My Outsourced Brain

Ubuntu for Research

2012-05-17T15:53:00.001+02:00

Every so often it's time to upgrade to a newer release of your operating system of choice. If you are using linux and you are working in research, this might be an article just for you. Here are some instructions about the installation of Precise Pangolin 12.04, the ubuntu long-term support (LTS) release which has just come out and is to be supported until 2017.

I wrote two posts before, which were dedicated to installing software for research in ubuntu. This is an update for Ubuntu Precise Pangolin (12.04) a long-term support release. Installation should be extremely easy and basically a one-line command. You just have to love package managers.

If you want to install from scratch, download the new release from the ubuntu site. Otherwise, if you want to upgrade press alt-f2 (or open the terminal) and type
update-manager -d

Once you are done with the basic installation or upgrade, you are ready for more. This means more software repository sources, more software, more libraries. Below comes a basic list, Please feel free to suggest other programs in the comment section.

Connectivity

The ssh server.
Google Chromium (Chrome) - because it's very fast and now supports smart bookmarks (at least in linux versions)
Dropbox - great for synchronizing files across computers and between users. Works with different operating systems.

Programming

Powerful editors such as vim and emacs,
gnu toolchain,
gnu screen,
subversion (svn), git,
file converter from dos to unix (tofrodos),

Statistical tools

Article writing and reference management

texlive,
many latex packages,
Mendeley
jabref and bibutils for converting to and from other reference formats.

Illustration

graphviz,
ImageMagick,
gnuplot, pdfedit,
inkscape,
Scribus,
gimp,
plugins to play media contents, etc.

Others

perl,
java RE and SDK,
blas
boost libraries
Zim is a note-taking/wiki application which is much faster than tomboy (presented some time ago on this blog).

Get a new and comprehensive ubuntu sources list from the ubuntu sources list generator. Choose your country, your ubuntu release (12.04) and all the software sources that you think could be useful. I chose for example the canonical partner, restricted, etc, and google linux repository among others. After pressing generate sources, you'll get a file that you should put as /etc/apt/sources.list (don't forget to backup the old one). On the same internet page, you find how to add the repository keys, which you should do before updating your sources (apt-get update).

For mendeley repositories do (you might want to check that 11.04 is still the latest release they officially provide packages for) sudo sh -c 'echo "deb http://www.mendeley.com/repositories/xUbuntu_11.04 /" >> /etc/apt/sources.list'

For the Adobe Reader repository do sudo apt-add-repository "deb http://archive.canonical.com/ $(lsb_release -sc) partner"

Download the latest package information. sudo apt-get update

I put all the software mentioned above and some more in a single command, so you have everything installed in one wash. No need to search or to sit around and try to fix things.

sudo apt-get install aptitude openssh-server build-essential gcc gcc-doc apt-file gsl-bin gsl-doc-pdf gsl-ref-html libgsl0-dev gsl-bin gsl-doc-pdf libgsl0-dbg libgsl0ldbl glibc-doc libblas-dev maxima maxima-share subversion subversion-tools git screen $(aptitude search R| grep -v ^i | awk '{print $2}' | grep ^r-) octave $(aptitude search texlive | grep -v ^i | awk '{print $2}') untex luatex perl fontforge context-nonfree context-doc-nonfree dvipng imagemagick graphviz gnuplot-x11 gnuplot-doc gnuplot libatlas3gf-base kdevelop kate kile vim-gtk vim vim-addon-manager vim-common vim-doc vim-latexsuite latex2html latex-beamer xpdf writer2latex jabref bibutils hevea hevea-doc wordnet cups-pdf djvulibre-bin djvulibre-plugin pdfedit inkscape scribus pdf2djvu pdf2svg pdftk python-gdbm ipython python3-dev python3-all python-scipy unrar tofrodos epiphany-browser epiphany-extensions scribes lyx claws-mail claws-mail-i18n claws-mail-doc claws-mail-tools libqt4-core libqt4-gui ubuntu-restricted-extras regionset soundconverter gxine libxine1-ffmpeg libstdc++5 libmms0 vim aptitude zim mendeleydesktop -y --force-yes icedtea-plugin sun-javadb-client gimp acroread wine colordiff moreutils

This will take a while...

