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!

I decided to write this post because I recently received an e-mail from BioMed Central stating that BMC Bioinformatics, one of their flagship publications, accepts a variety of different file formats in the submission process. This was already true when I submitted my articles. I wanted to know how they improved their submission process in this respect and if they now added open document formats (in a broad acceptance, not only the OpenDocument format somehow linked with OpenOffice.org).

My first comment is that the list of accepted file formats usually applies to all BioMed Central journals, not just BMC Bioinformatics, since they share the same publication platform. In the Instructions for Authors, the following file formats are accepted: Word, RTF and LaTeX (with the BMC template) for text, EPS, PDF, TIFF as well as PNG, Word (sic), PowerPoint (re-sic), JPEG and BMP for figures. In addition, they list CDX and TGF to represent chemical molecules. How disappointed am I!

I’m disappointed because some interesting open formats have been left out. And I can’t find interesting links stating that BioMed Central will support them soon.

With some stating that OpenOffice secured more than 15% of the business office suite market as of 2004 and despite an ISO standardisation (ISO/IEC 26300:2006), the OpenDocument formats are still absent. Many young scientists now use OpenOffice.org because it’s free (mainly free like in free beer, though), because labs can’t afford MS-Office licenses prices, even educational ones but also because it allow them to do everything they want. I agree that you can easily convert your ODF, ODS or ODP documents into their respective proprietary DOC, XLS and PPT. But it would have been nice to directly have the ODx documents. On the technical side, ODx documents are “just” XML files: tools exist to automatically parse them and transform them in the journal final format (I didn’t write it’s easy but it should be more easy than reverse-engineering closed, proprietary file formats).

I’m also disappointed because although the PowerPoint format if there, SVG is not. I guess it’s just because they only use bitmap versions of the PowerPoint files. All vector graphic editors supporting SVG (and all of them support SVG: Adobe Illustrator, Inkscape, Dia, …) have conversion functions to bitmap equivalent of your drawings. So it may have little impact. But it would have been better if BMC support for SVG was direct.

In conclusion, I’m hoping the extraordinary work done by BioMed Central in the publication area will extend to the formats they accept for submission. A partial example could come from PLoS submission guidelines (here for PLoS Computational Biology, especially for figures) where they explain a lot of technical as well as license aspects and cite free software as reference.

In my mind, I thought that third-party archiving (like arXiv or self-archiving) was one of the mandatory requirements for Open Access journals … and I was wrong. It seems JoVE is not giving the (technical) possibility to download the publication from their website (all what you can download is the abstract in text version). Now that this publication is a video and not a text/PDF version, it’s a problem for me (who cares?) and the Open Access movement (imho).

“Classical” Open Access journals are “just” an evolution of traditional, Closed Access journals (or rather a return to the original transmission form of scientific papers): usually, you can read the paper on the journal website but you can also download it and print it if you want (for offline reading or if you still prefer articles on paper). The problem with videos is that you can’t print them. Is it a sufficient reason to forbid the download of these videos?

Fortunately, there is a technical trick to allow you to download the video (it will still be in Flash 9 format but this problem is currently out of our scope). Once you are on the page of the interesting video (example), view its source code (Ctrl+U in Firefox) and look for the string “xml_file_name”. You can now copy the value of this variable and you can stop before the first “%26″ you encounter ; for our example, we’ll copy this: “http://www.jove.com/projects/VideoChapterXML/default.aspx?VideoID=211″. Enter this in your address bar and you’ll get another (XML) file (hence the name). Now on the first line, you’ll get the URL of your video in Flash format (flv); in our example: “http://source.jove.com/164.flv”.

In the future I wonder if JoVE will include a link to download its videos or it will obfuscate its source code in order to forbid further download.

Thanks to Biosingularity for the info.

The Association Electronique Libre is a belgian association protecting the fundamental rights in the information society.

The Association Electronique Libre supports the freedoms of speech, press, and association on the Internet and any electronical mediums, the right to use encryption software for private communication, the right to write software unimpeded by private monopolies, the right to access and preserve public domain and free digital information.
(from an old copy of the AEL website)

Although it was based in Belgium, the information it contained as well as the actions that were supported exceeded the small Belgian borders. The wiki was a very useful and valuable source of documents, links and comments about freedom in the electronic media. “Fortunately” we still have a 2007 version of the website on archive.org and some messages from the mailing-list were kepts on the mail-archive and open subscriber (and I will preciously keep my archives!).

