Posts for category 'University'

Day NaN: New toys!

Okay, they're for work, so they're technically not toys and they're also not actually mine, but this is still neat.

As some of you might know, the one thing that was still noticably absent from my desk at University was a PC. I had to use my own (old, slow) laptop to do my work, not exactly ideal.

Now, I finally got a PC. And quite a nice one it is too; quite a bit faster than the one I have at home. It's got an Intel Core 2 Duo 6600 (2.4GHz) CPU, 2GB DDR2 667MHz RAM, an nVidia GeForce 7950GT with 512MB RAM and two 250GB SATA hard disks. It far exceeds what I actually need, but you don't hear me complaining. :)

Perhaps the most amazing piece of equipment however is the monitor. It's a Samsung 225BW 22" widescreen LCD panel:

My desk at University

It's huge! The picture just doesn't convey how big it truly is. Working with it is like sitting front row in a cinema. I realize this may be old hat for a lot of people, but it's the biggest monitor I've ever worked with. When I came home today I couldn't help but think how small my own 17" CRT really is. :P

And it appears a fairly decent monitor in other aspects as well (especially considering its price). Response time is great, and colour clarity is good; definitely more than adequate for what I'm going to be using it for. The only drawback is that at 1680x1050 I think its native resolution is on the low side for a monitor this size. A bit higher, like 1920x1200, would've come a long way. But, I suppose that would've made it more expensive.

You may notice I'm running Vista on it. Unfortunately this is not because Leiden University is so up to date with their OS support: it's because due to a miscommunication they didn't have any Windows CD and key for me yet, so I temporarily used my own Vista DVD, installing it without a key (so it's not activated). In a few days I should get the proper XP CD and it'll be bye-bye to Vista. A shame, really, since this kind of machine is what Vista's made of, and not surprisingly it runs beautifully on it.

Categories: University
Posted on: 2007-01-08 17:30 UTC. Show comments (0)

Day 2: XML

Well, I'm happy to report Floris saw the light so DIAL will get an XML interface as well. Which means I can gladly forget about the whole YAML business. It also means there are no obstacles to using .Net, so I'll be spending the next three months working with the tools I like best. :)

Now might be a good time to give an overview of what I'm doing. As I said before, I'm working on a GUI for the DIAL genomics database. DIAL is a database that biologists can use for storing and processing DNA microarray data. As I said yesterday, there are currently four ways to interact with the server: perl, command-line, HTML, and YAML (and soon XML will be added to that). The current web interface is unfortunately not very user friendly so it's my job to make a better, wizard-based one.

The difficulty lies in the amount of flexibility it must have and the constraints I must work under. The first constraint is that DIAL is the way it is and besides small things they're not going to change it for me. Additionally, as new functionality gets added to DIAL, it must be as easy as possible to adapt my GUI to it. Using the soon-to-be XML (or the current YAML) interface I can basically "replay" the regular web interface. The data returned by the server is simply a list of all possible options that can be used by the user. The web interface simply displays those options as HTML form controls, where the YAML/XML interface just gives you a list of options. As you send input to the server to set different options, more options can become available. And sometimes there will be data included as well.

The options I get from the server are grouped, and I can discern the grouping based on the names of the options. For instance, all names starting with "Client::form_login" have to do with logging in. It is on this grouping that I plan to base the wizard. At its simplest, a group of options will become one wizard page in my GUI.

Of course, that's not all there's to it. There's more information needed that I won't get from the server because it's not in the currently existing web UI. For example, I divide the options into pages so it'd be nice if every page has a clear and concise title. Since the current UI doesn't use these pages, there's no titles. It can also be the case that a little more thorough restructuring of the options is necessary to make it user friendly; maybe we want to split a group of options into two pages, or combine two groups into one page, or change the order of the pages or the individual options on a page.

To allow for this, I plan to use a two-fold approach. First I will use additional data that will be combined with the data returned by the server that will allow me to define things like titles, page orders, and other transformations that might be needed. It will be possible for the GUI to use more than one set of this kind of "modifier" data; they will be loaded in order with each having the ability to override the settings from the last. This allows for e.g. user-specific settings that complement or override global settings. And second, I will make it possible to specify a custom server control to handle a specific group of options. That way, whenever something needs to be done that falls outside the regular options available for my GUI, it can still be done.