For google chrome I posted instructions earlier. This time I followed instructions other instructions, which are as follows:

wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | sudo apt-key add -
sudo sh -c 'echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list'
apt-get install google-chrome-stable

Linux is an international effort translated into many languages. Depending on the "locale" you choose, your week may start with a Sunday, Saturday, or Monday. Say, you are not a Christian or Jew? You might want to change the first weekday in your calendar to Monday. Here's how.

What I found had difficulty to find at first was how to add applications to the launcher sidebar. Press the windows key, search for "Main Menu." You might have to install it first (you will get prompted). That's the application for editing the application menu that pops up on pressing the windows key and from this menu you can drag and drop items to the launcher sidebar.

You might want to see other of my articles for more tips, such as (for a short selection) smart bookmarks for faster web searches, how to synchronize web browser bookmarks on different work stations, personalize the vim editor, set up a revision control repository, and automatically synchronize data.
You can also see the UbuntuScience community page for some additional information.
Enjoy. Please leave a comment below for questions and suggestions.

Analyzing Chess Positions Using Crafty

2012-05-14T19:58:00.000+02:00

When you play or analyze games with crafty, you can visualize the board as well as crafty's output with Xboard.via the Xboard siteIf you want to raise your chess playing skills to a higher level, you need to analyze positions and chess games. Even on off-the-shelf computers, chess programs are stronger than most grandmasters, therefore what could be more useful in this respect than chess programs? One of the strongest chess programs is Crafty, which is being developed already for many years by Robert Hyatt, who works as an associate professor at the University of Alabama at Burmingham (UAB). Let's see how to install and use crafty.

You are interested in the world chess championship, which is currently going on in Moscow or you want to analyze your past matches that you played on-line, for example on ?

As I just stated, crafty is one of the best chess engines out there, furthermore it's free as in beer and as in speech. You can get it following instructions at its official page. In debian based linux (such as ubuntu) you can install it doing
apt-get install crafty

In ubuntu, this will also install the Xboard interface, which I highly recommend using. For windows, you'll also find executables from the crafty homepage and for the interface you will find ports from the xboard site.

Xboard also works with other engines, apart from crafty, such as dreamchess, fairymax, hoichess, sjeng, gnuchess, phalanx, fruit, glaurung, toga2, and stockfish. The last one is particularly strong, however doesn't support endgame tablebases (EGTB). I'll get back to stockfish later.

I should note here that you should not use a chess engine to cheat on games you're currently playing. If using a chess program constitutes cheating is controversial, but on some on-line playing sites computer assistance is frowned upon or prohibited (compare gameknot's policy on using computer programs and the rules in the German Correspondence Chess Federation). You should only use chess programs where you don't get an unfair advantage. Unproblematic is post-match analysis that gives clues on missed moves and helps you analyzing games. As an example, you might want to use crafty to annotate your game files or you can put it in analyze mode while you step through the moves and look for sudden jumps of evaluation. I find it also very interesting to compare well-known high-level matches and play less explored lines that seem appealing (referring to reference material should be unproblematic).

Expert players not only have a highly developed sense of positions and tactical combinations, but also a broad repertoire of openings and a deep knowledge of endgames. To get this knowledge into crafty, you can supply it with an opening book and endgame databases, respectively. I found the on-line explanations about databases a bit sketchy, so here they come at more detail.

For the opening database you need to download a file with matches, so crafty can build statistics out of that for each position. This file can be a pgn file or you can convert it to pgn (in linux you have the convert-pgn utility). The "enormous" opening book database (careful, big file) you can find at this address, others from the official crafty page. Apart from the files that you find with crafty, you can download other files, such as specialized pgn files for different openings, for example from here.

You need to compile the opening database first (see readme). In crafty, you type
book create filename 60

EGTBs you can find here or on other sites.

Crafty needs to find these files if you want to use them. On my linux system, I put these databases in /opt/crafty. Crafty's configuration file is called .craftrc in linux (in your home directory) and crafty.rc in windows (no idea where to locate it). My configuration file looks like the following:

mt=2
tbpath=/opt/crafty/
bookpath=/opt/crafty/
egtb !
hash=384M
hashp=128M
cache=32M
ponder=off
smpnice=1
log=off
show book
exit

If you want to dumb it down to beginner level, put the lines set ply 5 and ponder off.

