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At the moment, I am spending a lot of time finishing programming projects before I swap jobs at the end of September.

It’s never too late to learn something and I am discover graphical user interface GUI programming, something that always fascinated me but that I had no experience of whatsoever (apart from the work on the MS Windows version of CHASM which is very limited in terms of user interface).

I have started to develop a small GUI for the C++ slope stability program (called hydrostab) for which I got NERC funding. I chose to implement the GUI with the Qt toolkit which is cross platform (so technically it can be compiled for MS Windows and MAC OS X although I have only developed on Linux so far). At the moment, it looks like this:

It’s not much yet at all, it’s very busy, badly organised and please forgive me the fact that nothing is properly aligned etc… So far, I have tried to make functions work and been mostly familiarising myself with the toolkit.

The important thing is that the application is multi-threaded. I have implemented the time loop in a separate thread. It means that the simulation can be controlled from the GUI during runtime. So far, the simulation can be started, paused, resumed and stopped. The example above shows a simulation that was started, paused, resumed and the confirmation dialogue before stopping it for good. It works very well so far and it will be really useful in the future. Imagine, you could for instance:

1. start the simulation, pause it, look at the first computed results and amend the parameters if necessary. No more need to wait for everything to finish.
2. set up several simulations (several slopes or several configurations of the same slope) and run them all together in separate threads. This is something some of my colleagues interested in optimisation and econometrics might be interested.

In a way, it is related to some of the high performance computing work that I have been involved with for another project but the whole graphical aspect is very new for me.

There is still a lot of work to do but it going in the right direction I think. The next step will be to create a GUI for designing the slope so that the program does not rely on the CHASM4 data format which is very limiting.

It’s been a while since the last update. A lot has been going on recently and the blog has been at the very bottom of my priority list…

To cut a very long story short, I will leave my post of Senior Research Fellow at Bristol University after the summer. I will be joining the Groundwater Unit at the Scottish Environment Protection Agency (SEPA) as a hydrogeologist. I will be based in the Dingwall office, a short bike ride from home (which will be nice). The exact start date has not been decided yet but the move will be sometimes in mid-September to early October.

There are a few reasons for the move. First of all I technically “left” Bristol almost two years ago and although my job at the university allowed me to work from home efficiently, getting a “local” job makes sense really. The new job will also be a great opportunity to get a lot of hands on experience about environmental science in practice rather than in an academic context; professionally, it is very exciting.
Finally, I think that it is fair to say that my position at Bristol was very unsafe for funding reasons. The position of a pathway 2 senior research fellow is not simple; I cost quite a lot and must find funds for a large part of my salary myself. In my case the large part was actually 85%. I had a very stressful first term in 2008 because of this and I don’t really want to be subject to that type of stress too often [note: some other types of stress are fine!].

It is a bit odd to think that I will be leaving Bristol University after the summer. I started there in December 1998, almost 10 years ago most of the friends I have in the UK I met in Bristol via work or the canoe club. Bristol is a lovely city and the job there allowed me to visit once a month or so which was good. I will miss seeing my friends during my regular visits to Bristol. There will be no excuse for them not to come and visit North Scotland though!

I am back from a trip in France visiting Electricité de France last week and I have now a lot of paper reading to go through. “A lot” is actually 323 unread papers published or “in press” in a range of journals over the past few weeks. Keeping track of papers as they are published, as you discover them and as you read them takes a substantial amount of time for an academic today. Luckily technology is your friend for that type of problem…

The problem
It is not really easy to keep track of recently published papers as there are so many journals and publications nowadays. I believe that there are two main issues with keeping track of papers for a scientist:

1. How can I be notified of recently published papers, even when I am not actively searching for them?
2. How to best organise a (growing) library containing all the papers I have discovered/read/annotated?

Being notified of new content
Luckily technology is your friend for problems like that. Indeed today, most publishers offer “web feeds” which are ideal to be automatically notified of new papers.