Following a small exchange of e-mails with one of the main guy behind AEL, the machine hosting the AEL is simply dead (the fact the machine was dying was announced a long time ago, no one apparently reacted). I guess (or rather hope) that the data is still available on the hard disk(s).

Now what? Beside the fact we are all getting “older” with other priorities in life, how come we don’t feel more concerned about our freedom in the cyberspace? Internet liberties are still in danger [1], the Electronic Frontier Foundation website has more and more issues, a paper-media publishing house is printing comics to “educate teenage youth about an array of issues ranging from privacy, free software, security and the impact of politics on personal freedom as it relates to the use of technology”, … Are we too lazy to try to understand what’s behind Facebook, LinkedIn, Orkut, Ning and other “social networking websites“? Maybe the technological gap between these polished websites and what indivuals can do “in their garage” radically increased since the advent of so-called Web2.0, inhibiting our will to actively participate in it [2], to make it ours? Did most of us “surrender” in front of the razzle-dazzle aspects of new communication media?

The idea behind this post title (AEL – New Generation?) is simply that something should be done to bring back to life a central, hopefully community-driven website to gather information about our freedom in cyberspace …

[1] Ironically, in this post, this reference is written by the main person behind the AEL
[2] About the “creativity” of people in Web2.0 applications, we could read with interest this article from C. Jonckheere and F. Schreuer (unfortunately in French only)

The last free software published is exams, an assessment management system (for on-line exams, …). They chose the GNU GPL 2, apparently without the possibility to upgrade to version 3 (I don’t know if it’s deliberate or not). And you can download the source code here.

What is even more interesting is that they provide a demonstration website if you want to test it in a nearly real setup (as examiners or students ; only in French). And the demonstration system is hosted by a commercial hosting company (OVH), indicating that it could be possible to use this system on very common platforms (only PHP/MySQL are required).

Now, we can dream of other software from the ULg released as free software, a subversion repository and a users/developers community around exams …

P.S.: of course, we already did all that since we published Gemvid in an Open Access journal (the Journal of Circadian Rhythms) and published it along with a lot of other tools as free software. But I don’t count this as an institutional push towards free software since it was mainly my decision and the development didn’t involved other people.

Lee Dirks, director, scholarly communications, Microsoft Research: “We are very supportive of the open science movement and recognize that open access publication is an important component of overall scholarly communications.”

I hope the other Microsoft divisions are going to follow this move and sponsor (or release their products as) Open Source and free software projects … More details on the announcement here.

What made me interested in Dasher is her introduction about the way we communicate with computers and how they help us to communicate with them. There are keyboards (even reduced ones), gesture alphabets, text entry prediction, etc. I am interested in the ways people can enter text on a touch-screen, without physical keyboard. Usually, people use a virtual keyboard (like in kiosks for tourists or in handheld devices). But they are apparently not the best solutions.

They come with an interesting way of entering text, where pulling and pushing elements on screen are used to form words (with the help of the computer that is “guessing” the words from the previous letters). It requires a lot of visual attention but this can be turned into a feature for people unable to communicate with hands (for physical keyboard and mouse ; one man even wrote his entire B.Sc. thesis with Dasher and his eyes!).

You can download Dasher for a wide range of operating systems and even try it in your web browser (Java required) (btw, it’s the first software I see that adopted the GNU GPL 3). After reading the short explanation, you’ll be able to easily write your own words, phrases and texts.

They are interested in the way people are interacting with the computer. They are using a language model to show the next letters. On the human side, I am wondering if this kind of tool has an influence on how the human brain works. Visual memory should be involved in physical keyboard (“where are the letters?”) but also here (same question but the location of letters is changing all the time). Here, letters are moving but one can learn that boxes are bigger if the next letter probability is bigger. How is the brain involved in such system? What is it learning exactly? Are there fast and slow learners in this task? It could be interesting to look at this …

Now people evolved and we are a lot to love the internet, free software and Wikipedia. But the openness aversion is still there and some people are trying to restrict freedom (net neutrality, DMCA, DADVSI, DRM, TCPA/TPM, etc.).

[1] Boyles J., “A closed mind about an open world“. Financial Times, August 8th, 2006, p. 9.

P.S. By the way, I discovered Prof. Boyle and his articles on his website. I’ll now have plenty of interesting things to read (as if I didn’t already have enough article and books to read …).

P.S. Although the name and logo can mislead you (and misled me), the primary origin of the name “GooDiff” is not Google. The “Goo” part comes from the Gray goo (in SF, “goo” means a large mass of replicating nanomachines lacking large-scale structure, which may or may not actually appear like a drippy, shapeless mass). I am learning new words everyday!