Mendeley instead of Endnote

I recently switched from using Endnote to Mendeley. There were several reasons behind this:

• It must be platform-independent. I have to work on an Apple Mac at work, and I enjoy working on my Windows 7 system at home, with occasional explorations into the Linux world. Writing a paper or a thesis and inserting references has to be possible on all 3 operating systems.
• It must be software-independent. It should not matter if I am writing on Word, OpenOffice or in LateX, references have to be easy to integrate.
• It must sync between different machines. 

I eventually stumbled upon Mendeley on the PLoS ONE website of my first paper where it was mentioned in the right sidebar. And bingo, there was a usable piece of referencing software!

Advantages

• It integrates into Word, OpenOffice and Bibtex, runs on Windows, Mac OS and Linux. I can't say anything about the performance in long documents with hundreds of references yet, but once my thesis is redone I will create a version with Mendeley references
• Mendeley synchronises the references between different machines. The free plan includes 1 GB of storage, which is enough for about 1000 references for me (with the odd badly digitized 5 MB PDF among more modern an smaller ones). 
• Unlike Endnote it is very good at finding document information from DOI addresses provided nowadays by all journals on their websites. It has some trouble though with recognizing them in some documents (PNAS, I'm looking at you!).
• It has also its own Chrome/ Chromium extension for easier import of websites and documents into the Mendeley library.

Problems

• Mendeley is, compared to Papers2, quite bad at reading the essential information out of a PDF file. It regularly fails to find the abstract in an automatically imported PDF.
• The software  is not open source, so development might stop at any moment due to financial trouble. Or prices might rise so quickly so high that I might have to hunt for yet another reference management system. 

But there is a nice way around the freemium system: Dropbox. I already have it, it synchronises files between computers on Mac OS, Windows and Linux (what I am looking for!) and there are quite often promotions to expand one's storage size without having to pay for it. Even the initial 2 GB free storage should be sufficient for quite an extensive library, about 2,000 references by my guess. Oh, and someone else has already done it before me, so there are actually some instructions on what to do already out there. There are some problems though, and often checks for duplicates are recommended.

Review: Logitech k400

It is meant to be used later on on my Raspberry Pi, if I can ever get my hands on one. For that I would like to have a second small keyboard with a tiny receiver so that I might be spared even more clutter on and next to my desk. Also, I need something else to do but only thesis revisions. Oh, and a wireless keyboard with a trackpad should work nicely with a TV-connected computer.

The k400 in all its beauty.

The good

• A few multimedia keys on top of the keyboard (mute, volume up, volume down, and a 'home' button to open a browser window).
• It worked without problem once the drivers were recognised and installed. It might have helped that the Logitech SetPoint software had already been installed on my home PC. The keyboard was also recognised at once on my work CrapBook.
• The keys work quite well once you're used to their size and their position.
• It takes normal AA batteries, and two of those babies were included. This opens the possibility for using rechargeable AA batteries.

The k400 from underneath with the battery compartment cover removed.

The bad

• The touchpad could be a bit more responsive and sensitive to fine manipulation. As these things go, I would guess that it is about 5 years behind in development of touchpads.
• The arrow keys are in a very bad position. It was quite easy for me to hit both up arrow and the shift key at the same time and then delete the marked line when hitting the letter that was meant to be capitalised. 



The badly positioned arrow and right shift keys.

• The enter key is a bit narrow for my taste.

The weird

• There is a 'left mouse click' button on the top left side of the keyboard. I don't know yet how useful that would be, given the full touchpad on the right side of the keyboard with single tap recognition and a left click button.

The weird 'left click' button on the top left.

• Instead of using only the tiny unified receiver one is supposed to use and additional bridge between that receiver and a desktop PC. I don't know why, but that makes the whole receiver larger than a standard Logitech one. And it worked fine without that connector on my desktop at home. Maybe it is meant for signal amplification when the receiver is connected at the back of a PC tower underneath a desk, but I used it on the USB dock on top of my desk.

The actual nano receiver on the left, the connector for PCs on the right.

[Update]

There is one thing I am missing: The touchpad does not support multi-touch gestures. The minimum I would like to have would be that a two-finger-tap would do a right click, but unfortunately I have to use the button. I personally got very used to a touchpad doing exactly that. Hell, even my ancient Dell Inspiron 6400 laptop did that!

Thesis submission

Just a week ago I finally submitted my thesis "Study of the mutual interactions of basic amyloidogenic peptides with polyanions". A last near-all-nighter (well, I got 3 hours shut-eye), and it was done. All I had to do was to convert a massive (35 MB) word document into a bound paper copy.
I spend a horrible Monday just printing that thing on our slow lab HP Laserjet 2605dn. Once more that thing was seriously struggling with printing any embedded image files because of its limited memory. If a image resolution of 300 ppi is seen as "high quality for printing" standard, why does it take more time to print the 15 full-page figures than the rest of the thesis? That should be easily done ... well, it is another Apple Mac OS X printer driver problem. Their printer drivers are quite bad in general.

