Lab Notes


Last week was a short one. Thursday was off, and in such circumstances, people here usually also take the Friday off, and enjoy a looooong week-end. More explanations about this phenomenon in this video:

I took this opportunity to work on a rather big project I’m truly dreaming of since years: plotting palynological diagrams with R! Since my Master studies, I’m using Tilia, which I became good at. I can produce complete, elegant diagrams, from scratch, in only a few hours.

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Coring the Mondsee

This week I’ve been coring two 12-meter long sediment cores from the Mondsee, a lake in a middle of a stunning landscape (see picture) near Salzburg (Austria). Colleagues from Bern (Switzerland) brought all the equipment and savoir-faire, and did most of the job. Thank you so much Sandra, willy and Armin! I was on the platform to help them, as well as Christophe and Gerry (thanks to you too). It was a great and funny adventure, coring a lake was a première for me, I learnt a lot. Next chapter will be the results of the pollen analyses from these sediments…

Here is also a nice paper about the project.

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Learning Python

This month I’ve attended the seminar organised by the Laboratory of Maths of Besançon about Scientific informatics. There was nothing about directly related to my research topics but I was curious and thought I would eventually get interesting pieces of information. I did. The talks about rights and ownership of data and databases provided me useful insights regarding a personal project of mine (I hope I can write more about this very soon). There were a couple of talks about Python as well. Python is a language I want to get familiar with since long (more information here), and these talks motivated me. The syntax is similar to R, actually. I’m currently writing a little converter, slowly learning. I’ll probably use it with Alfred for punctual needs, but I’ll do larger scale conversions with R, and I’ll share it as it’s ready 😉

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Pollen Symphony

During a trivial conversation with colleagues, we came to imagine what a counting session could sound like if PolyCounter would play a different music tone every time a key is pressed (i.e. a pollen is counted). With a counting history, and with Processing, I was able to produce such a pollen symphony.

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About Persicaria maculosa-type

I recently found a pollen of Persicaria maculosa-type. I didn’t know about this type before, and as the grain was not well preserved and folded, at first I thought about Armeria. But I wasn’t convinced about that, specially given the details provided by the Flora Helvetica, which didn’t fit with the study site at all, even long time ago. Hopefully, thanks to colleagues, we came to identify it as the old Polygonum persicaria-type. Looking in tela botanica, I found that Polygonum persicaria is now known as Persicaria maculosa, and is common at my study site. And finally, I found the Persicaria maculosa-type in Beug (2004)!

Reference Beug, H.-J. (2004). Leitfaden der Pollenbestimmung für Mitteleuropa und angrenzende Gebiete. München: Pfeil.

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So much to write

I’ve been writing so much last days on several manuscripts at the same time that, paradoxically, I haven’t taken time to write something on my weekly report. So here it is: I’ve been writing a lot in the last days 😛

I am currently preparing some more samples to analyze during the long wintery quiet Saturdays, and I will be back to writing during “weekdays”.

Additionally: I enhanced a lot my age-depth model plots with R!

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Christmas Holidays

Since exactly two years, I write a summary once a week to keep track of what’s happening, mostly about work matters, but occasionally about personal events also. I decided to write them here instead, as a public short lab notebook.

But, there is no much to say currently! I tried to achieved many things during the last days to get ready for Christmas Holidays. I’m finally back in France for two weeks, but you can still reach me by email 😉 More will come in the next weeks. In the meantime, I’m getting better with Illustrator.

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Scholarship in Sweden

I spent one month from mid-January to mid-February 2013 at the University of Kalmar (Sweden) to learn the theory of quantitative reconstruction of past vegetation. It consisted in courses and practical work to get used to the models developed by Shinya Sugita (including the models REVEAL and LOVE, as well as the Landscape Reconstruction Algorithm). This was the opportunity to apply these models to my data and represent so far the first attempt in the Alps.

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