# Harvard 360

I’m starting a new series of blog posts called Harvard 360 (a bit of my life and research on the Harvard campus). I’ll be posting 360 immersive pictures to provide a real feel for my work around Harvard University, and in particular during field work.

I kick off the series with an image of Harvard Yard. Harvard Yard houses the oldest buildings on campus as well as all undergraduate housing and several libraries. In front of the white building in the distance is the statue of John Harvard. [click the grey bar to load the image if not loading automatically, or click the link to access the VR Flickr page]

# Life cycle events and weather in the tropics (DR Congo)

Life cycle events in tropical forests, like their more temperate counterparts, are in part tuned to changes in the weather throughout the year. Unlike the more temperate regions the temperature in the tropics is not the main driver of phenology, as it stays more or less stable throughout the year. Below you see a summary graph of the temperature of Kisangani (120 km to the east of Yangambi), which averages around a ~25C or rather perfect growing conditions.

However, the region and most of the basin goes through two wet seasons. This is due to the fact that the intertropical convergence zone (ITCZ), a band of clouds and thunderstorms, moves back and forth across the equator following the sun’s zenith point. Given the location of the Congo Basin around the equator the ITCZ passes over the basin two times a year, due to tilt in the Earth’s axis, creating two rainy seasons. In the bar graph below you see the monthly totals, where values over 150mm are considered “wet” months.

If you compare an example of life cycle events of some of the intermediate Jungle Rhythm results you see that this particular tree flowers at the start of the wet season, while leaf senescence starts at the end of the dry season. Not all trees will show this pattern, as different species might take different environmental cues (which are or are not met depending on the seasonal changes or yearly variability). However, the example illustrates the relation between weather and life cycle events very clearly. The importance of these seasonal changes in the tropics can not be understated. A recent study also linked these seasonal changes to measurable differences in CO2 uptake from the atmosphere, a main incentive for me to document these life cycle changes in the Jungle Rhythms project.

# My Nature Climate Change grassland study is online!

My latest paper titled “Productivity of North American grasslands is increased under future climate scenarios despite rising aridity”, in Nature Climate Change, is finally online. After 1.5 year of work I’m rather pleased to see it “in press” !

The short version of the paper reads:

1. Grasses will adapt to a more arid world by shifting their growing season
2. This leads, counter-intuitively, to a slight increase in ecosystem productivity
3. However, at the same time this puts rangeland managers at a disadvantage due to this more variable growing season.

You can read the full version HERE if you have access to the Nature publishing group content. Alternatively, you can find a full copy on Research Gate (or email me).

Some popular press coverage can be found here:

http://scienceblog.com/483100/in-grasslands-longer-spring-growing-season-offsets-higher-summer-temperatures/

(header image courtesy of Russ Scott)

# Mendeley grievances and quick hack

I was recently reminded by Mendeley that I ran out of ‘free’ space on my account (i.e. 2.Gb of pdf storage). As a previous paying customer (who reverted back to a free account as they bumped it from 500mb free to 2Gb) I was more than happy to pay again, so I thought.

However, in the 3 years since I last payed, their storage offer has not kept up with the times. For a \$55/yr you now get a WHOPPING - 5Gb - of pdf storage space, a Pro plan goes for \$110/yr and an impressive 10Gb, while unlimited storage will cost you \$165/yr! Given that Mendeley is now owned by Elsevier, a dominant if not the biggest scientific publisher around, their database of pdfs can easily be reduced by an order of magnitude (as most files are already stored by Elsevier!). Given this large overlap their storage overhead should be smaller than before their acquisition by Elsevier, warranting a price cut not a price increase relative to other / previous services. In comparison, a Dropbox account costs me \$100/yr for 1Tb! Even better deals are possible with a Google Drive account (however I like Dropbox’s integration and Linux support better).

In short, given the current state of cheap storage these price points are less than impressive, and it reeks of profit maximization using some user statistics and marketing parameters (at which price point are people likely to pay for  a given feature). Sadly, I’m of the opinion the charge does not reflect the true value of the service.

As such, for anyone who has cloud storage and does not want to pay extortion prices for pdf storage:

• just disable your pdf syncing feature (click 'Edit Settings' next to the All Documents tab title)
• create a soft link between wherever your pdf's used to be stored and a location within your cloud storage.

An example below for the standard configuration on OSX:

# move all your files to your cloud storage (e.g. Dropbox)
# on OSX your Mendeley Desktop folder in Documents stores all your
# pdfs

mv ~/Documents/Mendeley Desktop ~/Dropbox

# now create a soft link between the new folder and where the folder
# used to be

ln -s ~/Dropbox/Mendeley\ Desktop ~/Documents/Mendeley\Desktop

# Migrate the database to your Dropbox (for convenience)
# the link below if for linux, look up the locations for Mac
# and Windows on the Mendeley website
ln -s ~/Dropbox/Mendeley\ Ltd./ ~/.local/share/data/Mendeley\ Ltd.

# now do this for all your computers. Your database will keep up to date
# through Mendeley (and Dropbox), while your files keep in sync
# through your cloud storage service

The above hack will allow you to keep your references in sync using the Mendeley database, and platform while at the same time keeping your files in sync through your cloud storage service. This way you can bypass their rather questionable business model.

Given this hack and an ironic twist of fate they now miss out on my \\$55/yr. If they would have provided 10Gb I would have payed, as the markup from my current quota is significant and a worthwhile upgrade. Sadly, I now have to resort to tricks, albeit legal, to keep the same functionality (a basic reference manager).

I guess this is one example of software as a service gone wrong. I hope that they will change their business model in the future, so I can become a paying customer again.

DISCLAIMER: You will lose the ability to read your pdf’s from within the Mendeley app on iOS or Android (but you could still do so using e.g. the Dropbox app)!

# Jungle Rhythms pre-processing

The Jungle Rhythms project at the surface seems rather straightforward in it’s setup. However, there are a lot of behind the scenes preparations that went into project. One of these tasks was cutting the large tables into yearly sections.

Below you see a picture of one page of the original tables, halfway through pre-processing. Each of these tables was first rectified (making sure that all row and column lines are roughly vertical and horizontal - to the extend possible) and cropped (as shown below).

Next, I marked all column widths and the width of one row, as well as the bottom right corner. Using this information I could calculate the approximate position of all yearly sections (outlined by the red lines).

The yearly sections were then cut out of the original images (with some padding) and saved with additional information on their location (column and row number). The final result of this operation would be an image as shown below and presented to you in the Jungle Rhythms project.