lbossers's blog

Zotero, the best thing that happened to me research-wise: THIS IS IT!

As some of you might know, I blogged to ask for a document management system and something that could deal with references. Extremely fast, I had a very useful responds that Zotero might be what I was looking for (many thanks!). Zotero is not only what I was looking for, but has so many options that I cannot stop myself telling how wonderful it is to anyone that seems to be listening. The reactions very from: “really nice program you have” to “WOW, that would have made my life so much easier” (yes that's right, no negative replies). I think that everyone (not only the people I meet) should have the opportunity to benefit from this Firefox plug-in. So, now I’m telling the world!

First of all: Zotero is ridiculously easy to work with. Besides, the documentation on http://www.zotero.org/ makes it possible for people that are “as good with computers as my mum” to fully understand and use all the facets of Zotero. Secondly, automatically obtaining information required for referencing by doi-number or ISBN saves a lot of time: instead of writing everything down yourself, you only need to check what Zotero come up with. If it is not to your liking you can easily adjust title (incl title case and lower case), author and so on. Furthermore, you can add notes and tags, categorize your documents, all to find them later on in only a few seconds. At the moment, I have about 400 items in my library and the search speed amazes me. I don’t need to make myself a cup of thee I only blink and before I have opened my eyes Zotero came up with a search list through all my data (that is: scientific articles in pdf format, notes and tags made in Zotero and documents written in OpenOffice)! And just to get back to the referencing part: you can export references in Word, OpenOffice, Gmail, LaTeX and possibly also other programs (I, however, don’t use those programs so I cannot give you feedback concerning that). Anyhow, this means that citation of references can in most cases simply be done by drag and drop. Furthermore, you can adjust the format in which the citation is made. And if that is not good enough: Zotero allows you to share your library with other people and allows you to access your library from different computers due to their server. Obviously the space on the server is limited and if I would want to use this I have to buy more space or work on only one computer since I just have too many files in my library. Anyway, the space they give you for free is more than enough to get a feeling of the value of this plug-in (I had almost 200 articles in my library before Zotero warned me that I didn’t have enough space on the server to sync my library).

A couple of things I haven’t tried yet and questions I have for the long run are:

-          Will I be able to use this program without major crashes up to at least the duration of my research (3 years)? Most likely the answer is yes, but I have to see that before I can believe it. I’m also not sure how to restore data if that would happen.

-          How does portable FireFox (combined with Zotero) work? In case I don’t have internet at hand... or can I simply open my browser and have zotero at hand? (I strangely enough never use my computer without internet. You may call me addicted.

-          What is best for exporting my references to LaTeX? Especially if I want to refer to many scientific articles? I have tried it with 1 article and that was ok. but I think that it can be done with less effort from my side (or maybe I’m just getting lazy seeing what is possible at date).

-          LyX , well that’s just one of those things I also have to try, I guess.

For now, I’m just extremely happy I found Zotero. Therefore, great many thanks to JFM who said that this might be it for me. You were right J.

If someone has any questions about this plug-in or how to deal with it and cannot find it on Zotero’s homepage, I’d be happy to help you!

 

 

The fastes way

The fastes way to get my boyfriend respond is via this medium... Emails and phonecalls don't work. Letters, well... don't even bother to send those to him. Luckily, there is a way to get him involved in my (computer)life. I just had a phonecall and he was really helpful explaining me what is and is not an error I should worry about. @Kanarip: I'll thank you later (K).

Crash, error and me freaking out

At the moment I wish I was more eager to learn how to deal with computers in a more advanced way. I think I'm more advanced than an ordinary user, but well... not good enough yet to understand why my computer crashing every freaking day. It is annoying. Anyhow, what sort of information should I have trying to solve this is my question?

Few things I noticed:
- First crash occurred 28th of February (can I somehow obtain information about what sort of software I installed that day or just before that day?)
- I'm installing a lot of programs lately. These were: Zotero, XdrawChem, WinDrawChem, PSPP, Chemical Calculator, SpecViewer. Furthermore, I keep all my software up to date.
- My memory is used to the fullest almost constantly. (for example: 44% in use by programs and 55% in use as cache).
- My network is often down (damn wireless)
- I am almost always on the internet when I work on my laptop.
- I've taken a screen-shot of the errors I have had lately...