If you want to use a graphical user interface (GUI), there's XBoard, which you can call like this:
xboard -fcp "crafty"

That's so much for crafty, but crafty does not give you statistics about moves, which is useful especially for choosing between opening lines. Scid comes with this functionality.

You can create opening books for scid, which uses a different format (the same that fruit and togaII use) in polyglot (e.g. polyglot make-book -pgn BDG2.PGN -bin poly.bin -max-ply 60. You have to copy the generated file to /usr/share/scid/books/).

However, this book format does not include win/loss statistics. If you want that you have to create a new database in scid, open a pgn file (for example enormous.pgn), and then you can use the opening report (ctrl+shift+o). The opening report includes among other things a section "Moves and Themes" with frequencies, scores, etc. for different moves and positional themes.

You can use stockfish and other engines in scid, over tools->analysis engine. Alternatively, for stockfish, use this command:
xboard -fcp stockfish -fUCI

Cheers! Please leave a comment below for questions and suggestions.

Estimation of Impact Factors

2011-09-14T22:11:00.000+02:00

Scientific excellence is often burned down to some numbers. For academics, it is publish or perish and bibliographic analysis is an important factor for academic careers. A bibliographic analysis includes how many papers somebody published, where they published, and how many citations their publications received. One of the numbers that sums up the quality of publications is the impact factor, which classifies journals and is often taken as the quality of individual publications published in those journal. There are services that calculate these impact factors, most prominently isiweb of knowledge, however they provide limited access (they are subscription based) and they only publish impact factors for journals that exist already for at least four years. Here I discuss shortly a method based on google scholar to estimate impact factors and I use it to estimate an impact factor for the journal frontiers in systems neuroscience.

What is the impact factor?

I am only paraphrasing slightly from the wikipedia article on the impact factor:

In a given year, the impact factor of a journal is the average number of citations received per paper published in that journal during the two preceding years. [...] Papers published includes citable items, which are usually articles, reviews, proceedings, or notes; not editorials or Letters-to-the-Editor.

There are alternative strategies to evaluating journal impact, such as eigenfactors, which are probably a better indicator of importance than the impact factor, however the impact factor is commonly used and cited.

Average citations

I am trying to estimate impact factor from google scholar, using the publish or perish software as search front-end.

Search for journal Frontiers in systems neuroscience between 2009 and 2010. Results from publish or perish below.

Papers: 110 Cites/paper: 4.82 h-index: 13 AWCR: 239.50
Citations: 530 Cites/author: 182.54 g-index: 16 AW-index: 15.48
Years: 3 Papers/author: 41.93 hc-index: 17 AWCRpA: 81.49
Cites/year: 176.67 Authors/paper: 3.25 hI-index: 4.02 e-index: 7.55
hI,norm: 6 hm-index: 7.98

The number we are looking for are the cites/paper: 4.82.

Discounting

The impact factor counts only citations received during the year after the publication period. Therefore, we should discount for citations during that time. This is not easily possible in google scholar. Therefore, because citation patterns over time should be similar over journals within a scientific domain, I suggest to discount by a factor suggested by other journals for which the impact factor is known. Probably the citations follow a log-curve over time, however a scalar discount factor could suffice for our purpose.

I will now calculate a discount factor based on impact and citation data for two journals, Neuron and PLOS Biology.

According to google scholar, papers in neuron published during 2009-2010 received an average of 20.25 citations since publication. Neuron's impact factor according to Isiweb is 14.027. Therefore, the discount factor should be 14.027/20.25 is roughly 0.69.

For PLOS Biology (impact factor 12.472) the average citations since publication for papers during the period 2009-2010 is 23.755. The discount factor should therefore be 12.472/23.755, roughly 0.52.

The higher discount factor for Neuron could mean that articles in PLOS Biology have a shorter half-life (i.e. Neuron articles get cited for longer periods of time).

