Worst. Cough. Ever. But science cheers me up!

I thought I only had a little cold – that’s why, instead of resting and going to bed early, I had to prance around in the rain late at night for our Ikeodyssey. When my cough didn’t get better until yesterday and my voice started to disappear, I went to the NHS walk-in clinic in Soho. They had a staff shortage and a waiting room full of coughing people, so I neatly fit in.

After two hours, I was able to see a doctor, who in turn told me that I have a viral infection in my throat. Medicine and antibiotics won’t help, so I’ll have to rest, drink lots of fluid, and not talk for a few days. Good thing I can type rather quickly.

As I’m typing this, I’m sitting at my kitchen table, about to finish my second litre of peppermint tea laced with honey. And I just came across the funniest account of an experiment ever. It’s titled “Electron Band Structure In Germanium, My Ass“, by Lucas Kovar:

Now, let’s look a bit more closely at this data, remembering that it is absolutely first-rate. Do you see the exponential dependence? I sure don’t. I see a bunch of crap.

Christ, this was such a waste of my time.

Banking on my hopes that whoever grades this will just look at the pictures, I drew an exponential through my noise. I believe the apparent legitimacy is enhanced by the fact that I used a complicated computer program to make the fit. I understand this is the same process by which the top quark was discovered.

Reading it made me laugh (and cough) hard. Ah, the joy and wonder of science.

Via Worst. Result. Ever.

HOWTO: Mendeley on OS X/Linux/Toaster

Update: We now have native versions for Windows, OS X and Linux, so I have crossed out the instructions on how to run Mendeley using WINE and Darwine. The instructions for running Mendeley on your toaster remain valid.

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[June 13, 2008]: My name is Mike and I’m a software engineer. No, I won’t fix your computer. However I will get Mendeley running on it because you’re such a nice person.

I’m hard at work at the moment making Mendeley work on Linux. For those who care this involves moving from a Visual Studio based build-system to one using CMake and also fixing some of the inane rubbish that the the MSVC++ compiler seems to think should be valid C++.

At the moment you can use WINE on Linux/FreeBSD, Darwine on Apple OS X and Mendeley-shaped bread in your toaster to fulfil all your unsated academic document management needs.

Running Mendeley on Apple OS X

  • Install Darwine from http://www.kronenberg.org/darwine/ into the Applications directory.
  • Install TRiX from http://mike.kronenberg.org/?p=69 into the Applications directory.
  • Run TRiX from Applications.
  • Make sure the following options are selected: In the “General” tab: “MS Arial, Courier, Times fonts“, “MS Tahoma font (not part of corefonts)”. In the “Libraries & Runtimes” tab: “vc6redist from VS6sp4 (mfc42, msvcp60, msvcrt)”
  • Press the “Install” button.
  • When done (i.e. Terminal displays “All done, no errors”) install Mendeley (double click on .exe file – Darwine will do the rest. Allow it to install into the default directory: i.e. “C:Program FilesMendeley Beta”). If “All done, no errors” did not appear then try and click “Install” again until it does.
  • Open a new Terminal.
  • Run the following commands: “cd ~/.wine/drive_c/Program Files/Mendeley Beta/; /Applications/Darwine/Wine.bundle/Contents/bin/wine Mendeley.exe
  • The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
  • KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on Linux/FreeBSD/BeardOS

  • Install Wine from your package manager.
  • Download Winetricks from http://www.kegel.com/wine/winetricks.
  • When downloaded run “sh winetricks” from a terminal, when in the same directory as Winetricks.
  • Select “allfonts” and “vcrun6” and press “OK“. Press “OK” when the VC6 installer pops up.
  • When done (i.e. the terminal displays “All done, no errors”) run “wine Mendeley-0.5.4.0.exe” when pointing at the correct downloaded installer and change the version number to be correct. Allow it to install into the default directory: i.e. “C:Program FilesMendeley Beta”).
  • Run the following commands: “cd ~/.wine/drive_c/Program Files/Mendeley Beta/; wine Mendeley.exe
  • The last command should have launched Mendeley! If it didn’t or you are having any other problems then post them here and we’ll try and help.
  • KNOWN Problems: Depending on your language, “Program Files” may be something like “Programme” instead. If the above command doesn’t work then try to run “ls ~/.wine/drive_c/” and use the results to see where you should “cd” to.

Running Mendeley on your Toaster

  • Get a piece of Bread.
  • Cut the piece of Bread into the shape of the Mendeley logo.
  • Insert into Toaster and set heat to at least 5.
  • Wait patiently for the Toast (toasted bread) to pop out of the toaster.
  • Optional step: Use a Knife and a Spread (any bread-compatible spread will do) and combine them on the toast.
  • Consume the toast.
  • The last command should have launched Mendeley made you less hungry! If it didn’t or you are having any other problems then post them here and we’ll try and help.

Worst. Result. Ever. Brilliant!

By chance, I stumbled across One Big Lab yesterday, a very interesting blog on Open Science maintained by (as far as I can tell) four Stanford bioinformatics Ph.D. students. One of the many gems to be discovered there is a series of t-shirt designs called “Worst. Result. Ever.”:

You’ve been there, done that. Spent hours, days, weeks… months?… just to discover that your hypothesis (or “hope-othesis”) is completely wrong. Finished a data analysis only to see that what you’ve just produced can only be described as the Worst. Result. Ever. […]

Each one is named after the hapless student who had the pleasure of seeing something very much like it in their own research.

I’ve had nightmares of the Magda, and once pulled a Bernie, too. Once the shirts become available, buying them will support the PSB workshop on Open Science in… what? Hawaii?! I need to go there!

Are you advising Master Theses?

Well, I am. Currently I have six students writing their master thesis under my supervision, and if you’ve ever done this before, then you know the amount of work that goes into that job. Especially when you have to compile and distribute literature lists to each of the students, it can be quite a hassle to pluck this list from your own pool of references – depending on how well you’ve organized your library. In the end you want to have an up-to-date list of references which you can give to the student, and you also want your student to be able to directly use and analyze these references for his own work.

This is, again, one of the day-to-day problems of researchers that we’re aiming to solve with Mendeley. In Mendeley, you’ll be able to just set up document groups according to the different topics you are currently researching, and drag & drop references from your library into these groups. You could then either export a formatted list or, even better, give the student access to this group so that he would be able to import this information into his Mendeley account and start building up his own library. And every time you add a new reference to one these shared groups, your student will see this new reference in his library as well.

Obviously, this would also make the lives of research groups easier. I believe we could figure out plenty of additional scenarios which make sense in this context. If you have some ideas, just send us an e-mail and let us know!