I actually tried jabref, but it struck me as not having many functions beyond holding a list of all my papers and generating a bibtex . . . → Read More: classifying papers]]> Every few months I ask myself the question again: “What to do with my scientific library?” I’ve run across solutions here and there, bu none which convinced me: jabref, zotero, papers, etc.

I actually tried jabref, but it struck me as not having many functions beyond holding a list of all my papers and generating a bibtex file. Zotero is hosted on servers far away somewhere and my work doesn’t allow this. (Well, they might allow it, but to be prudent I host all work related files locally.) Papers seems awesome, but is unfortunately mac only. The situation seemed desperate until I saw gPapers! I thought I finally had found THE program of my dreams. Alas, gPapers is rather unfinished. The person who developed it originally doesn’t seem to have contributed in a while. What to do? Well, contribute of course! Though I have been known to file bug reports and test alphas, I’ve never contributed actual code to an open-source project, so this is my first experience. It seems like the timing and circumstances are perfect for me to get involved:

• gPapers is written in python, which I’ve taken the time to learn lately;
• I’m tired of looking for this perfect software and have gotten frustrated enough that I’m willing to write it;
• right now, the feature-set of gPapers seems contained, so the initial deciphering of the code shouldn’t be impossible (it’s not like I just decided to rewrite the whole linux kernel);
• there are few developers and the pace is slow, so I should have time to get up to speed without having the software go through three major revisions.

The only problem is: the active fork of gPapers is hosted on github. I have no idea how git works, let alone github. (I DO use version control, but I’m a svn user right now and have no experience with distributed version control.) I managed to create an account on github, create keypairs and upload the public key to github and…that’s pretty much where I was as of this morning. After a few days of looking, I came across a great tutorial containing the information I had been looking for so far. It basically answers the question I’ve been stuck with for a while: “Ok, I’ve created an account on github and now I want to contribute to a project. What do I do?” (spoiler: the answer is basically that you fork the project, as surprising as it may sound to svn users.)

Getting started with GitHub from Charles Max Wood on Vimeo.

As for gPapers itself, I got the software to run a few days back and now I’m off to see if I can actually make it work. Let’s see how much has to be done to make gPapers better than papers.

[Update 11/17/2010: I was corrected by a commenter. You can use zotero entirely locally. I'll give zotero a whirl again sometime in the next few days then. I'll probably still try to contribute to gpapers, be it only to learn how to use git properly.]

Now, the German foreign ministry is in the process of migrating its 11 000 desktops to linux with about . . . → Read More: FOSS taking over the world]]> The french legislature switched from windows to linux in July 2007. ZDnet ran an article a year later (in french) with several first hand accounts of the effects of the transition. The conclusion was that everything went well.

Now, the German foreign ministry is in the process of migrating its 11 000 desktops to linux with about half of the work completed. Interrestingly, a source in the foreign ministry says that the cost of operating the desktops has gone from about 3000 euros to 1000 euros per year per computer. While the situation may be a lot more complex (maybe the foreign ministry has linux wizards on its payroll) it is definitely something to consider if you’re running a business that uses any number of computers. With a potential economy of 66% of your operating costs, even a small business using only a handful of computers, it may be beneficial to switch. The cost of transition (per computer) may become quite high, but with such savings in operating costs, I bet a migration to linux will be self-financing in a very short time.

It may be beneficial to run the numbers for your business. Then again, if I had to run the numbers for a business of mine, I wouldn’t know where to start. There may be money to be made here.

So the wikimedia foundation just announced a deal was accepted by everyone that would . . . → Read More: Wikipedia licensing will be compatible with creative commons]]> [I know I'd promised this post would be about the great idea I have and which I've been dangling around without really being descriptive, but as far as I can see, this has just come out and I need to talk about it.]

So the wikimedia foundation just announced a deal was accepted by everyone that would make the GFDL (the gnu free documentation license) compatible with the creative commons license. Wow, ok, so what does that mean? Two short points.

1- What’s a license again?