Estimated impact factors

For the journal Frontiers in Systems Neuroscience, discounted according to the model by PLOS Biology, the estimated impact factor would be 4.82*0.52, roughly 2.51. According to the Neuron discount factor, the estimated impact factor would be 3.33.

I tried this out with other journals. For the journal of neuroscience, publish and perish's limit of 1000 papers was reached, so the estimate (11.04) is skewed by publications with higher impact that come first in search results. Maybe introduction of some arbitrary search queries could help, but I am moving on to other journals. For Plos Genetics I got "Cites/paper: 12.15" which would be 6.44 and 8.38 discounted, respectively, while the impact factor of 2010 is 9.543.

The the journal of computational neuroscience reports an impact factor of 2.325 on its web page, while I get 4.43 cites/paper, which would be discounted to 2.35. Frontiers in computational neuroscience has an impact factor (as of 2010) of 2.586 and I find 3.13 cites/paper from google scholar; discounted this would amount to 1.66 and 2.16, respectively.

So the estimate from google scholar is sometimes very crude, but maybe indicative for similar journals.

Conclusions

As indicated before, this estimation has to be taken with a grain of salt. Google scholar results are ordered by pagerank, so you have to take care not to loose the less-cited paper in the analysis. Important in this context is that frontiers in very well-indexed (DOAJ, CrossRef, PubMed Central and PubMed, Google Scholar, SCOPUS) which means that no papers get lost, otherwise we might loose papers that are not indexed or not cited. This could mean that estimates for frontiers journals from google scholar are better than for other journals that are not as well-indexed.

Google scholar takes into account a very broad spectrum of journals and many conferences. Isiweb impact factor includes only citations from journals. It also excludes self-citations, however self-citations (as I found in some study) do not co-vary (at least not significantly) with the number of citations of a paper (which means self-citations do not distort results if you compare different results at least).

Please leave a comment below for questions and suggestions.

Handwashing Behavior - Or: Should I take the Peanuts?

2011-02-08T22:04:00.005+01:00

Minuscule particles between dermal ridges in the hand, hardly seen by the naked eye. via wikipediaI don't think I am obsessed with personal hygiene, although, I am averse to certain behaviors, such as when you pick your nose next to me and then flip your snot in my direction, or when you reach out to touch me after having been touching dirty things on the street. What sometimes sets me off is seeing people exit the bathroom without washing their hands. I was also surprised, that when toilets featured shared faucets, to see this frequently with women (or should I say rather, not to see it). Now what about the peanuts in the bar? The guy, who just grabbed 10 more peanuts than his hand could hold and let half of them fall back into the bowl, what did he touch before? Should you really eat any of the peanuts? How many people wash their hands anyways?

In 1847 Ignaz Semmelweis showed that hand washing of midwives helped to reduce significantly mortality rate of childbed fever, from aroud 10 percent to around 1 percent, although at the time, he became rather unpopular for it. In 1890, Robert Koch demonstrated that anthrax was caused by the bacterium Bacillus anthracis and provided evidence for Pasteur's germ theory. Despite the implications for hygiene being so clear, it is again a case of theory against practice as case studies show.

Results from studies on hand washing behavior vary, debited in part to experimental protocol. Amanda Stinson concluded in her article "Hand washing behavior of women in public bathrooms", that due to an increased self-awareness, subjects were more likely to wash their hands when someone else was present washing their hands. Stinson distinguished between three conditions in her study on hand washing behavior of women:

No observer was visible
A person is talking on the cell phone next to the faucet
A person is washing her hands

She found that overall only 40 percent of young women washed their hands. In the hand washing condition (3), the subjects were more likely to wash their hands, 56 percent, while in the cell phone condition (2), subjects were less likely to wash their hands 27 percent. Stinson also found a strong and highly significant negative correlation between the time of night and whether or not the subject washed her hands.

In some studies it is not very clear whether the social factor mentioned above was taken into account so it is difficult to compare data over different studies. It also becomes clear from another study (see below), that age and education could be correlated variables. I therefore mention only one more study to compare men and women's hand washing behavior.

In the study "Gender and ethnic differences in hand hygiene practices among college students" by Anderson and colleagues it is not completely clear how they observe people in restrooms, however they make no mention of controlling the social variable and I would speculate that the difference from the results above could be explained in terms of social pressure.

