as the 2003 London power cut). In the case of the London Underground, its past is not only the history of the network itself, but the experiences of those who travelled on it.

That is what makes this exhibition of Bob Mazzer’s photographs, taken on the Underground in the 1980s so intriguing. Recently featured on Annie Mole’s Going Underground Blog, they offer a fascinating glimpse of London’s social history through the lens of a commuter at the time.

The exhibition runs until 13th July at the Howard Griffin Gallery, 189 Shoreditch High St, London, E1 6HU. I will certainly be making the effort to go and see it.

Train “Delay Repay” Forms Online


I frequently travel by train when visiting family and friends, which in the UK is expensive – especially during ‘peak’ periods, if you are not eligible for a railcard, or are unable to purchase advance fares which permit travel only on booked trains on specific dates.

One way to reduce costs is to claim money back when your train is delayed, as many operators offer compensation if a journey is more than 30 minutes late. This is often 50% of the value of the ticket for delays up to 59 minutes, and 100% for more than an hour. Compensation is provided in Rail Travel Vouchers, which can be redeemed at ticket offices.

Claiming this used to involve filling out a paper form and sending the original tickets to the company, but several companies now offer this electronically. You will need a good quality scan of the tickets to upload, and full details of your journey.

As many of my journeys are to Cambridge, the relevant operators for me are:

Three “Feel at Home” Roaming Map

UK Mobile operator Three announced last week that their “Feel at Home” service would be extended to five new countries on 1st July, on top of their previous expansion in December 2013. When the service debuted in August 2013, it was available in 7 countries.

Although the Three website offers a map of the areas covered by Feel at Home, it uses a pin to mark each country. I wanted to visualise the actual territory covered, so I’ve quickly created a map using a Google Fusion Tables and publicly shared KML boundary data. This is complete except for Macau, which wasn’t in the boundary file – I’d be happy to include this if there is a more complete country boundary dataset available.

Feel at Home is now available in: Australia, Austria, Denmark, France, Finland, Hong Kong, Indonesia, Italy, Israel, Macau, Norway, the Republic of Ireland, Sri Lanka, Sweden, Switzerland, and the United States (countries in italics are from 1st July 2014).

About Feel at Home

Feel at Home allows Three customers to use their monthly inclusive texts and minutes while abroad in participating countries to contact UK numbers as if they at home in the UK. There are some restrictions: if you have all-you-can-eat data, calls or text these are limited to 25GB data, 3000 minutes and 5000 texts respectively. The tethering/personal hotspot facility is also not available. In spite of these limits, it is a pretty generous deal.

I discovered just how much difference this can make with two visits to the United States in 2013. In July I accrued more than £20 of roaming charges through light use in a couple of days, while in December – when I stayed for longer – I was able to use data as much as I needed without incurring any charges. As Three’s plans are pretty good value anyhow (mine is less than £20/month), this is a bargain.

Other than brief calls to family in the UK, I don’t find myself using texts and minutes from abroad, but the ability to access mobile data without worrying about the cost when you’re in an unfamiliar environment is fantastic. You can also use services such as WhatsApp and iMessage for messaging, and Skype or FaceTime for calls if needed. I find Feel at Home invaluable when I’m visiting a country where it is available, and hope it is extended to other countries soon.

The European Parliament will abolish charges for roaming in the EU by December 2015, which is long overdue and very welcome, but in the meantime (and for the non-EU countries it covers) Three’s Feel at Home is a good start.

On Apple Macs

Apple Command Key by Fi20100, on Flickr

Apple Command Key by Fi20100, on Flickr

In late 2009, I finally purchased my first Mac. My five-year-old self-built PC was on its last legs, and I had coveted a Mac Pro for some time. Alas, this was somewhat out of my budget and I settled for a Mac Mini (since passed on to my parents when I purchased a MacBook Pro the following summer).

I had intended at the time to document the transition from Windows to Mac but never got round to it, so this will be a series of occasional retrospective posts on the practicalities of that transition.

Moving from a PC to a Mac did take some getting used to. As a power user, I found that re-learning keyboard shortcuts was most challenging – I continued to use a PC at work, and still do, which probably didn’t help. Most common shortcuts were pretty much the same, substituting  (Command) for Ctrl in shortcuts such as Ctrl + C (copy), Ctrl + P (print) and so on.

More challenging to commit to muscle memory were those that were more significantly different. The trickiest was getting used to ⌘ + O for open, rather than Enter/Return, closely followed by ⌘ + Tab to change between applications being distinct from ⌘ + ` to change between windows within an application. This is quite unlike Microsoft Windows, which makes no such distinction with Alt + Tab to cycle between all open windows, regardless of application. Other things such as the inability to cut files (only to copy/paste them) also initially threw me.

After a few months, this ceased to be an real problem – I guess my muscle-memory just adapted to using both systems on a daily basis. There are still moments when I curse that MacOS X doesn’t have something Windows has, or that Windows does something illogical when the equivalent is very straightforward on MacOS X. But generally I am well settled into the Mac world, which I generally prefer to battling with Windows, and when the time comes I suspect that this MacBook Pro will be replaced by a MacBook Air…

A Protracted Absence

More than four and a half years have passed since I last updated this blog. It’s about time that changed!

