First month of KAPing along the coast of Spain and Portugal. My experiences and best pics.

August 27th, 2009

In the beginning of April 2009 I made a post on the Kite Aerial Photography forum and asked to recommend me a beginner rig and kite. I explained that I would join friends on a sailing trip from Breskens in the Netherlands to Lisbon in Portugal, and that that trip would be the perfect opportunity to finally get started in Kite Aerial Photography (KAP).

I ordered a Sutton Flowform 16, a BEAK-Servo and a GentLED CHDK from KAPshop. I had asked for the “Becot” variant of the kite, so Peter - the owner of KAPshop- had to do some modifications. And because I had posted the question only a week for departure, the kit didn’t arrive in time at my home address. Luckily, a fourth crew member was delayed for personal reasons as well, and when he hopped on board in Cherbourg, France, he had the KAP gear with him. As soon as he was on board we departed for a 4-day non stop sailing trip to cross the Bay of Biscaye, so the first time I actually opened the box with KAP items and could take a decent look at its contents was in La Coruña in Spain.

There is a small castle on an island not far from the yacht harbour (Castillo de San Antón) that looked like an ideal target for my first try at KAPing. The wind was quite light, but I did get the kite up without any problems. Since this was my first kite flight since childhood I used it mainly to get acquainted with the Flowform. At the end of the session I even attached the BEAK to the line, but the wind was too light to lift the rig. I unhooked it and carefully put the rig back on the ground. For this I used both my hands: one for holding the kite-line the other for unclipping and with the reel under my right foot. Just as I put the rig down on the ground the reel slipped from under my foot and the kite flew away! The reel tumbled down the rocks of the peer and the kite fell into the water. After climbing down the rocks to the reel, I easily dragged the kite back in (together with some seaweed), but first lesson learned: never let go of the reel. Since then I always made sure that I had my climbing harness on while KAPing, and attatched my kite-line to my figure-eight.

At that point I still hadn’t succeeded in putting CHDK on my G9 (due to the 4GB card being FAT32 instead of FAT16). A few days later I also broke the LCD screen of my G9 in a non-KAP related accident and hence the menu options weren’t accessible any more. That meant I couldn’t use the GentLED CHDK for triggering the camera. Luckily I had also ordered a servo mechanism for pushing the camera button (which I had intended to use with a watertight film camera) so in Vigo, Spain I installed that and went for my first picture-taking KAP flight. The conditions were very good, strong stable wind blowing in the direction of the peer I was standing on and I’m very happy with the results I got:

KAP flight preparation in action
Picture taken from the boat with me getting the FlowForm airborne

Mijn fototoestel aan een vlieger gehangen, en dan krijg je foto's zoals dit!
The result from the air

The four-masted barque in the background of the right picture is the 114.4 m (376 ft) Kruzenshtern which was in Vigo to participate in the Tall Ships Atlantic Challenge 2009. (And yes, I have contemplated doing a KAP session closer to her, but since I was just getting started with this KAP thing I didn’t feel at ease doing this standing somewhere in the middle of the massive crowd visiting the boat nor did I want to have my kite line tangled up with her yards.)

A few days later we anchored in front of the Islas Cies, a group of islands near Baiona. Once a pirates’ haunt, Cies is now an uninhabited and pristine national park and the beach was number one in a list of ‘Top 10 beaches of the world’ in a Guardian article. Stunning vistas there so I tried to lift the kite several times, but each time there was barley enough wind to lift the kite, let alone the rig. We even hiked to the top of the island in the hope of finding more wind there, but alas. (As an alternative, I took some shots from the top of the mast.) The best shot I got was this, while anchored before the southern Illa de San Martiño, with the camera only one meter out before I had to reel it back in.

Poging tot vliegerfotografie terwijl we voor anker liggen
My friend Klaas looking intensly while I try not to drop the camera in the water with the low winds

The second succesfull KAP flight was in Baiona, famous for its Parador (now a four star hotel) built in the style of a Galician manor house within the walls of a medieval fortress. The fort was built to protect (not always successfully) the port of Baiona from enemies and pirates. Again, I am very satisfied with the obtained results (except for the upper left corner in the fourth picture which was overexposed by the sun).