What they found is that men washed their hands in 38 percent of cases and women in 62 percent,hand hygiene in females would be better than in males. In the discussion, Anderson and colleagues reference earlier similar evidence. They provide the argument that females' higher compliance could be associated with their tendency to practice socially acceptable behaviors. This however would also mean that having somebody watch you in the bathroom would have a stronger effect on women than on men, so that the question of who is more hygienic, men or women, cannot be answered conclusively.

Interestingly, Anderson and colleagues found that the minority students exhibited better hand hygiene practices than the Caucasian students. Comparing other studies they find that hand washing behavior in this college student population was only slightly higher than in populations of middle school and high school students. As for adequacy of hygiene, they report that only a small proportion of those who washed their hands did so for 20 seconds.

To come back to the original question: should I take the peanuts? I think that's a question of priority: just how hungry are you?

Enjoy those peanuts. At least as long as you can. Please leave a comment below for questions and suggestions. If you liked this article you might also want to read about the speed of nail growth.

Atheism around the World

2011-02-07T22:56:00.004+01:00

The rate of atheism or agnosticism in different countries is a question which can commonly sneak up in discussions over dinner or lunch. Atheist writers, such as Richard Dawkins and Christopher Hitchens, argued that belief in "a bearded man in the sky" — to take a somewhat provocative verbal expression — interferes with perception of reality.

While there are few people who would go as far as to actually claim that rate of religious belief is inversely proportional to national intelligence (see below), some people may take a high rate of believers as a measure of backwardness. Intuitively, I would guess it is probably relatively safe to claim that atheism rate is indicative of education level and economic well-being. I found a map of atheism worldwide, which I show, I outline the argument around atheism, and give a short discussion.

The data in the map come from different sources and are subject to different sorts of methodological differences and should therefore be taken with a grain of salt. Please, click on the link for a list of sources and to get a bigger image.

In many developed countries, people go to church on at least four occasions baptism, confirmation, wedding(s), and funeral(s). Some time ago, I wrote an article about belief in evolution worldwide, with a graph included that looked quite similar to this one.

I promised a discussion of the argument that religious belief is a sign of backwardness, so here it comes.

Is National IQ Related to Atheism Rate?

Richard Lynn, one of the discoverers of the Flynn effect, published together with others the study "Average intelligence predicts atheism rates across 137 nations." In it, after reviewing previous supportive studies, the authors find further evidence for significant negative correlation of IQ and religious belief within nations.

So, there you have it.

However, then the problems begin and I have to take this detour to distance myself from other results of this study.

They then go on to correlate national atheism rates with national IQs as Lynn previously had compiled in a book, mostly based on Pisa international education assessment studies and find again a negative correlation of educational success and religious belief over populations of different countries.

Rather than arguing for a correlation of education with atheism, the authors argue for a correlation of national IQ and atheism rate, which is not unproblematic. The main problem are methodological confounds about how to define/calculate national intelligence. They include factors of economic development (see below). Further, the authors argue backwards, saying basically that people are religious and uneducated because they are stupid (genetically).

The Flynn Effect and Atheism

It is worth to point out at this point that Lynn's claim to fame beside the Flynn effect is his quest to find racially conditioned differences in intelligence. I am therefore making a detour to point out the confusion of concepts and because I don't feel comfortable in citing a study by Lynn without qualification. Lynn states on his departmental web page:

In 1991 I extended my work on race differences in intelligence to other races. I concluded that the average IQ of blacks in sub-Saharan Africa is approximately 70. It has long been known that the average IQ of blacks in the United States is approximately 85. The explanation for the higher IQ of American blacks is that they have about 25 per cent of Caucasian genes and a better environment.

An abstract of one of his papers, Sex differences in intelligence and brain size is no less controversial: A paradox resolved, reads:

Males have larger brains than females, even when corrected for body size, and brain size is positively correlated with intelligence. This leads to the expectation that males should have higher average levels of intelligence than females. Yet the consensus view is that there is no sex difference in general intelligence. An examination of the literature shows that the consensus view is wrong. Among adults, males have slightly higher verbal and reasoning abilities than females and a more pronounced superiority on spatial abilities. If the three abilities are combined to form general intelligence, the mean for males is 4 IQ points higher than the mean for females. Among children up to the age of around 14 yr the sex differences are smaller because girls mature earlier than boys. The evolutionary selection pressures responsible for greater intelligence in males are discussed.