My thesis before binding: 2 copies in the paper box, 1 on top, and two copies of thesis summary and thesis submission form.

The binding could not be done on the same day anymore, but stroke 9:00 on Tuesday morning (20/03/2012) I submitted two bound copies of my thesis and two copies each of the thesis submission form and the thesis summary form. The most anticlimactic ending for a thesis imaginable.
Relief and relaxation came only on the following weekend.

Endnote trouble

While writing my thesis I cam across quite a few problems with Endnote. As you might know, this software allows you to maintain a reference library for writing scientific articles or something like a PhD thesis. It can insert references and format them according to different journal styles (e.g. Science random number or human readable PLoS ONE etc.) and create a reference list in a Word document.

But there are many problems

• It makes working with Word a pain. Each time a reference is inserted it's having a big think and then reformats the whole reference list. During which time both Word and Endnote are unusable. Also, if this coincides with with a Word autosave all your work progress since last save will be lost because Word will crash.
• It is slow. As soon as you hit about 10 references in a document updates take forever. 
• Occasionally it gets the styles wrong up to a point that you would be better off writing the reference list yourself. Science journal is not a book, so the city it is published in is unimportant!
• It is expensive. £200 for a single license, and there is a new version out every year. Also, older versions do not support newer versions of Word and don't receive updates.

All in all I will try to never use it again. It is just too clunky and buggy. I only have to find some alternative that works well on Windows, MacOS and Linux (just to be prepared for all eventualities).

How to make a 500 mM EDTA solution

Getting EDTA into solution is easier said than done. I just needed 50 ml of a 500 mM EDTA stock, but it really does not dissolve well. Buying it was not an option since I couldn't find any solution that was not buffered, and I wanted it as pure as possible. So I prepared it myself.

First Try
In the beginning I made the mistake of starting with the pure acid which has to be completely deprotonated before it goes into solution, and that is a long way to go. A nasty surprise was that such a solution goes up to a pH of 8 when a NaOH solution is added, but then decreases to 7.8 within a few minutes without any visible effect of dissolving the salt. I had to discard this failure because I exceeded the 50 ml maximum volume.

Second Try
Next time I tried to use water and pure NaOH tablets, again starting with the EDTA acid. This resulted in a white sludge (I did not keep a proper record on the number of NaOH tablets added after various waiting times) which spilled out of a not properly closed Falcon tube. In the end I got it into solution, but because of the leak I did not trust the concentrations anymore and dumped it.
I finally got the idea that starting with an acid and taking it's pH up is not the best thing to do if there is already a disodium salt available.

Third Try
Eventually I managed to do it like this (for 50 ml of 500 mM EDTA with a pH of ~9):

• 9.3 g EDTA disodium salt dihydrate (the stuff we had on the shelf, 372.24 g/mol) in 50-ml-Falcon tube. Watch out, that stuff is charged and reacts to static electricity!
• Add 40 ml water. Mix and watch the precipitating EDTA settling down.
• Add 10 tablets of pure NaOH. Mix and wait for 1 hour. Feel the warmth spreading through the tube.
• Add another 10 tablets of pure NaOH. Mix and wait for 1 hour.
• The solution was now clear. A pH check gave me 9.71, which was good enough since this was a stock solution to be added to some buffer. Next time I will be more careful about the second lot of NaOH tablets.
• Fill up to 50 ml and filter with 0.2 µm syringe filter (just to have done it).

This is probably more than I will ever need.

A nice Sunday walk in the mud

I don't have much time for walking these days, but I try to get at least twice a week out there for some fresh air and some dirt on my boots.

The walk two weeks ago gave me the opportunity to test the camera of my new phone, the Samsung Galaxy Nexus. It was holding out quite well when compared to that of my old HTC Desire. The built-in panorama function is working great! Just point the camera at the landscape, and the phone does the rest. Just don't go too fast: That led to the  aberrations on the right side of the image. 

Panorama view somewhere north of Cardiff

There are some alternatives out there, but unfortunately I hadn't thought to compare them on the spot. The app Pano does not take the images automatically, but the user has to take them one by one (with some help from the app). And one has to be careful to not twist the camera which leads to a distorted stitched image.
An alternative I used with my proper cameras is Microsoft ICE which allows me to stitch the images together after I got them off the camera. This works quite well, and one can create stitches in more than one dimension, i.e. take pictures in a grid and then create a composite. I will add some examples later.

Other than a testing ground for the phone camera the walk was quite muddy, and it was worse than these images suggest:

Left foot

Right foot

Usually the ground is quite easy to walk in that area north of Cardiff, but the recent rain and the heavy use by horses turned some of the horse paths we ended up walking on turned them into shallow bogs. But at least the first daffodils were out, although we are not sure if they will make it through the spring: 

The first daffodils

One of the surprises we found is this sign of some hiking path leading into nowhere. It seems no one has been using that path for a long time, and nature claimed it back. Not sure if the owner of the land would actually care ...

A path to nowhere

... since the house just across the fence is derelict:

Anyone home?