A fresh install of WordPress was first on the agenda, though the layout may change as I tweak the site. A number of the old posts were no longer relevant at all – such as a test of GNER Wifi when it was new – so I have not reinstated them. I have left are those that might still be useful (or simply quaint, such as my early thoughts on the iPhone and the iPhone 3G when it was announced).

More regular updates to both this blog and the site will be forthcoming…

iPhone 3G

Although I’ve been too busy to blog in the last couple of months, after my previous entry I was keeping a pretty close eye on the iPhone rumours as they trickled (flooded?!) onto the net.

The announcement of the iPhone 3G last Monday has created a bit of a stir, though the release of a 3G iPhone was probably one of the worst kept tech secrets this year.

So what of my predictions/wishlist, which included 3G, GPS, more memory, and a video camera, as well as a general comment on the cost of the device?

  • 3G: Check, though there is currently some debate which network speeds the “UMTS/HSDPA” listed in the specs will actually support (1.8, 3.6 or 7.2Mbit/s, though one of the first two seems more likely).
  • GPS: Check. Although the SDK states that “[a]pplications may not be designed or marketed for real time route guidance” amongst other things, I imagine that Apple could come to a suitable arrangement with well-known companies such as TomTom or Garmin.
  • More memory: No, and this surprised me somewhat at first. But a 32GB iPhone would presumably compete with the iPod touch, and I imagine bumping that up to 64GB to maintain product differentiation would make it prohibitively expensive and start competing with the iPod Classic
  • Video camera: No (and not even an upgrade of the existing camera).
  • Price: Slashed. On a £35/month contract (600 mins, 500 texts) with O2, the iPhone will be £59(8GB)/£159(16GB), whilst on a £45/month contract (1200 mins, 500 texts) it will be Free(8GB)/£59 respectively.

In addition subsidizing it on a contract, O2 will be offering a pay-as-you-go version, though the price has yet to be announced, and one of the key benefits of the contract is unlimited/fair use data which would probably cost a lot on PAYG. iPhone users will also have access to more than 9000 commercial wifi hotspots for free, with the announcement that O2 have also partnered with BT Openzone, adding a further 3000 wifi hotspots to the 6000 available through The Cloud.

There is also a suggestion that tethering the iPhone 3G to a laptop may be officially sanctioned by O2 – if so, this is fantastic. If not, I imagine that once jailbroken software is released, such tethering will be achievable sooner or later.

So, all in all, not a truly groundbreaking revision of the iPhone. The lack of Flash support is still a pain, as is the fact that there is still no cut and paste. I imagine these features could both be shipped in a software update, if Apple wants to…

Something which could not be upgraded like this is the capacity: it is a real shame there has not been an increase in capacity with the iPhone 3G. With the App Store on the way, in addition to personal music and video content, more than 16GB on the high-end iPhone would have been good. I imagine there will be a revision of the iPhone 3G, perhaps around Christmas, which will increase the capacity to 24 or 32GB.

So, will I get the new iPhone? I’m not too sure yet. My current phone is slowly dying, the lack of 3G – my major objection to the iPhone – has gone, and it is priced much more attractively than before. But I’d still have to pay off the remainder of my existing contract, and it would be nice to have more than 16GB of storage. I imagine I’ll sit it out until maybe a month or two after the release date and see how things look then. At least it should be jailbroken by then!

iPhone Developments

A pretty cool video presentation by Steve Jobs et al demonstrating the forthcoming iPhone 2.0 Software including Enterprise tools and the SDK.

I’ve held off the iPhone bandwagon so far. The main reasons were as follows:

  • iPhone cost (£269 + £35/month tariff on O2 with 200 minutes and 200 texts – very stingy).
  • Not enough storage – I would use it as an iPod as well, and 8GB does not cover my music collection.
  • No SDK, so unsupported hacks to run anything which isn’t a web application.
  • No 3G – ubiquitous Wifi is not a reality yet, resulting in slow web browsing… and web applications.
  • (Last, but not least) an existing phone contract that would need to be paid off.

Since its original release though, changes in O2’s pricing structure, a minor iPhone upgrade, and now the announcement of iPhone Software 2.0 have changed the situation significantly.

£35 per month gets you 600mins & 500 texts, in line with other phones. 16GB solves the storage problems for me, the initial extra cost of purchase being negated by the fact that it is useful as an iPod. The SDK opens the door to native iPhone applications which are not limited by the speed of the internet connection. The Apps store allows Apple to control the platform – and you cannot complain about the cost if you wish to release a free application! If you wish to charge, is a 70/30 split fair? Is it possible to make an app for personal use only – do you have to release it to the Apps store in order to get it onto your iPhone… and if so, will this stifle development?

I am still on my old tariff, so I won’t be getting a new phone just yet. If I did, the iPhone is now looking very attractive indeed – the only significant issue for me is its lack of 3G – without this, I’d be very reluctant to buy one. However, I am an optimist, so here are my wishes/hopes for the next hardware revision:

  • 3G – essential. If iPhone v2 has this and nothing else on this list, I am still likely to buy it as my next phone.
  • GPS – becoming commonplace in high-end phones, and with the SDK would allow some very cool applications.
  • More memory? Flash prices are falling and with (hopefully) lots of interesting applications being developed, a little more storage would be nice, though not essential.
  • Video camera? I’d not use it that much, but again a common feature on phones these days and nice to have now and again.

We shall see what happens… I think 3G is almost inevitable.