Personally, I think doing a good PhD means:

Doing a PhD represents several years of supervised training, developing oneself to become a researcher capable of independently contributing to, and participating in, a scientific discipline.

Contributing to a scientific discipline means that a PhD candidate is supervised to create scientific products of the highest possible quality, and does so in an increasingly independent manner. Participating in a scientific discipline entails presenting these scientific products to others, frequently discussing these with colleagues, and collaborating with representatives of that discipline.

The core of that statement is being trained to independently contributing to a scientific discipline.

Based on my (clearly limited and selective) experiences, I learned that in New York (US?) PhD students really are … students. This by no means is a negative comments, but it is clear that the PhDs I met have a different set of skills. Generally, my impression is that their course load results in them being familiar with a wide overview of the literature on several topics, but (at least during the first few years) are less experienced in doing research with some level of independence. It’s a trade-off: some of the exams seem to be gruesome, with students faced with the taks of familiarizing themselves with a whole field of research. This is well beyond the relatively simple exams we have in the Netherlands, but getting your hands ‘in the dirt’ while doing some actual research yourself also is quite the experience.

Also, I noticed that it is much more of a struggle to do your PhD in the US. In New York life is expensive, and most PhDs are not employed by their universities as in the Netherlands. This means you have to find yourself some funding, but also that it really is a disappointment if your proposal is rejected. Not getting those funds really means you have to rethink your options. Many PhDs also need to have a job – besides writing their thesis, that is. Many teach or assist a professor, tasks that we do in the Netherlands as well. The difference, I think, is that the workload (again, besides writing a thesis which is a pretty decent workload by itself) is much higher in the US.

If every individual is under quite a lot of pressure, I wonder how that works out in terms of being able to form an academic group. I learned of one example of a PhD only providing to help to others when being paid on an hourly rate. I understand where that’s coming from, but also wonder how it affects the livelihood of an academic community of shared ideas, discussion, and collective interest.

Devesigned by ‘automattic‘, the same people who wrote the WordPress code (“code is poetry”), released their WordPress application for iPhone today. I downloaded it and found myself writing this post within a minute. Really, that’s how well it works! The app has been redesigned and in nothing it resembles the WordPress admin screen.

The interface allows thevuser to sign up for several blogs. I only had to fill in the URL, my user name, and password. When logged in to one of my blogs, thirty of my recent posts are shown and can be easily read and edited. Using a single button, a new post is created, including a title field, categories, and tags. All the categories created on my blog were shown on my iPhone, but it is also possible to add more categories on the run. Drafts are stored locally, so that you can write even when not connected to the internet.

Not all that is possible from the WordPress admin screen, can be done using the iPhone app. For starters, you can’t do anything but write a blog post, but I feel that in that limitation the strength of this app lies. Some other limitations are due to the fact that we’re writing from an iPhone: for instance I don’t see myself writing posts with a thousands of words length due to the relatively small keyboard.

Some other things might perhaps be added to future versions of this app, however. For instance, it is at present not possible to add a link to another page or blog on the web. Also, you can’t manually change the permalink of the post, nor can abstracts be added to the posts.

All in all I find this app strongly suited for writing a quick post on your Worspress blog. No long and detailed academic posts can be expected to be written using this app, but I do believe that it is very well able to result in nice concise contributions. Especially in a dynamic environment where you don’t want to be lugging around too much equipment, for instance on a conference, I see how this WordPress app can be put to great use.

Soon I will be attending the useR! 2008 conference in Dortmund. I already planned to do some conference live-blogging, so now I have found myself the tool to do so.

Most academics will recognize the problem: how to properly manage the abundance of articles, book chapters, and papers that our work is based on. How do we store them, and more importantly, how do we retrieve them after a while? Personally, I very much like to write on the papers I read, indicating and coding important sections. This generally means printing, while I also want to bring the papers I read along, facing me with the impossibility of lugging hundreds of articles around. So what to do? Some papers I only use for quick reference I don’t print, but those meant for close reading, I did. I’ve always been looking for a method to read digitally while allowing me to take notes.

Until recently, that is. I think that I may have found a good combination of two software packages that allow me to orderly store my loads of articles, and to read and annotate them digitally. Ladies and gentlemen: I present you BibDesk and Skim!

Bibdesk

BibDesk is a little piece of software meant for bibliography management focused on the BibTex format. It is thereby specifically focused on integration with LaTeX, but that happens to the way I prefer to write my papers. However, even if you don’t work with LaTeX, it is still suited to work with. It automatically stores files to a given location and shows the bibliographic information in a nice overview. It also allows the user to search in repositories as PubMed and Web of Science, including the ability to download the references to articles of interest. In the sidebar a preview of the article is shown.
I’ve been able to find only a single drawback to BibDesk: it allows the user to create folders and store articles in these folders, thereby keeping your bibliography in an orerly fashion. However, it is not possible to create such folders within folders. Thereby, it is not possible to create a folder for a specific topic or paper you’re presently working on, including some sub-topics.

 

Skim

When it comes to reading the nicely stored papers in BibDesk, it works together in an integrated manner with Skim. Skim allows you to read papers stored in .PDF and, more importantly, to take notes! Just clicking in the text creates a yellow field in which some text can be typed. These fields can be adjusted in size, color, and position. Many more different types of markers are available as well, such as underlining text (just select and click the icon), arrows, and boxes / circles. Also, you can make longer notes which just have an ‘anchor’ in the text which reveal the note when clicked on. Again, these anchors can have a variety of icons. All in all, this allows the user to develop his or her own coding-system. Most interestingly, in the right-sidebar a list of all comments is shown, which can be searched independently of the text. When in full-screen reading mode, this sidebar can be called forward by simply moving the mouse-pointer to the right edge of the screen.

The integration between the storing in BibDesk and the reading in Skim is strong. Skim can easily be called forward from within BibDesk. Both being very light-weight software packages, this works very fast and smoothly. Moreover, the notes you make in Skim can be directly read from within BibDesk. It is also possible to export your notes exclusively, thereby allowing the usage of these notes in other software.

What we thus have here is a system that allows the easy on-screen reading of papers, while taking notes in the actual paper itself. It surely requires some getting used to, but soon it seems to work nicely and speedily. I can surely see how Skim would into my workflow.

 

Both BibDesk and Skim are freeware and open-source, a software philosophy I gladly adhere to. Designed for MacOSX, they both run perfectly on my operating system of choice. The only drawback is that since both are far ahead of the competition, some compatibility issues might arise. This is especially clear when using Skim: it stores the comments in an ‘additional pocket’ to the actual .PDF files, a feature not yet supported by all file systems. So, for instance, when e-mailing the .PDF or when storing it on an old USB-disk, the comments may be lost. It is however possible to export a .PDF document with the comments stored inside, so that other people still can read your thoughts. But then again, all software has some compatibility issues.

To conclude, I must say that I’m already looking forward to go reading again using BibDesk and Skim. To all mac-based researchers I would like to suggest to give it a try. Please report back your own experiences!

UPDATE: I wrote a how-to on syncing your BibDesk library to your MobileMe iDisk.