The “copyleft movement” doesn’t claim that it won’t use copyright, rather it encourages creators to voluntarily give some or all rights away formally, but within the confines of copyright law. How do you do that? You use a license. As an example, let’s take wikipedia. Formally, everytime you modify a page on wikipedia, you own the copyright to that page as a derivative work of all the stuff before… until the next edit of course. By using the wikipedia framework (the wiki, the site itself, etc…) you agree to post your copyrighted stuff according to a license. In this case, wikipedia uses the GFDL, the GNU Free Documentation License. It says many things, but the summary is that everyone is free to use the stuff freely for non-commercial or commercial uses, at will. What you have to do though, is that whatever is licensed under the GFDL has to be distributed under the GFDL and also carry along with it the whole text of the GFDL (which is pretty long). It also says that if you make a derivative work of the stuff (which is what you do when you edit a page) you have to distribute it under the GFDL, so that if you use something that’s licensed under GFDL as a base, you have to make your end product licensed under GFDL as well. It’s not as bad as it seems as the definition of a derivative work isn’t all encompassing. For example, if you quote something from wikipedia in a book, you don’t have to distribute the whole book under the GFDL. Is the GFDL the only license of that type? Absolutely not. There are dozens and they’re not all compatible, which has caused headaches at time. Another license which is pretty close to the GFDL is the CC-by-SA (creative commons attribution share-alike license). Now you may think, “wow!What’s that?!” Let’s describe it.

2-Wow! What’s CC-by-SA?!?!

CC-by-SA stands for creative commons attribution share-alike license. The creative commons is a not for profit organisation that came out of Stanford and whose purpose is to design license agreements that allow you to easily understand what you’re doing and easily give away some, all or none of your rights away. To achieve that goal, they have crafted a whole set of lienses (and are crafting more) as well as have ported them to different jurisdictions (different countries). So hte CC-by-SA is only one of those licenses. What does CC-by-SA say? Well, basically the same thing as the GFDL. It says you can use the work as you like, but you have to say where it came from and the resulting work has to be licensed with the same terms. Now, it’s nice and simple, but it’s not compatible with the GFDL? So at this point, you may ask “Why?”

3-Why are GFDL and CC-by-SA not compatible?

Simple. In fact, right now, the incompatibility is only one-way. You can take stuff that’s licensed CC-by-SA and integrate it (or just release it) under something that’s GFDL, because the GFDL has the same terms as CC-by-SA. You can’t take something that’s GFDL and release it under CC-by-SA because the GFDL says the derivative work has to be licensed under the same license. CC-by-SA only says the license has to have the same provisions, but it can be a different license. Annoying heh? Two things achieving the same goal can’t talk to each other. So now you may think “Well, that’s nice legal stuff, but why should I care?” Let’s look at that.

4- “Why should I care?”

Well, at least I (Charles) should care because I administer websites and I have to deal with these licenses. If you look at the right bar of this website, further down, you’ll see a little logo with the name of the license. That’s right, this site is licensed under a creative commons license. Neat heh? I don’t actually mind people reusing what I write here. I just ask that they be nice about it and follow my conditions. Now that’s nice, but I don’t often use wikipedia stuff in here. In fact I don’t. One area where this was a problem was wikiscuba. I started that website with a british diver and we had to decide, at the beginning, which license we were going to use. We wanted to have a creative commons license so that we could interface with wikitravel. Wikitravel is a travel wiki and since we have listings of dive sites, we wanted to be able to re-use stuff from wikitravel in ours. As a matter of fact, we did. Way at the beginning, I copied the country pages from wikitravel to give us a start and some structure in the dive site section. The problem is that we also have a techniques/gear/instruction kind of part of the site and it would have been nice to have GFDL licensing so that we could take stuff from wikipedia. We had to make a choice. We picked creative commons. With the hindsight, we could have picked both. It’s possible to dual-license all the stuff. We didn’t. Why? I don’t remember. That’s where the headaches start, you see. Thanks to this new move (I’m not sure whether it’s a done thing, but when it comes, you’ll know for sure, wikiscuba will gain about 1000 pages overnight and I’ll happily add information on there!) we won’t have to choose. Now we can just get back to the business of creating more information, adapting more information and distributing it so people can use it.

5-”That’s nice, Charles, you’ve told us why you should care, but why should I care?”