Of course, this is just my preliminary idea. Tomorrow I'm having a meeting which will involve getting some feedback from real users on the system as it currently is, and next week I will join a demonstration of the system at the VUMC in Amsterdam, and I'm sure that will influence the design.

Categories: University
Posted on: 2006-12-05 16:59 UTC. Show comments (0)

Day 1: YAML

Today was my first "real" day. Sure I'd been over to work last week too, but that was not a full day and I spent a lot of it just getting set up. Plus I worked mainly on my thesis research (as I said before, we're going to continue that a little).

But today I worked a full day, literally nine-to-five, on the DIAL project. I'm still very much in the "how" phase; I'm just trying to figure out how I'll be doing it. Even the implementation platform isn't set in stone yet (I'm trying my best to get them to let me do it in .Net :) ).

One thing that I do know is that I need a way to communicate with the server, and so far that can be done in four ways: via the Perl modules, via a command line interface, via a web interface, and a YAML interface. Since my stuff won't necessarily be running on the main DIAL server the first two are out. A web interface that tries to communicate with a server through another web interface is too weird even for my tastes, so that leaves YAML. A brief look at YAML didn't reveal any problems with this.

Unfortunately, a detailed look reveals more than a few problems! For one thing, good YAML parsers are scarce. Really the only decent ones I could find are for Perl or Python. There is as far as I can tell only one parser for .Net and it doesn't work properly. That means I have two options: roll my own parser, or convince the DIAL guys to give me a different interface.

Since the YAML spec is very hard to read, and YAML in general is extremely hard to parse (it's designed for human-readability, severely compromising machine-readability), writing my own parser wouldn't be fun. The grammar for YAML is context-sensitive, determines scope by indentation, and has far too many ways to do the same thing. I could decide to limit myself to the subset of YAML that the server seems to be using, which makes it slightly more possible, but it's still not my first choice.

That leaves trying to get a different interface. I've briefly looked at the DIAL code, and the YAML generation is pretty much a matter of calling YAML::Dump from the YAML CPAN module. Which to me at least makes it seem like he could pretty easily use the XML::Dumper module instead. Here's to hoping.

Categories: University
Posted on: 2006-12-04 18:47 UTC. Show comments (0)

Not quite used to it

Today for the first time I really went to University to work. I've been there a few times this week for various things but today was the first time I really got to sit down at my desk and work. I don't actually have a computer yet (I used my own laptop), but at least I have a desk, and an office.

And that's just weird. It takes an enormous amount of effort just to open the door to my office without knocking. Sure, there's other people in there too, but I don't need to knock on their account. It's just, for six years if I wanted to get work done at Uni, I'd go to one of the computer labs. The only time I spent in an office is in meetings in someone else's office. And now I've got an office myself. It really helps to drive home the fact that although I'm still going to University, I'm not a student anymore; I'm an employee.

Even weirder perhaps was when I had to fill out some forms for personell services regarding my employment. It was basic stuff: name, first name, title, date of birth. Suddenly, I realised I actually have something to put for "title" now.

Categories: University
Posted on: 2006-11-30 20:47 UTC. Show comments (0)

Sven Groot, MSc.

Yesterday it finally happened: I received that one piece of paper that says that I am now a Master of Science in Computer Science!

Of course I've been done for a while now, but now that that final formality is done it feels much more final. It's weird to think that now, I'm really not a student anymore. Of course, since I'm staying at University to work and will continue in the academic world (as you know, hopefully in Japan) it's not as weird as I imagine it would've been if I would've left University for ever and went to a "real" job now. But it's still weird.

The proof is in the pictures: here I am after just having received my degree from Professor Wijshoff (whom I'm shaking hands with).


So today, I can officially call myself Master of Science. Or if I so choose, I can use the old Dutch title "Doctorandus" as well (that would make me Drs. Sven Groot).

And to add to this, today is my 25th birthday, so it's a double party. I already had some people over this afternoon, and I'm expecting lots more this evening.

It's strange to think that last month, I was still working on finalising my thesis, and now I'm done. It's even stranger to think that if things go well, I'll be in Japan in less than six months. And it's strange to think that I've been alive for a quarter century already.

Strange, but good. :)

Categories: University
Posted on: 2006-11-25 17:43 UTC. Show comments (1)

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