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My Akademy talk proposal was not accepted, but the organizers were kind enough to offer me the chance to hold a BoF on the same subject. Now I bet you wonder on what I’m going to discuss, and I think the title already gives you an idea:

KDE and bioinformatics: the missing link

Although in the KDE community we have our fair share of scientists (hey there, Stuart!), my BoF will focus on the adoption of KDE in the field of bioinformatics (my day job, not-so-by-chance) on the "outsiders" front and how to improve the current situation. To elaborate further, bioinformatics is a rather broad field where biological data are treated with computational methods. The oldest and most famous branch of bioinformatics is sequence analysis and related field, where sequences of DNA are analyzed, for example, to find common ancestors among several species, or to reconstruct the genetic code of an organism by comparing it to a related species. Another recent example is related to high-throughput technologies, technologies which produce huge amounts of data from a very small number of experiments ("ultramassive sequencing" and DNA microarrays are examples of such a technology).

Either way, bioinformaticians have to deal with large amounts of data all the time, and usually there’s no "shrink-wrap" solution to the problems they have to face, software-wise. That’s because we do research, so we need to find something new. So the solution is often to write algorithms, or re-implement existing ones in a form that is suited for the tasks at hand. So, bioinformaticians also write software, although they’re by no means (usually) professional coders: some have a mathematical or statistical background, others (like me) come from an experience at the lab bench. What kind of programs bioinformaticians write? Normally scripts and small stuff, but in certain cases even full blown-algorithms and applications. Some become so famous that are even trend-setters.

Which brings us to the heart of the matter: how does KDE stand in all of this? Sadly, not too well. I’ve done some research in the published literature, but there’s just one hit returned that’s proper: a KDE application for neuroscience (based on the 3.5.x Development Platform) published in 2008. I know that big research places like CERN use KDE, but to my knowledge smaller realities such as research group code in the majority of the cases for Windows or for web-based solutions. Given that at least a signficant portion of bioinformaticians uses UNIX-like operating systems, the question we need to answer is: why?

The first and foremost problem is related to market share. Research groups don’t even know that KDE exists, so it’s unlikely they develop something using the Development Platform (even now that’s becoming more cross-platform). This is where some promo efforts could help. Secondly, the problem lies in the "difficulty" (notice the quotes!) of developing using the KDE Development platform: most bioinformaticians, as I wrote, are not professional coders, and few of them know C++. The most used languages in bioinformatics are Perl and Java (with some Python and Ruby thrown into the mix). Thus, the need for proper bindings. The bindings are there, thanks to the excellent work of the kde-bindings team, but documentation is still lacking (namely in the examples department, but also in tutorials and getting started guides that aren’t aimed at C++). Some documentation is auto-generated, and while the KDE API docs are usually not too hard to read, they can still scare off newcomers. Of course this is not the fault of the kde-bindings team: namely, more help is needed.

Promo efforts and better bindings are the keys to spread KDE more in the field of the bioinformatics. This is what my BoF is about, plus an informal discussion on the use of FOSS in academia and related matters.

Interested? If you are, you can come to the BoF which will be on Tuesday, 6th July at 15.00 in the Area 2 of the main room at Demola.

I’ll also be around later till the following morning (sadly, two days is the best I can do to attend) in case you’re interested for a chat.

Those who use PyQt and PyKDE4 are certainly familiar with the syntax used to connect signals and slots:

from PyQt4 import QtCore
from PyQt4 import QtGui
from PyKDE4 import kdeui

class MyGUI(QtGui.QWidget):

    def __init__(self, parent=None):
        super(MyGUI, self).__init__(parent)
        self.pushbutton = kdeui.KPushButton()
        self.pushbutton.setText("Push me!")

        QObject.connect(self.pushbutton, QtCore.SIGNAL("clicked()"),
                               self.button_pushed)

    def button_pushed(self):
        print "Button clicked"

The main advantage of this syntax is that it’s very close to the C++ equivalent, and so you can translate easily from C++ to Python. Unfortunately the advantages of this syntax end here. The disadvantages, at least from a Python coding perspective, outweigh the advantages:

• It’s extremely error-prone: make a typo, and not only your signal won’t be connected, but you won’t even get a warning, your program will simply do nothing;
• In case you have overloaded signals, you have to type the exact signature, going back to the first problem;
• It’s not Pythonic at all.

So, in recent PyQt versions (and thus also in PyKDE4) a new style approach was introduced (although the old style is always present should it be the need to). Using the new style, the signals become a property of the object that emits them. and then you use the connect function of that property. Here’s the example using the new style-signals:

from PyQt4 import QtCore
from PyQt4 import QtGui
from PyKDE4 import kdeui

class MyGUI(QtGui.QWidget):

    def __init__(self, parent=None):
        super(MyGUI, self).__init__(parent)
        self.pushbutton = kdeui.KPushButton()
        self.pushbutton.setText("Push me!")
        # New style
        self.pushbutton.clicked.connect(self.button_pushed)

    def button_pushed(self):
        print "Button clicked"

As you can see it’s much clearer, and much more Pythonic. Also, typos will trigger an AttributeError, which means you’ll be able to track where the problem is.