Ah! Good question. Well, in today’s world, it’s easy to create content and distribute it. Do you have blog? Did you take a picture of your dog and put it on it? Then you’re distributing content. (Just for the record, it could also be a picture of you, your boyfriend, your niece or anything else.) What about the text of your blog? What if you wrote down something, put it on a webpage for everyone to see? You’re distributing content. What if you sing a song you recorded? You’re distributing content. What if you write a piece of software and you put it on your webpage? You’re distributing content. (There are licenses specifically for software, for example linux is licensed under the GPL which is also very popular. There are, for software also, a lot of different licenses and they’re not a priori compatible, either because of the terms they use or of some technicality. Firefox, for example, is free and open source software, but is not distributed under the GPL.)

So as you can see, in today’s world, it’s easy to create and distribute content. (As a corollary, it’s also easy to copy someone else’s copyrighted content and distribute it.) An example which is hopefully more interesting to the scientist-readers of this blog, is the following:

If you write a report, produces plots, integrate it all in a pdf and put it on your webpage, you’ve created and distributed content. Now, what do you want? Do you want to make sure people know they can cut out a figure and re-use it in their Ph.D. thesis while attributing you as the source? This is probably something most scientists want. One option would be to release your work under the Creative Commons attribution share-alike license, the CC-by-SA. [Just for the record, I don't work for creative commons and I don't get anything from them for saying this or anything else.] In today’s massively interconnected world where fast communication methods are available to many, it’s important to know about copyright. Especially when it’s so easy to break the law by copying someone else’s copyright these days.

So that’s the long story about the short announcement. This is a great day. Interoperability between “open source” or “copyleft” projects is important or, at least according to me, desirable. Sometimes you don’t want interoperability. For example, I believe the license which governs the BSD operating system (most people have microsoft windows, mac people have MacOS, the free and open source operating system normally talked about is linux, BSD is another such free and open source operating system) allows people to take the source, modify it, compile it, package it in a machine and distribute it around, making people pay for it, without ever giving the program away. (If I’m wrong, someone correct me, but I believe it’s the BSD license which allows that.) Now I don’t think that’s wrong. It’s a choice. And the BSD people, at the beginning, made that choice. Linux, on the other hand, says that you can re-use linux code (well, GPL code really) as you will but you have to give the source away. Again, it’s a decision. It has good effects: the license basically tends to multiply and your code would never end up to disappear from the usable-for-free pool (which could happen to BSD although it’s quite unlikely). It also has undesirable effects: there are people who might want to use the code base and create something really awesome that you’d actually want to buy, but they won’t because they don’t want to give the source away. The original linux people made a choice.

My final point is that when you create content and distribute it, you have to make a choice as to how you’re going to distribute it. You can give all your rights away and put it in the public domain. You can give no rights away and simply not license your creation at all (or basically only license it for viewing). You can give some rights away in between those extremes. Still you have to know what you can give away and what your choices are. I recommend the creative commons website as a good start with information although there are more ressources out there.

[Originally seen on slashdot and Jamendo Blog]

I were just told about an bikerouting application for Gotheburg, Sweden. It’s all in swedish but may be interesting anyway. It is at <http://demo.triona.se/cykel/>, try for example enter “parkgatan 7″ as start/Från and “torggatan 1″ as destination/Till and then click “Beräkna rutt”. You get a route in green . . . → Read More: “Google Maps” for bicycles]]> Just saw this on the OpenStreetMaps mailing list:

I were just told about an bikerouting application for Gotheburg, Sweden. It’s all in swedish but may be interesting anyway. It is at <http://demo.triona.se/cykel/>, try for example enter “parkgatan 7″ as start/Från and “torggatan 1″ as destination/Till and then click “Beräkna rutt”. You get a route in green in the map and a list of turns in the lower right part. There are setting for if you cycle slow, medium or fast. Also if you want the “most appropriate” or fastest route.

/Jonas

This is cool. For those not in the know (and I assume there’s a few of you, not so long ago I had no idea that OSM meant more than Orchestre Symphonique de Montréal), OSM stands for Open Street Maps. It’s community effort, people riding/walking/driving around with their gps units and recording where the streets are. So far, it’s basically an “open source google maps”. Except, as in most open source projects, it ends up being more than that. People don’t just record the location of the streets, they record the location of pubs/restaurants/parks… Ok, so far it still looks like something Google does with the added burden of the randomness of data availability. Except it’s not only that! Mappers also record the position of walking paths, cycling paths, etc. Now that’s definitely something Google doesn’t do, at least not right now. So why bother when google does it for free? Well, for starters, the bike routing example I gave just above is a great idea that’s impossible with Google. There is someone who decided to reuse this free data to make something cool and innovative. It might not be so useful in the land of Uncle Sam, but in other countries with a developped cycling infrastructure, this would be wonderful. Granted locals learn how to cycle somewhere quite fast without needing to constantly use a map, this would still be a perfect tool for a slightly longer trip. I could see myself having used such a tool back when I lived in Montréal, in Québec.