Especially the attachment screenshot.jpg worried me (though it was gone after a restart). I hope my laptop will survive my PhD, which I just started... Can anyone say that it is not that bad and that it is only inconvenient at times? My laptop has his maintenance soon enough (2 weeks from now, at least if my boyfriend allows me to use him for this).

OLPC Dinner Party

The FUDCon in Toronto brought me, besides some really nice memories, a laptop referred to as OLPC. Last night I had a dinner party. I saw this an opportunity to explain them about the project and let the 30year old kids play with it. The first thing we noticed was that we are brainwashed by normal operating systems. We don't know how you can get to the main menu after you entered a program. However, we were all very enthusiastic about the project and we are sure that the kids in the age range well below us are more flexible and learn it quickly via trail and error. One of the guys explained that a similar project was run in Portugal. I'm googling and see that the XO is the big winner during a trail in Portugal. Somehow I cannot suppress this feeling of being proud, whereas I honestly haven't done a thing for the project. Only... well, let's just say I'm a good person to spread the news on open source software. Since I could explain why the kids can truly benefit from this type of laptop more than software that isn't open source, one of my friends saw the light: "SOOOO COOOOOOL". And indeed it is. It is good to develop yourself via educational exploration and have the possibility to look at what others have written to develop the software (you may be using). This way of learning most likely doesn't work for all of us, but it is an under-appreciated manner of learning if you'd ask me (in the Netherlands that is).

Presents for my birthday

I had my birthday on the 27th of feb. Nothing special, though I was gladd some people did give me a call on that day. Like my boyfriend. When he was in Cardiff last weekend, he wanted to buy me something for my birthday. So... I picked a couple of things: straws, tissues and passport photo's. Isn't that great? He gave me exactly what I needed. Well, more to be honest because he himself added some cookies with chocolate dips (can't go wrong with chocolate :))! Everyone in favour of no nonesence presents say I................................... I

Exit Code 127 while converting my LaTeX made file in .pdf (apparently important for the viewing part)

Hi there,

By now I realize that the error I got was not my mistake. Something is wrong with the Kile-program: viewing pdf does not work as is indicated with Exit Code 127. I can open the pdf file that I made on the location where the pdf is stored, but it is just not that convenient if you want to see what you're doing. However, for people using KDE this problem was fixed using a package (2.1.0~svn963524-1), see https://bugs.kde.org/show_bug.cgi?id=191090.

Is there a fix for someone using Fedora 12 and the most recent version of Kile?

Cheers,
Lydia


This approach worked for me the last time, let's see if someone can help me out this time :).

Exit Code 127 while converting my LaTeX made file in .pdf (apparently important for the viewing part)

Hi there,

By now I realize that the error I got was not my mistake. Something is wrong with the Kile-program: viewing pdf does not work as is indicated with Exit Code 127. I can open the pdf file that I made on the location where the pdf is stored, but it is just not that convenient if you want to see what you're doing. However, for people using KDE this problem was fixed using a package (2.1.0~svn963524-1), see https://bugs.kde.org/show_bug.cgi?id=191090.

Is there a fix for someone using Fedora 12 and the most recent version of Kile?

Cheers,
Lydia

This approach worked for me the last time, let's see if someone can help me out this time :).

Document Management

I love to be organized. Especially because I'm not. I can read an awful lot and remember it all, but if you ask me to tell you where I have gathered all that information or make a nice story out of it... Well that's where I struggle. I just started my PhD and I know that because of this I really need a good document management system. Someone told me about a program called Papers. And it really looked good. Unfortunately it is not FOSS, it is MAC's. My boyfriend shouted at me when I brought it up. Hmmm, maybe I didn't really explain myself good enough. All I want is a program that works well for referencing literature (preferably automatically because then I cannot make stupid mistakes and explain myself when I defend my research) and a system to store my literature in a way I can find things again.

Has someone an idea (and don't you say EndNote!)? Anyone?

If you don't understand what I'm talking about that's fine too, but just say so. Then I'll try to explain myself more clearly. For now: thanks in advance!

PhD Wales

Hello everybody,

Once again I'm dragging my boyfriend to a place in the world he probably wouldn't visit otherwise. I mean New South Wales, Australia and Wales in the UK may well not be the most exciting places for him...

Anyhow, I myself look forward living there and hope my boyfriend will eventually come on over too. Anyhow, let's talk about me and one of the more exciting things in my life. I intend to do a PhD project on the analysis of drugs in hair (see my facebook website). The research subject really sounds good to me, and I might even have the opportunaty to do some consultancy on the side. Next week I'll check out the University of Glamorgan and so on... Excited to go,

Lydia

FUDCon @ Toronto

At the moment I'm writing this, I am in Canada. Even though I haven't been able to explore the country as I would normally do, I have the impression that Canada is more similar to the US than I expected it would be. I think having a healthy life style is more difficult over here than in the Netherlands. On the other hand, how often do I go out for dinner and worry about the amount of sugar and fat in food in the Netherlands? And from the supermarket I just visited I can tell that there is enough fresh food to prepare a decent dinner myself.

Well, let's talk about something I do know instead of the impressions I have gathered over the last few days: FUDCon, the reason I am in Canada... I expected a group of computer geeks, but this was certainly not the case. If I would have give some thought about how social fedora contributors would be, the social aspect would not have been as much a surprise to me. I mean, these people operate in a community and they would only be valuable contributors if they can understand what others want and explain their own views on what the future of a project should be like. Hence, no loners.

 

At times it does cost me a lot of energy to find the things I'm interested in, because frankly I honestly don't care about the technology side. I mean, what do I care about computer-related stuff such as Ruby? (a project my boyfriend can talk about for days. Luckily, he knows not to talk to me about this stuff) What I do care about is the vision behind open source, how it can be applied in other fields, the reason people devote a lot of time to free software projects and last but certainly not least what a part of my boyfriend's life looks like (what kind of people he meets, what the activities at a conference are like and what makes him tick).

So, what have I learned? Well, I'll start with the basics I already knew. This way it may be more easy to understand where I come from. First of all, let me introduce you to the Fedora project (http://fedoraproject.org/). Fedora is a Linux distribution. Unlike Windows and Mac, Fedora is free and open source. And don't get me wrong; free definitely does not mean it is free of cost though I do run software that I can get at zero price. What it does mean is that one has access to the code, can freely modify it to one's liking and can distribute the modified code. The Fedora project is all about these modifications and sharing the (modified) software with others most prominently upstream. Great minds think about how to solve bugs, incorporate features and discuss the future of a software project. Non-technical people (like myself) can also contribute to the project by, for example, filing a bug report or request a new feature.

Up to now, my only contribution was to request a feature with the words: “will I ever see you [Jeroen van Meeuwen] again in the living room?”(https://fedorahosted.org/revisor/ticket/136). I must admit, I do not really consider this a contribution. Mostly, I just do not care enough about bugs as am easily satisfied as a user and instead of filing bugs I myself adjust when software works a bit differently than I expect. The only program I use enough to care about is the GIMP. So maybe I will get involved if there is something with this program... WTH, I might even be learning how to program software if it is important enough to me. I mean, if I do not try to change the program to my liking, I should not be allowed to complain about it. And as a side effect, I might do the other users a favor that may have the same problems as me. To me, as a user, this is the strength of Free and Open Source software; The possibility to get involved, get your problems fixed, your expectations met, all as part of this upstream process, so that others may enjoy the solution(s) or feature(s) as well.

I would say the main advantage of Free and Open Source software is the inherent transparency that allows you to fix bugs that annoy you (or others) and add interesting features. However, I'm not like the people that write code. As I understand, they mock around with the code just for fun. And why is it fun? Because it is a challenge. And of course, with this method of working you are able to excel and learn from others, since the community will respond on your actions. And though I do not understand why you would be interested in excelling in this type of activity I do understand the motivation if I think about my interest to work in the field I'm most interested in (let's just say I don't have a 9-to-5 mentality).

What I have learned at FUDCon is some technical stuff such as how to file a bug report.

  • Where?
    Bugzilla.redhat.com, bugs.kde.org and/or bugzilla.gnome.org (it does depend what you need to report. To really get involved with the GIMP I would directly go to the upstream GIMP website, same thing applies to the other software projects in Free Software).

  • What kind of information is wanted?
    What package it belongs to, what version of fedora you are using, whether it is a RFE (request for enhancement) or a bug report, a screen shot of the problem/ error, what hardware you use. In case it was a bug also information such as: what you were doing when it went wrong, what you think should have happened and try to reproduce it. Hence: a lot of information. Don't be put off by this, because filing a report without this information could be just as valuable. Of course, I won't deny that it is more likely that the bug gets fixed when more information is available. I mean, the developers should be able to understand enough of the problem to deal with it. A good way to get a problem solved is to provide all information a developer might need to reproduce the bug on his development workstation.

Another thing I have learned is that Free and Open Source Software is absolutely not free in costs since maintenance is expensive. I mean: time is money, right? A lot of very enthusiastic people work for the fedora project and this is the only way that it could work. Without a doubt it is nice to hear people talk about this since it simply means that they are extremely passionate about something. They all think that anybody could do it. And maybe they are right. The only question is: do you want to spend time to figure this out? Needless to say, everybody answers this question differently. All I ask of you (if you are not a contributor) is that you set aside your excuses and answer the question honestly. If you can't be honest to yourself, think about what this says about you. Do you feel morally obliged? Or do you want to spend your time on something that is more important to you?

So, what about the money stream in a Free and Open Source (FOS) world? Instead of paying for the product one would pay for a service done by skilled people. If a company wants to have the software designed slightly different the company can wait and wait and wait and meanwhile hope that their request or bug report gets enough attention from a skilled developer. This, however, may not be the most efficient and effective way to deal with a problem or deficiency. Hence, why not pay someone to do it for you? In addition, pay someone to maintain the system as well. That is how in a FOS world someone obtains money: getting paid by doing a service rather than selling a product. Don't get me wrong it's not all about the money. I, however, do think that money is a helpful tool for trading one's spare time for the stuff he/ she wants to obtain regardless of whether that is an experience or material stuff. Anyhow one thing does become more difficult in a FOS world. Ever since other people think for us users products are made that we got used to. In fact we don't really know what we need or what we want, because that has never been an issue. Hence, in an FOS world it suddenly becomes important that one realizes what it own demands and wishes are, that one can communicate this with the person that will work on this and that that person is able to understand the demands and wishes. At times another person to help (with this process of realizing the needs and with a clear communication between the user and developer) would be a wise idea. Another thing that can be handy in this process is to make a simple sketch of how things will finally look like. Think about a mock-up for a website. More honest feedback will be given then. After all, people realize that it is relatively easy to make changes in a sketch whereas it is not so easy to modify a written code accordingly to the feedback. A piece of useful advise for a design is that one should group different objects when a design is (almost) done just to protect the design. Since accidentally moving one tiny object is not as noticeable as moving a whole group of objects. Honestly, this is a bit besides the point, the point is that in a FOS world people are still able to make money, but in a different way in which communication plays a huge role. The reason I speak of world and not software is that this story does apply to software as well as other fields such as science. Instead of access to the code, one would have access to raw data in science.

Of course I heard an awful lot more. Mostly technical stuff, like that RPM 5 is worse than RPM 4 and only to be used for one package. But hey: do you care about this? Or how certain patches are required for such and such? I know I don't care so let's stop writing right here.

 

selection pics me and kanarip in Australia

Hi Everybody, Rather have a selection of the pictures kanarip and I made in Australia? Check out the subalbum I made @

. Not only I made a selection but I also manipulated a few pics (a girl needs to do what a girl needs to do, isn't that right?). So, even if you already seen the pictures, now you've got the chance to get a better impression... Cheers, Lydia


Self-Introduction: Lydia Bossers

Dear reader,

My name is Lydia Bossers and I'm the new kid on this block. Can I join the cool kids?

I'm using Fedora on my workstation as well as my laptop since there's no way any Windows will ever be installed at home on anything but the Christmas tree (purposefully obtained free copies of the media, of course).

I've been using Fedora for quite some time now... Actually now that I think about it I've been using Fedora ever since I'm dating kanarip.

Anyway, Jeroen has added my blog to Fedora Planet and so he wanted me to blog about *something* so that my new hackergotchi would show up on Planet.

I'm also on Twitter: @lydiabossers

LaTeX

The last few days, I've been thinking about what I want to use as text editor for my final report. Most likely, this report will contain numerous images and therefore I rather not use a texteditor such as OpenOffice.org Writer. Then again, is it worth learning how to use another texteditor? Probably the answer is "yes". Especially because I'm not the most patient person in the world and well, my laptop does get annoyed by the language I use when I spend my time with him.

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