Zelfportret vanuit de vlieger
I was standing behind a wall with canons with steady wind from the sea.

Strand van Baiona
The beach and yacht harbour, parts of the medieval fortres wall visible to the right

Speedboot vaart uit
A speedboat enters the ‘Ria’ of Baiona

Parador de Baiona - luxues viersterrenhotel binnen de oude fortengordel die de haven beschermt
The four star Hotel Conde de Gondomar

The next opportunity I got to go KAPing was in Lisbon. I had chosen my spot carefully, and had positioned myself with the Torre de Belém on my right side, with the Padrão dos Descobrimentos to my left side, a nice lighthouse tower behind me, and the wind pushing the kite steady over the river Tagus. Except, this time I had pointed my camera way too low, so most of the 50+ pictures where of boring grey river water without any features. The few shots that did include some scenery also failed to impress: there was one with a small, unsharp Torre de Belém in the upper right corner and the shot from the Padrão dos Descobrimentos was heavily overexposed by the sun. I tried to save them in post-processing, but didn’t manage. So another lesson learned: besides looking for a good location and keeping an eye on the wind, take also in account the position of the sun and your camera angle.

IMG_2301_zelfportret_met_toren_en_bouwwerf.JPG
The only picture that I have slightly tilted in post-processing, all the other pictures are straight out of camera

IMG_2315_overbelicht.JPG
Is there anybody here who can make a decent picture out of this?

So, in summary: a great hobby, I had lots of fun, got some mighty nice shots that I wouldn’t be have gotten otherwise and will certainly come back for more.

(For those interested, the complete set of pictures from my sailing trip can be found on my Flickr page.)

Google Summer of Code Project Proposal

March 26th, 2007

Project Title

Evolve Unix phyloinformatics tools into Ajax applications

Synopsis

Phylogenetics is the study of evolutionary relatedness among various groups of organisms. Many of the powerful software applications that scientists in this field use, like xrate or PHAST, are only available via the Unix command line. Biologist are often more comfortble working with a browser than a CLI, so these tools need to become accessible over the web in a user-friendly way. This project would focus on providing an Ajax interface for xrate.

Wordle: Google Summer of Code Project Proposal

Project Background

xrate (1) is an open source software tool for genome annotation based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. The software takes two datatypes as input: a multiple sequence alignment in Stockholm Format and a grammar in a format based on Lisp S-expressions. Depending on the mode of operation in wich it is run (training, annotation or phylogeny mode) the software produces different output which can be used to estimate rate parameters or make predictions.

Project Plan

First step would be to build a web-based interface for xrate, comparable to what Pise (2) has accomplished for many other command line bioinformatics tools in the past. Next we want to enhance the user experience by using asynchronous javascript for the output (eg. phylogeny tree viewers & navigators). Javascript toolkits such as Dojo, Script.aculo.us, Mochikit, and Zimbra will be evaluated and used where appropriate. During the development of the Ajax Genome browser, much of the code involving dragging, track managment, tile caching, etc. had to be written from scratch (slide 20). Dojo now provides a lot of these tools (eg. drag-and-drop frameworks, events, i/o) already out-of-the box. The ajax-enabled xrate would build further upon the alignment viewer, but with added asynchronous functionality so that xrate can be called on the server, and a client-server rendering scheme which produces bubbleplots & graphviz state diagrams (for the xrate format files) and alignments & phylogenetic trees (for the Stockholm format files). Like in Google Maps, you will be able to seamlessly zoom in and out, drag around, and toggle labels on and off in these diagrams and trees. Likewise the input could be enhanced by providing an interface that validates the S-expressions (or even gets rid of the need of “writing” them altogether). Finally, an API should provide an easy interface with other web-based bioinformatics platforms, so that the output from one program can be exchanged in a machine-readable form into another. (Overview of which programs can be “piped” into each other.) The project will be build in rapid iterations, following the eXtreme Programming guidelines, with extensive testing and documentation.