There’s more to this than a cycling navigator, though. The data is free (as in free speech and free beer), which means you can take it and reuse it. How does that impact your life? As an example, let me take wikiscuba. It’s a wiki and all the information is free (as in free speech and… you know). This site would benefit a whole lot from having maps included. We have installed all the required code on the site to use the google maps applet and it works. Some people have started using it. It’s completely legal. It’s free, as in free beer, but not free as in free speech. What this means for us is that we can use the google maps applet with no legal worries, but this restrict the further uses that can be done with out site. While it’s legal for us to display google maps within the wikiscuba site, it makes it illegal for someone to print off the page and distribute it to people. So if, at some point, we have enough information on a page for a dive shop to say “Ok, let’s just print off the page from wikiscuba and distribute it to students so they know where to go for the certification”, they wouldn’t legally be allowed to. At this point, you may thing it’s probably not a big problem. After all, Google is probably not going to tour all the dive shops of the world to make sure they haven’t printed a page from our site with one of their maps. Sure. Only, our data is completely free. So theoretically, someone could decide to write a book using the stuff we have written on the wiki. But they wouldn’t be allowed to use the maps. You couldn’t, also, directly make a set of pdf files from pages from an area that interests you and just distribute those on your website. You’d have to edit the maps out beforehand. Something like “The expanded guide of scuba diving sites in Northern Europe”. Now that starts restricting what you can do with our site. At this point, you may think “So what? Just edit the maps out!” and you’d be right. It’s just not as nice. I’d like to be able, on the licensing page of wikiscuba, to say:

“Go on. Do what you will. It’s free! (as in free speech)”

But I can’t. I have to say:

“Almost everything on wikiscuba is free. The text is all licensed under a creative commons license and you can use all the text you want in other uses. Images should also be similarly licensed, although it’s a good thing to check. Some of them may be in the public domain, in which case you can do anything you want with them. In other cases, some images may be licensed under various flavors of the creative commons licenses and certain restrictions may apply. Above all, you are not allowed to re-use the google maps applet information…”

Not as nice. Not all of it is Google’s fault, you’re right. The bit about the images will have to be there no matter what. But “some images have some restrictions and many have absolutely no restrictions” sounds a whole lot better than “you can’t re-use the information.” Reading the bit about google maps, stumps the reader. It may make re-using our data appear more difficult than it is and lower your desire to undertake a project that would re-use what we offer. I don’t like that. There’s really no incentive for us (who legally own wikiscuba and make it run) to restrict the way in which you use our data.

Now, at this point, you may be thinking “I disagree. If you restricted what can be done with the information on your site, you could make money everytime someone reuses your data!”

And you’d be right.

But you’d be forgetting one, small, detail; This is a community effort.

People don’t like to work for something and then not be allowed to use it if they want to.

Nobody would contribute to our site if we did that.

The site wouldn’t be cool.

I wouldn’t have a great scuba diving encyclopedia (although we’re still far from that) when I’m looking for info about a dive site.

I wouldn’t sleep well at night.

Again, I’m not blaming Google. They’re not sharecropping here. They license map and satellite data from companies and government and use it on their site. In fact, it appears that the restrictions they put on their maps and the google maps applet is because of those licensing deals. So it’s not entirely clear it’s even their fault from the start. Still, OSM is better in that respect. The data is free. Yes, the data is spotty. You don’t have good coverage in the US and in many other parts of the world. But the coverage is expanding. Companies are licensing their map data to the OSM community for use in the project. So, some bits of the world see their coverage expanded very, very rapidly at times. It’s a relatively young project. It’s getting there. When their coverage is really good, maybe I’ll be able to include that data in my site instead of google maps. That will be a great day. Oh yeah, and I’ll be able to have great street navigation on my gps without having to pay 200$ to garmin. That’ll be even better!