Open-Source

FluTE is an influenza epidemic simulation model written by Dennis L. Chao at CSQUID. It works out-of-the box on GNU/Linux (just type make and run it). I wanted to see how it works. But since I’m temporarily stuck with a Windows laptop, I downloaded a free C++ compiler for Windows ( wxDev-C++), imported all the files in a project and compiled. For those who want to try, here is the project file and the specific makefile in a zip file (2 kb). Just decompress the FluTE archive (I used version 1.15), copy the two files from the zip file above and launch the IDE. In the project options (Alt+P), specify the custom makefile (in the “Makefile” tab) as the one from the zip file above. Compile (Ctrl+F9). Done. ...

Three months ago, I complained about the fact we can’t see comments made in PDF files in Evince. With a recent update to Fedora Core 12, Evince was also updated to version 2.28.2 and, among many improvements, comments ( annotations) added to PDF files are now visible :-) Bye, bye, Adobe Acrobat Reader ;-)

Evince defines itself as “simply a document viewer” (for Linux/Gnome and now for Windows too). However it can already read a lot of formats: PDF, TIFF, PS, DVI, DJvu and plans to support a lot more in the future. But for me there is one important feature missing: the ability to read comments in PDF files. I sent PDF versions of draft documents to my PhD thesis promoters and they send them back with their comments. Open them in Evince: you’ll only get the balloons but no possibility to click on them (see Figure 1 below). Open them in Acrobat Reader and not only you can see that there are comments but you can also see their content (see Figure 2 below). ...

I really like gthumb to have a look at my photos, quickly perform some basic modifications or effects and display all the photos to people around me. But there is one thing that is annoying me: it seems impossible for my gthumb version (2.10.11) to upload to Flickr, where I put some of my pictures. There is an " issue 73" in the GNOME’s GHOP Contest page from 2007 and the development seems to be done ; it’s just not yet in the main branch. ...

If you get error 404 with your permalinks and RSS feed after an upgrade of your Wordpress installation to version 2.8.3, it’s worth to check the “Permalinks” section (under the “Settings” tab in the admin panel). Try set it up to “Common”, save changes and then put it back to your previous structure (“Month and name” in my case). This should solve most of current 404 errors after upgrade. If not, check the Wordpress support forum.

This morning, it was impossible to post tweets on Twitter so I finally gave in to install a Twitter client. Amongst many software available, Pwytter seemed interesting to try: free software, written in Python were my two criteria. Unfortunately, the installation process is not straightforward (although its use of the general python setup procedure). Here is how to install it on Fedora 11 from the command line: Download Pwytter, unzip it, enter directory pwytter-0.8 Install ImageTK: as root, type " yum install python-imaging-tk" ( in Fedora, ImageTK was renamed python-imaging-tk) Install simplejson: as root, type " yum install python-simplejson" (optional) launch: python setup.py build launch: python setup.py install Complete the installation by copying some files with the 4 lines below (type them as root too) ( a comment in pwytter blog helps to solve the pwCache installation bug): cp pwCache.py /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg cp pwCache.pyc /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg cp -r media/ /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg cp -r theme/ /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg Now you can launch pwytter from any user! In addition, since the source code is available and Identi.ca supports a Twitter-compatible API, let’s see if it’s easy to modify pwytter for Identi.ca :-) ...

IPGphor2reader is a software meant to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. I previously hosted it on my personal website and just moved it to Sourceforge, here. Amongst the various reasons for this move, I wanted the possibility for anyone to participate in the project and no hassle to manage this. Slowly, slowly, most software on my website will be hosted on Sourceforge or Bioinformatics.net. ...

BioMed Central is one of the main Open Access publishers in the world of Science, Technology and Medicine. On a side note, that’s where I published my two articles (in Proteome Science and the Journal of Circadian Rhythms). One might think that, given their support to Open Access, they would also support Open Source software and Open Format documents. For the software side, it’s not very clear. Although they ask authors to consider releasing software described in publications under a free (or at least open source) license, they also support and advertise for a bunch of proprietary software. While it’s not a bad thing per se (it enlarges the number of potential authors), it’s sad to see they don’t cite popular free software like OpenOffice.org (to write your article), Gimp (to edit your figures) or Zotero (for reference management). These are the three main software in each category but the free software world has many more of them! ...

This week, I nearly emptied my internet quota by downloading and seeding the new Fedora Core 11. For those who don’t know yet, Fedora is a Linux-based operating system that showcases the latest in free and open source software. What I particularly like in this GNU/Linux distribution is that its developers prefer to make changes to the original software instead of applying fixes specifically for Fedora ; in this way, all the other distributions may also take advantages of the improved software. You’ll find many reviews and " tours" on the web about this new Fedora. In the next paragraphs, I’ll just highlight some of the most interesting points I saw until now. Coming from a Fedora 9 also helps to pinpoint the major improvements (mainly from a user point-of-view). ...

Oracle and Sun announced a few days ago that Oracle will buy Sun. Others are more apt than me to comment on the financial and strategic impacts of this move (for example, in the Guardian, the New York Times, the Wall Street Journal or on Slashdot). I’m more interested in the potential implications this move could have on some Open Source projects which were backed by Sun. I indeed believe Oracle will continue the development of his contributions to Open Source software, whether they are notable ( Btrfs or Oracle Enterprise Linux) or less visible. ...