Archive for the ‘hard research life’ Category

6 April 2010 by Ricardo

As a PhD student I find myself roaming the Internet quite a bit in search of literature for my research project which can be really time consuming. Looking for the right keywords, opening each relevant result into a new tab, downloading each paper of interest, finding the cryptically named PDF file and then adding it to your library in an organized fashion (phew). So anything that can cut back this strain of accessing and organizing research papers is most welcome.

In previous posts I’ve mentioned Mendeley’s web importer, which helps retrieve papers directly to your Mendeley Web account. That’s all good, but what about papers that you already have on your computer spread about in different folders or hard drives?

There are multiple ways to import files from your hard drive directly into Mendeley Desktop. You can add one file at a time, a full folder in one go or even make a specific “Watched” folder.

A “Watched” folder is basically a folder that Mendeley keeps an eye on for any new files and automatically imports new documents with minimal interaction on your behalf. Just drop or download your PDF documents into your watched folder and Mendeley will do it’s thing (I mean auto-extract it’s metadata and add it to your library!).

So we now have a web importer for online retrieval and an automated watch folder. Looks like we are set!

My references and documents are all nice and organized within Mendeley Desktop and accessible online but when I look at the files on my computer, I notice something. In fact, I notice the lack of something: meaningful file names.

hard research life design research tools  An organized folder is a sign of a… file organizer

As you can see in the image above, the file names are not very explanatory and whenever I have to pick a file to send to a colleague or open it directly for some reason, it becomes a guess-the-mystery-file name game. Not to mention that every time I add a file to that folder with a similar name, I get this fantastic message:

The file you are trying to copy “sdarticle.pdf” already exists. Cancel or overwrite?

Good question, do I want to overwrite sdarticle.pdf? Do I have any idea what is in that file? The most probable answer to both these questions is no. Once again, Mendeley has considered this situation and provides an effortless way to organize your files with a built-in feature called: ‘File Organizer’.

As the name suggests, this feature can organize your files for you in a few different ways. You can store your files in a centralized folder with all the files renamed to a specific format. The format is easy to customize by simply dragging the naming categories from one input box to the other.

hard research life design research tools  An organized folder is a sign of a… file organizer

As you can see in the image above, I chose to rename my files and keep them in one folder with the file name following the format Author – Year – Title. I did not add the journal to the file name, but could have easily done so by just dragging it down into the file name.

There’s an option to organize the files into sub-folders, however I chose not to do so. That’s just my personal choice even though I know colleagues of mine prefer to separate things into sub-folders by year.

Once I’ve picked how I want my files to be sorted and renamed, I go ahead and click apply. Folders get created, files get renamed and I’m done:

hard research life design research tools  An organized folder is a sign of a… file organizer

These file names are much easier to understand and are categorised how I want them. This feature has not only organized my files into a folder with proper file names, but it will keep any new documents I add in the same orderly fashion. Neat huh?

20 January 2010 by Mendeley

Great news! We’ve been picked by Chinwag and the UKTI to don our cowboy boots and Stetson hat before jetting off to the great Lone Star State on a Digital Mission.

“39 of the UK’s leading digital companies have been selected for the second annual Digital Mission to South by South West interactive (SXSWi), taking place in Austin, Texas from 11-17th March 2010. [...] The successful companies were chosen from over 120 submissions by an advisory board of industry experts drawn from the UK community including: VC’s, export specialists, journalists and industry pundits to take part in the Digital Mission to SXSWi.”

(You can find the full list of participating companies here.)

There are some great presentations in the line-up at SXSWi, some of the ones we’ll be looking out for include: Can the Real-Time Web be Realized?; Crowd Sourcing Innovative Social Change and Is The Brain The Ultimate Computer Interface?

start up life hard research life community relations  Mendeley on a Digital Mission to TexasWe also hope to swot up on doing business in the US (not by watching re-runs of Dallas) but attending some special events and seminars set up for tech entrepreneurs. SXSWi brings together some of the brightest minds in the tech world and a line up of special programs showcasing websites, video games and start-up ideas. If you are planning to attend, let us know and we’ll be happy to hook up.

A big thanks to Digital Mission for making it possible and we’re looking forward to a great event!

27 November 2009 by Andi

Happy Thanksgiving: Around 5pm yesterday Mendeley services ceased when all of our servers went offline simultaneously; we quickly realised that something was very wrong with our connection to them and this was confirmed by our hosting provider’s customer service calling us to let us know.

start up life progress update hard research life  Where did Mendeley go?

The details are not completely clear at the moment however we do know that the data centre suffered a very serious power outage, and it appears that there were some faults with their back-up generator and batteries too. In summary, we didn’t have much influence: our servers were stuck in the data centre without power, unreachable for around 2 hours, due to issues sadly outside of our control.

After we re-established contact, the process of checking data integrity, restoring backups as necessary, and testing the system took us another 8 hours – although some of us were up much longer doing their very best to ensure everything was back to normal. Well done Ben and Fred – excellent work! I hope you’re having a well deserved lie-in…

Please be aware that if you were syncing your data around 17:12 UTC yesterday then it would be worth checking everything is ok and contacting support if you are having any problems.

As we are growing in size, we continuously work on scaling Mendeley further. However, yesterday’s combination of events borders on the absurd, and if it were a Mr Bean movie, it would have been funny.

Our apologies that Mendeley was away for so long – we will surely have a word with our data center providers…Normal service has now resumed. Enjoy!