What about overloaded signals? Normally the first defined is the default, but you can use a dictionary-like syntax to access other overloads (signal names are completely made up here):

# One signal is without arguments, the other has a bool

# Signal without arguments
self.my_widget.connected.connect(self.handle_errors)
# Signal with a book
self.my_widget.connected[bool].connect(self.handle_errors)

Signals are emitted with the emit() function and disconnected with the disconnect() function:

# Emit a signal
self.pushbutton.clicked.emit()
# Emit a signal with a value (an int)
self.my_widget.valueChanged.emit(int)
# Disconnect another
self.my_tabwidget.currentIndexChanged.disconnect()

To define new signals, you can use the pyqtSignal function, specifying which values will the signal take (if any): just define that as a class constant (like in the example) and then you can access them like the wrapped ones:

class MyWidget(QWidget):

    # Signal with no arguments
    operationPerformed = QtCore.pyqtSignal()

    # Signal that takes arguments
    valueChanged = QtCore.pyqtSignal(int)

I merely scratched the surface with this. For more information, check out PyQt’s reference manual, which also covers other cases.

Recently, I investigated how to perform some checks on web addresses using KIO for Danbooru Client. My old code was synchronous, so it blocked the application while checking, thus causing all sort of troubles (UI freezing, etc.). Therefore, making the switch to KIO was the best solution. However, I had one problem: how could I check the HTTP response?

I knew already that the various ioslaves can store metadata, consisting of key-value pairs which are specific on the slave used. Normally you can get the whole map by accessing the metaData function of the job you have used, in the slot connected from the result signal. For some reason, however, in PyKDE4 calling metaData() triggers an assert in SIP, which ends in a crash (at least in my application; I stil need to debug further). KIO jobs have also the queryMetaData function, which returns the value of the key you have queried. Unfortunately, there was no way I could find the name.

Thus began my search for the right key. Googling didn’t help, and on IRC I got the first answers I needed but not enough to reach the goal. Until I saw a commit by David Faure in trunk/kdelibs/kio/ which touched a file called DESIGN.metadata (link is for the branch version). After checking with webSVN, that was exactly the thing I was looking for! It lists all the keys for the metadata, indicating also to which ioslave they begin. After that, the solution was easy.

Of course I’m not leaving you hanging there and now I’ll show you how, in PyKDE4, you can quickly check for the server response:

from PyKDE4.kio import KIO
from PyQt4.QtCore import SIGNAL
[...]

class my_widget(QWidget):
[...]

    def check_address(self, url):

        # You can add optional flags such as KIO.HideProgressInfo
        job = KIO.get(KUrl(url))
        self.connect(job, SIGNAL("result (KJob *)"), self.slot_result)

    def slot_result(self, job):

        if job.error():
            # Bail out if there's an error
            return    

        # Get the HTTP response through queryMetaData
        http_response = job.queryMetaData("responsecode")
        print "Got response: %s" % unicode(http_response)

This snippet does a few things. Firstly, it gets the specified URL, using KIO.get (KIO.stat doesn’t set the required metadata). Notice that the call is not wrapped in the new-style PyQt API because result (KJob *) isn’t wrapped like that (there’s a bug open for that). In any case, the signal passes to the connecting slot (slot_result) where we first check if there’s an error (perhaps the address didn’t exist?) and then we use queryMetaData("responsecode") to get the actual response code.

If you want to do error checking basing on the result, bear in mind that KIO operates asynchronously, so you should use a signal to tell your application that the result is what it expected or not.

I wonder if this should be documented in Techbase…

It’s been a while since I blogged about anything non-FOSS. This time I’ll be sharing some impressions on one of the games I’m playing at the moment, that is, Ar Tonelico III (which arrived at my doorstep two days ago). I admit I haven’t been a fan of Gust games (aside from Ar Tonelico, they’re known mostly for the Atelier series), mostly because technically wise they didn’t really perform that well. While I understood they’re a small company, sometimes it was a little too much.

I bought this one because from the movies and information disseminated throughout the net it looked like it was better, so I started reading information, which in turn prompted the buy: it’s also a good way to keep my Japanese in order, as I need to keep up with the language if I want to understand things.

Right now I’ve just played a couple of hours, and it looks decent, although with some technical issues (the characters glide over the terrain, rather than walk). I’ve also seen the infamous Purge System in action (look it up online), which made quite a number of fan sneer for a various number of reasons. As of the story, I can’t say anything at the moment: I’ve just started. At least it is moderately fun.

Here’s a hands-on (Italian) which covers more details. I’ll try to post a few updates in the future (if I don’t forget….)

And here’s a quick video I made with my camera: