Trueg is the KDE-Nepomuk dude, and has been running a few cool blogs, for example about Nepomuk Virtual Folders - The Next Level, We Don't Search... and Fetch, Nepomuk, fetch!
Tagging is the future. Overcoming typos in tags, synonyms is a conflicting feature, but does not limit the wide applicability of being able to tie information together. Now, Nepomuk is a bit strict on the type of metadata allowed, which is why Strigi has a super ontology (as in super set), to which we can add chemistry bits.
I have yet to install KDE 4.1, assuming that a good deal of truegs work found its way into that. At least, the virtual folders bit, I hope. But just imagine tying together PDFs, PDB entries, etc, I have on my desktop, all belonging to a diabetes, by just typing this URL: nepomuksearch:/diabetes.
On a different note, this tagging if available in Kmail would provide a powerful approach to organize the processing of my inbox; I can tag emails with todo, toreply, toread, toarchive, ...
Oh, and let me squeeze in this statement too (sorry, jriddel) : Kubuntu 8.04 has required me to tweak to work around bugs than any other previous Kubuntu release. Things tend to be encountered by others earlier, so that Googling generally helps sufficiently. But missing dependencies is a bit ugly (sorry, forgot which program it was, so can't link to the bug report). And, still am a happy Kubuntu user!
Showing posts with label KDE. Show all posts
Showing posts with label KDE. Show all posts
Monday, May 12, 2008
Saturday, February 02, 2008
Synchroning KDE settings; Plasma updates
First of all, thanx to all who gave replied to my previous blog item KDE 4.0.0: no Yukuake for Kubuntu?"! I got my desktop machine run KDE4 now, with Yakuake and with being able to lock the screen.
Now, regarding the taskbar; I haven't placed it on top of my screen, as I could not find those coordinates adz21c was talking about. That's really a minor thing. Now, the Plasma taskbar has seen many improvements over the last days, like the two row taskbar, and the ability to make is somewhat smaller.
Riddel wrote a tool to synchronize KDE settings between machines. It's actually amazing that in the era where KDE is able to have a central architecture for 'personal information' (Akonadi), and we have technologies like bzr, svn, that we still have to hack workarounds to synchronize our desktop environments. Of course, I already have the data of my desktop synchronized via repositories, but things as far from automatically done...
The tool made by Riddel is such a workaround, a really promising one (looking forward to the Kubuntu package! BTW, does it support both KDE3 and KDE4?), but it is surprising that it is not the default yet.
Now, regarding the taskbar; I haven't placed it on top of my screen, as I could not find those coordinates adz21c was talking about. That's really a minor thing. Now, the Plasma taskbar has seen many improvements over the last days, like the two row taskbar, and the ability to make is somewhat smaller.
Riddel wrote a tool to synchronize KDE settings between machines. It's actually amazing that in the era where KDE is able to have a central architecture for 'personal information' (Akonadi), and we have technologies like bzr, svn, that we still have to hack workarounds to synchronize our desktop environments. Of course, I already have the data of my desktop synchronized via repositories, but things as far from automatically done...
The tool made by Riddel is such a workaround, a really promising one (looking forward to the Kubuntu package! BTW, does it support both KDE3 and KDE4?), but it is surprising that it is not the default yet.
Friday, November 16, 2007
Friend-of-a-Friend (FOAF) support in Strigi
Last week I have been hacking on a Strigi plugin for FOAF files. Now, one will not expect FOAF files on ones desktop soon... unless, you start indexing your Konqueror history. I have not seen that feature yet, but not overly difficult to implement for a skilled Konqueror developer (just use the dbus interface for Strigi).
However, HTML files may have this line in the <head> element:
This could be the trigger for a Strigi plugin, to download this file and provide that as substream for the HTML file. I am aware for security issues at immediately pop up, but that is something we can surely deal with.
Using this approach the whole semantic desktop takes shape. Say, I am searching what I have on my desktop on some topic, then, additionally, Strigi will make me aware that I recently read the blog from someone who showed interest in that topic too. Moreover, it will even allow Strigi to tell me which projects on SourceForge are related to this topic.
Far fetched? No, it's really just around the corner. If interested, you may find the source code in KDE SVN under trunk/playground/utils/strigi-foaf. The Konqueror history hack is not implemented yet, as I need to know first what efforts are ongoing in that respect.
However, HTML files may have this line in the <head> element:
<link href='http://blueobelisk.sourceforge.net/people/egonw/foaf.xrdf'
rel='meta' title='FOAF' type='application/rdf+xml'/>
This could be the trigger for a Strigi plugin, to download this file and provide that as substream for the HTML file. I am aware for security issues at immediately pop up, but that is something we can surely deal with.
Using this approach the whole semantic desktop takes shape. Say, I am searching what I have on my desktop on some topic, then, additionally, Strigi will make me aware that I recently read the blog from someone who showed interest in that topic too. Moreover, it will even allow Strigi to tell me which projects on SourceForge are related to this topic.
Far fetched? No, it's really just around the corner. If interested, you may find the source code in KDE SVN under trunk/playground/utils/strigi-foaf. The Konqueror history hack is not implemented yet, as I need to know first what efforts are ongoing in that respect.
Wednesday, August 22, 2007
MDL SD files as folders: opening a single molfile
Alexandrs Google Summer of Code project is over, and he is wrapping up his code and blogging about his resource. He just blogged about one of his achieved goals: opening SD file as folders using Strigi's jstream technology. It provides tight support of chemistry on the KDE desktop: browse a SD file as a folder, open a single MDL molfile entry from the SD file with the FileOpen dialog, all in addition to finding a specific molecule by InChI in the SD file. Check the screenshots that Alexandr put online.