Web feeds are a popular way to be notified of a change on a website. A feed contains a summary of what has changed, the date of the change and also a link to the original. The websites which contains web feeds usually display a specific icon (shown on the right). For information, subscribing to a podcast is simply subscribing to a web feed that happens to contain audio or video content.

You usually manage a set of feeds using a “feed reader” or “feed aggregator” which will keep a eye on a set of feeds and update you when one of them has changed. There are a range of feed readers available. The latest editions of Mozilla Firefox and Microsoft Internet Explorer for instance allow the user to subscribe to feeds directly. I personally use Google Reader, an online service from Google. I like it because it allows me to access my feeds even if I am not using my own computer. Microsoft and Yahoo offer similar services.

This is what my “Google Reader” looks like at the moment:

On the left hand side is a list of all the feeds I have subscribed to. The main panel on the right contains a list of all unread articles that I need to go through, where they were published, when and the title. Google reader offers a range of keyboard shortcuts to quickly “mark as read” the articles that don’t interest you. When you are interested in an article, you just click on it to see an extended summary and then a button allows you to navigate straight to the journal website if you require more detail.

Some useful feeds for the hydrologist

It took me a while to build my list of feeds so here is an extract of my feeds related to hydrology.

• Advances in Geosciences
• Computers & Geosciences
• Earth Surface Processes and Landforms
• Environmental Modelling & Software
• Ground Water
• Hydrological Processes
• Hydrology and Earth System Sciences
• Hydrology and Earth System Sciences Discussions
• International Journal of Heat and Fluid Flow
• Irrigation and Drainage
• Journal of Hydrology
• Natural Hazards and Earth System Sciences
• Non linear Processes in Geophysics
• Waste Management

Some journal don’t seem to offer web feeds but luckily the ZETOC service in the UK generates feeds now. So here area few for which I had to use ZETOC:

• Water Research
• Water Resources research
• Hydrological Science Journal
• Journal of Groundwater Hydrology

Organising a personal library

Now that you have found the papers that interest you, you have to file them in your personal library. I believe that , again, this is best done using online services.

I personally favour CiteULike, a web based tool that allows you to organise a library of papers online. It comes with plugins which allows you to extract information out of most publishers websites (Wiley, Elsevier, AGU, Sciencedirect etc…) by pressing a specially crafted bookmark button called a bookmarklet. As CiteULike is a “Web 2″ or “social” service, you also rate papers, tag them or share them with others using the notion of groups. For instance, we have set-up a UoB-Hydrology library for the members of the Hydrology Group at Bristol University.

I discovered CiteULike about 18 months ago and have been using it extensively since. It is a very nice way to organise your collection of electronic papers. Have a look at my library and you could even subscribe to my library using a web feed too!
It is also possible to import/export to EndNote, therefore it can be used with Microsoft Word but it’s not directly integrated like EndNote Web. It’s a free, community based initiative. There is a proprietary equivalent called Connotea pushed by the Nature Publishing Group.

Outlook

Using web feed and a virtual library makes it a lot easier to follow the publications of scientific papers. I wish it was even easier though. I guess in the future, publishers will offer web feeds that for a set of keywords rather than the name of a journal. These keywords (or tags) could even them be automatically be used in the virtual library.

In a way, it is already possible! You can search for “groundwater hydrology” on ScienceDirect for instance and subscribe to a web feed of the results, i.e. your search is alive on and the feed will notify you of new hits in the future. I need to investigate that in more detail more actually.

In January 2008, my friend Catherine Wilson got married to Rob Branston in Ireland and then had a wedding party in Wales, near Newport.

Congratulations and best wishes for the future!

I was lucky enough to go to their wedding reception with my friend Katerina Michaelides from Bristol University. We had a great time … and great food - massive hog roast, yum!

(*) In the case of Catherine, maybe I should use “hydraulician” rather than “hydrologist” but anyway…

I have just received great news from the Natural Environment Research Council; my small grant application has been successful. I was initially surprised but I am now ecstatic.

I am really excited as it will allow me to spend some time working on slope stability again. The research is entitled “Modelling vegetation growth and its impact on slope hydrology and stability”. I have some good ideas on how the model should be built and overall, the project will span most of 2008.