Deliverables

  • website with a working demo of an Ajax-enabled xrate
  • website describing the project, including software documentation
  • API for interaction with other web-based applications.

Project Schedule

I expect to complete this project in 3 months.

March 14 - March 26 : Students submit their applications

May 27 - April 10 : Mentors review applications

April 11 : Accepted student applications are announced

April 12 - April 19 : Introduce myself to the community

April 20 - April 29 : Read the scientific literature about phylo-grammars

April 30 - May 6 : Experiment with different javascript toolkits

May 7 - May 13 : Experiment with the Ajax Genome Browser

May 14 - May 20 : Experiment with SWIG

May 21 - May 27 : Make first sketches for implementation

May 28 - June 3 : Start coding

June 4 - June 10 : Write the web-based interface

June 11 - June 17 : Ajaxify the xrate output

June 18 - June 24 : write the API

June 25 - July 1 : Early prototype is finished

July 2 - July 8 : Upload code to code.google.com/hosting

July 9 - July 15 : Mentors begin mid-term evaluations

July 16 : Mid-term evaluation deadline

July 23 - July 29 : Usability testing with end-users

July 30 - August 5 : Extensive debugging

August 6 - August 12: Write documentation

August 23- August 19: Students begin final evaluations

August 20- August 26: Mentors begin final evaluations

August 31 : Final evaluation deadline


Bio

In 2004 I obtained a Masters degree in Biology from the University of Antwerp on a bioinformatics thesis, titled “comparison of methods to prioritize candidate disease genes according to their presumed involvement in human hereditary diseases” (in Dutch). For it, I wrote a computer program in Perl which combined and compared four techniques to prioritize candidate disease genes. The program worked, but involved a lot of screen scraping and some sub-optimal statistics.

I also noticed that my knowledge of algorithm design lacked, so I enrolled at the Open University Netherlands to obtain an additional Masters degree. This time in Computer Science. I’m currently in my first year, specializing in bioinformatics.

Besides Perl for my thesis project, the main scripting language I currently use is Python. Ocasionally, I also play with Ruby, Haskell, Erlang, J and Scheme48. I am in the process of learning Java and C for my university courses.

Since 2002, I have been using Linux as my only operating system (first Red Hat, then Freebsd, now Ubuntu).It has given me a good understanding of UNIX system administration.

I have wide ranging interests, see for example my del.icio.us bookmarks. Tags that frequently appear include bioinformatics (358 times), webdesign (211), Ajax (97), Javascript (94), data visualization (57) and machine learning (29).

Motivation

Since my youth I have a passion for both design and science. My father is an industrial designer, and from a very young age made me aware of things like typography, minimalist architecture and ergonomics. My mother on the other hand stimulated my inquisitive mind, and -as a biologist herself- introduced me to the scientific method. While growing up, I became interested in diverse fields such as information visualization, data mining and graphic design and noticed how they all solved an isolated part of the larger problem: making sense of the ever growing amount of data. The Aha-erlebnis came when I saw how Ben Fry brought these disparete fields together in a singular process titled Computational Information Design. That’s also the way I want to go with this project:
bridging diverse cultures by making the software more accessible, and presenting the data in an enhanced visual way.

Name

Jeroen Van Goey
on the net, also known as BioGeek (for example at reddit)

Contact

‘jeroen.vangoey+soc’ (@gmail.com)
http://jeroen.vangoey.be

IM

GoogleTalk

References

  1. XRate: a fast prototyping, training and annotation tool for phylo-grammars Peter S Klosterman, Andrew V Uzilov, Yuri R BendaƱa, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, and Ian HolmesBMC Bioinformatics. 2006; 7: 428.
  2. A Web interface generator for molecular Unix Catherine Letondal Bioinformatics. 2001; 17:73