Friday, April 27, 2007
GSoC Meeting with Alexandr
Yesterday I met with Alexandr to discuss things around his GSoC project, like time schedule etc. During the mentors meeting to work out the final rankings, one fellow mentor argued that this project is too specialized for KDE. We, therefore, discussed how we can maximize the effect on the rest of the KDE project, and ideas that came up include a dedicated query tool for complex data (such as chemical data). Anyway, this will be discussed in our blogs soon.
Meanwhile, I have registered to the new Planet SoC which was announced on the Summer of Code Blog.
Meanwhile, I have registered to the new Planet SoC which was announced on the Summer of Code Blog.
Saturday, April 14, 2007
GSoC: towards a chemical semantic desktop
Now that I am officially a Google Summer of Code mentor for KDE's participation, it was more than time to get my KDE4 install up to date. Meanwhile, Jos' Strigi toolkit is well integrated already, and Jerome has updated the chemical kfile plugins to the new Strigi based architecture.
I was talking to Phreedom on IRC about ontologies used by Strigi, and added one for chemistry. It currently has the fields chemistry.inchi, chemistry.molecular_formula, chemistry.molecular_weight, chemistry.pdbid, and chemistry.xray_resolution, but more are expected to be added. I already updated kfile_chemical to make use of these fields, and updated it for a few fields from the more generic ontologies in Strigi.
Extracted metadata
Strigi currently focusses on metadata only, as do the kfile_chemical plugins: they extract metadata from the file, and do not generally create metadata based on the file (actually, Strigi calculates sha1 hashes). These are typically fields like molecular formula, title, X-Ray resolution (in case of PDB files), identifiers (e.g. InChI, PDB id), etc. However, there can be a lot more interesting information in those files, which require some more tought. For example, PDB files cite one or more publications, which might be present at ones hard disk too. The idea is here, that Strigi actually links the PDF with the publication and the PDB file. This is where Nepomuk comes in, and where Strigi is currently disabled. Similarly, any general organic chemistry publication will mention many molecules, each of which might have other publications discussing them, or even have 3D coordinates or other properties defined.
Created metadata
Another interesting thing one can do for chemical documents, is calculate metadata: for example, calculate InChI's for mol/xyz/hin/... files, using OpenBabel. Or Rule-of-Five properties, e.g. using the CDK. This is where the GSoC project comes in which I am mentoring, and on which Alexandr (a former CUBIC student) is going to work.
Oh, and like most desktop search tools, it can simply work on your HTML cache too, so that all these cool things will work on the webpages you search too. That should trigger some more ideas :) It does for me at least.
I was talking to Phreedom on IRC about ontologies used by Strigi, and added one for chemistry. It currently has the fields chemistry.inchi, chemistry.molecular_formula, chemistry.molecular_weight, chemistry.pdbid, and chemistry.xray_resolution, but more are expected to be added. I already updated kfile_chemical to make use of these fields, and updated it for a few fields from the more generic ontologies in Strigi.
Extracted metadata
Strigi currently focusses on metadata only, as do the kfile_chemical plugins: they extract metadata from the file, and do not generally create metadata based on the file (actually, Strigi calculates sha1 hashes). These are typically fields like molecular formula, title, X-Ray resolution (in case of PDB files), identifiers (e.g. InChI, PDB id), etc. However, there can be a lot more interesting information in those files, which require some more tought. For example, PDB files cite one or more publications, which might be present at ones hard disk too. The idea is here, that Strigi actually links the PDF with the publication and the PDB file. This is where Nepomuk comes in, and where Strigi is currently disabled. Similarly, any general organic chemistry publication will mention many molecules, each of which might have other publications discussing them, or even have 3D coordinates or other properties defined.
Created metadata
Another interesting thing one can do for chemical documents, is calculate metadata: for example, calculate InChI's for mol/xyz/hin/... files, using OpenBabel. Or Rule-of-Five properties, e.g. using the CDK. This is where the GSoC project comes in which I am mentoring, and on which Alexandr (a former CUBIC student) is going to work.
Oh, and like most desktop search tools, it can simply work on your HTML cache too, so that all these cool things will work on the webpages you search too. That should trigger some more ideas :) It does for me at least.
Saturday, April 07, 2007
A Chemical KDE desktop: the Google SoC
Two Google Summer of Code ideas have been written up for the KDE project, and students wrote 10 applications based on those. Today is an important day, as the final ranking will be determined which is send of to Google. See my bits on this some days ago, and earlier in this blog. Both ideas have a reasonable chance of getting one student accepted, but the final decisions will not be clear and made public before 11 April.
Thursday, March 08, 2007
Chemical KDE GSoC Project Ideas
Very likely KDE will participate again in the Google Summer of Code. At this moment two project ideas are written up related to chemistry: The second is my personal favorite, and I have worked on this topic in the past myself. See also Carsten's post on this.
The only thing I really miss in the full list of ideas, is the idea of completing a Greasemonkey plugin for Konqueror. I could not mentor a project like this, and, therefore, cannot put it up on the idea list :(
The only thing I really miss in the full list of ideas, is the idea of completing a Greasemonkey plugin for Konqueror. I could not mentor a project like this, and, therefore, cannot put it up on the idea list :(
Friday, February 23, 2007
KDE GUI's for OpenBabel's chemical file conversion
Jerome Pansanel has written Qt and KDE based GUI's around OpenBabel, allowing file conversion of chemical documents. You can download it here.
Together with the chemical mime type package, and chemistry indexing support in strigi, this should make KDE a perfect desktop for handling molecular data. I won't be able to make FOSDEM once more, but looking forward to the transcripts.
Together with the chemical mime type package, and chemistry indexing support in strigi, this should make KDE a perfect desktop for handling molecular data. I won't be able to make FOSDEM once more, but looking forward to the transcripts.
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