In 2006, Jones et al. wrote a paper entitled “An assessment of the tracer-based approach to quantifying groundwater contributions to streamflow” in Water Resources Research concluding that the interpretation of tracer based studies of pre-event contribution to streamflow might need re-interpreting. After discussing the methodology used in this paper at the 2006 European Geosciences Union Spring Assembly with Hannah Cloke and Markus Weiler, we submitted a comment to Water Resources Research. Our comment was published in September together with the reply from the authors of the original paper.

However, Hannah, Markus and I are disappointed by the answer from Sudicky et al. to our initial comment because it does not really answer our criticism. As the comment system in Water Resources Research does not allow comments on a reply (to a comment…), we wrote this short comment in October and sent it to Sudicky et al. who were invited to reply. They have not yet provided us with their answer. We will update this page and make their answer available here when we have received it.

Read our full comment below or download it (PDF version, 36KB) from the website of the University of Bristol.

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… and the NERC deadline is now gone. Good

It’s the end of a very busy week that I spent in Bristol working on two research proposals to NERC (Natural Environment Research Council) with Kat Michaelides and Wouter Buytaert. Both proposals are very exciting. As usual, lots of time was wasted playing with font size to make everything fit inside the 8+2 page long template. Anyway, now we simply have to cross our fingers for a while and hope they go through.

On a different note, I taught the (two!) MSci students how to build from scratch and in Fortran a particle tracking model for solute transport. I am very pleased with the progress so far and it looks like they will build a great model.

I am now finalising two technical reports for EDF. We have a new asynchronous time loop in ESTEL-3D now and it’s quite a nifty algorithm. I’ll blog about it later on.

I recently went to the TELEMAC Users Club 2007 which was held at HR Wallingford in Oxforshire on Thursday 8th and Friday 9th November. This is a yearly two day workshop. The new developments in the codes of the TELEMAC system are presented to the users by the developers; I presented the recent developments in ESTEL-2D and ESTEL-3D and Minh from EDF focuses on the particle tracking module in ESTEL-3D. The users also present the type of application that they carry out using the TELEMAC system; Regina Nebauer from EDF presented some of the large ESTEL-3D models that are built at EDF for the study of nuclear waste storage. Unfortunately I could not attend the second day of presentations.

We had a developer’s meeting on the Wednesday afternoon prior to the users club itself. It looks like a big package of work on High performance Computing will be done in 2008 by EDF so that ties in nicely with what I am involved in here in Bristol.

On Thursday afternoon, we also visited the facilities of HR Wallingford. The large physical models were quite impressive but the highlight was visiting the “ship simulator” a real scale ship platform inside a virtual reality immersion system. They use it to simulate the entry of ships of different sizes into a harbour and can also test different harbour configurations. The currents and waves are calculated using TELEMAC.

Physical model (airport expansion on the Isle of Man) and ship simulator at HR Wallingford

The Hydrology Group at Bristol University has really increased in size this year (new staff, new postgrads, new visitors). We had our first group meeting about a month ago. This was followed by a social at a local pub

It’s nice to see we can occupy a whole table in the pub now!

I have been teaching a course about hydrological modelling for a few years at Bristol University. The course is an “attempt” at describing how numerical models work to an audience of geography students. This year, I am testing e-learning and the course is delivered mainly via the Internet using Blackboard, the online learning environment at Bristol University.

For this purpose I have converted my 10 lecture course into 18 units, each unit being about 20 minute long. Within Blackboard, the students can play a screencast of the unit; i.e. watch the slideshow on the screen and listen to my recorded voice at the same time (example). They can also download the handouts, the slides and use a discussion board. Audio and video files that can be downloaded on portable audio/video players are also provided.

It is too early to say whether it is working well or not. There have been a few technical problems, including the removal of the podcast feature from Blackboard which means that students cannot subscribe to the course in iTunes for instance. Also, nobody has used the discussion board yet. I will be meeting with the students next week so hopefully, I will have a better idea on how the concept is received. It’s generating tons of work for me so I hope it works somehow!

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