19 August 2009 by Victor

As an addendum to Jason’s earlier post, here’s a story of scientific discourse gone horribly wrong. It would be funny if it wasn’t so.. somehow really not funny.

How to Publish a Scientific Comment in 123 Easy Steps

Via björn.brembs.blog.

11 February 2009 by Victor

Today a user told us that Websense, the internet censorship “content-control” software, hard research life  Websense is blocking access to Mendeley... dictators around the globe rejoicehas marked the Mendeley website as “Illegal or Questionable” and blocked access to it. I wonder how that happened?

At least we’re in good company. Websense is blocking access to Amnesty International in many parts of the world (wait… now it makes sense! I’m a member of Amnesty!), and has also been blocking GMail and the MIT website just because they can.

Also, I think their logo exhibits a slightly flawed sense of humour. Yes?

21 July 2008 by Victor

Well, what can I say! The EuroScience Open Forum 2008 in Barcelona has turned out great so far. Due to its considerable greatitude and excellent greatishness, Jan decided not to let me have all the fun by myself and joined me yesterday.

On the downside, the heat and travel stress didn’t exactly help me get rid of my still-persisting cough/throat inflammation. I was barely able to sleep again for the first two nights in Barcelona, and I will need some more days rest at home when I return to London. Nonetheless, we attended some very inspiring sessions and received enthusiastic feedback on our presentation today (more on that in a later post) – let me recapitulate.

Saturday, the most interesting session was on “Open Science” or “Open Notebook Science”, on which Prof. Peter Murray-Rust from Cambridge gave a very spirited talk…

start up life hard research life academic life  An excellent EuroScience adventure, Part I

…followed by a not-so-spirited talk given by he-who-shall-not-be-named and in which every slide looked like this:

start up life hard research life academic life  An excellent EuroScience adventure, Part I

Anyhow, “Open Notebook Science” is a fairly recent idea which has gained more and more exposure in the past few months. The basic premise is that researchers should not only share their publications through Open Access outlets, but also freely publish their raw data alongside it so that it can be validated, re-purposed and aggregated.

This, of course, entails some problems: Academic careers and tenure decisions depend on publications, so how can you incentivise researchers to lay open their data before they’re certain that they have “wrung” all possible publications out of it? I believe that our “Last.fm for research” model, i.e. the chart-like tracking of which papers are being widely read, which authors are up-and-coming etc., could also be extended to raw data – thus giving credit to people who have created the raw data that others are successfully using.

Two other highlights yesterday and today were the keynote speeches by Prof. Marcus du Sautoy from Oxford and by Physiology/Medicine Nobel laureate Dr. Richard J. Roberts. Both described how they had discovered their love of science and the fields they wanted to dedicate themselves to. Little known facts:

start up life hard research life academic life  An excellent EuroScience adventure, Part I

Prof. du Sautoy originally wanted to become a spy (to get a nice black gun like his mum, who had worked for the foreign office) and thus tried to learn many different languages. By his own admission, he failed miserably because he did not find languages to be logical enough. Fortunately for him, Mathematics – and especially Symmetry, his field of expertise – offered him a way of describing and understanding the world in more logical terms. Finally, despite his obsession with symmetry, he had this wonderful quote from the 14th-century Japanese Essays in Idleness:

In everything [...] uniformity is undesirable. Leaving something incomplete makes it interesting, and gives one the feeling that there is room for growth… Even when building the imperial palace, they always leave one place unfinished.

This reminded me strikingly of the Law of Closure in Gestalt psychology which describes how the mind will try to complete figures if they are unfinished – hence deliberately leaving something incomplete will engage the mind’s creativity.

Today, then, Dr. Roberts spoke about his way from unruly, almost-expelled-from-school teenager to molecular biologist and Nobel laureate.

start up life hard research life academic life  An excellent EuroScience adventure, Part I

Dr. Roberts had actually wanted to become a professional snooker player – back in the 1960s, he was West England snooker champion. That was also when he received what he described as one of his most profound life lessons:

During a snooker tournament, he had sunk an incredible “lucky shot” – but then failed to make the next one. After the game, an old man came down from the audience and said to him:

Listen, if you sink a lucky shot like that, you have to concentrate twice as hard on your next shot. Everyone can be lucky, but if you get lucky – don’t feel bad, instead work extra hard to take advantage of it.

Seems to have worked out alright for him! After the talk, I hopped onto the stage to give Dr. Roberts a brief pitch of Mendeley, since he’s now actively involved in the Open Access movement. I’m sure that he gets loads of requests like these, but if we’re lucky, who knows – he might just find our idea interesting enough to give us some feedback.

Finally, here are two pictures of me wearing a brain helmet, looking at my brain activity (and oddly, not seeing any?!):

start up life hard research life academic life  An excellent EuroScience adventure, Part I

start up life hard research life academic life  An excellent EuroScience adventure, Part I

Phew. I should stop writing now. Must sleep. Will tell more of our exploits later. Adios!

3 July 2008 by Victor

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:highlighting research hard research life  Worst. Cough. Ever. But science cheers me up!

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.

13 June 2008 by Mike Arthur

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.

—————————————————————

[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 Files\Mendeley 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 Files\Mendeley 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.
12 June 2008 by Victor

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.

research miscellanea open access hard research life design research tools academic life  Worst. Result. Ever. Brilliant!

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!

8 May 2008 by Jan

hard research life academic features  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!