The article "Why national IQs do not support evolutionary theories of intelligence" delivers rebuttals for most of the claims (emphasis is mine):

We show that these studies assume that the Flynn Effect is either nonexistent or invariant with respect to different regions of the world, that there have been no migrations and climatic changes over the course of evolution, and that there have been no trends over the last century in indicators of reproductive strategies (e.g., declines in fertility and infant mortality). In addition, we show that national IQs are strongly confounded with the current developmental status of countries. National IQs correlate with all the variables that have been suggested to have caused the Flynn Effect in the developed world.

In fact, in the book mentioned above, Lynn and his co-author, Vanhanen, find correlations between the national IQ, as they calculate it, and many other factors. The human condition index (QHC), which they derive in the book, is found to be very highly correlated with national IQs. The QHC is composed of the following:

purchasing power parity Gross National Income (PPP-GNI) per capita 2002
adult literacy rate 2002
gross tertiary enrollment ratio
life expectancy at birth 2002
the level of democratization 2002.

One of these factors is education, which they use to calculate their IQ scores, so a high correlation is not too surprising. Basically the whole argument of national IQs boils down to saying religious belief correlates negatively with factors such as purchasing power parity, literacy rate, education, life expectancy, and others. I find it both ironic and sad, that Lynn forgets about the effect he helped to discover.

Concluding, religious belief (or rather the absence) seems to be one of the indicators of development.

Sleep Patterns as a Function of Age

2011-01-29T19:07:00.000+01:00

Sleep is not the same over a human life time. The time to fall asleep, the efficiency of sleep, and the amount of sleep vary with age. I found a great article about age-related changes in sleep patterns and thought it is of general interest to show some of the graphs that show these changes. It also shows that there is a difference between depressed and normal people. Read on to see them.

I found this in an article called "Age-related changes in sleep in depressed and normal subjects" by Gillin and colleagues published in the journal Psychiatry Research (vol 4, nr. 1) in 1981. They did all-night electroencephalography during sleep of people diagnosed with depression (78 people in total) and controls (who were not diagnosed as depressed, 36 in total). Both groups of people were unmedicated.

They found that healthy (non-depressed) people sleep more than depressed people.

Interestingly the total sleep time of sleep decreases over age. This trend is very much pronounced in depressed people. Another chart shows that the REM latency (the time to reach REM sleep) decreases over time, so people over age, become better with age in reaching REM sleep.

They also found that depressed people took longer to fall asleep as evidenced in the graph below.

From looking at the other charts, the time to wake up seemed to be inversely correlated on the latency (time to fall asleep) and of sleep duration. Depressed people took much longer to wake up. Depressed people not only sleep less, but also they wake up more frequently during the night.

(Please note, that the colors are inverted for depressed and healthy people (between the two graphs.)

Enjoy. Please leave a comment below for questions and suggestions.

Dynamic Javascript Loading on Scroll

2011-01-04T16:16:00.001+01:00

If you have a lot of widgets on your webpage page, you can try out many tools in order to speed up page loading, however there is a limit to optimization. It is often tried to put heavy javascripts at the end of page loading, putting them before <head> or using the window.onload function. In this post, I show an alternative that has the advantage of shorter initial page loading and a smoother user experience than these methods.

I had the idea when I was researching social toolbars. Often the social toolbar would appear only when the page was scrolled. Therefore page scrolling should be detected and if the page was scrolled down the toolbar would fade in.

I thought that the same code could be applied for dynamic javascript loading. Many libraries are not needed initially. Some widgets are only visible once the page is scrolled. I implemented some code myself for scroll event detection, however in the end, I use the ajax library for this purpose.

Here comes the general pattern:

<script src='http://ajax.googleapis.com/ajax/libs/jquery/1.4/jquery.min.js' type='text/javascript'/>
<script id='aptureScript' type='text/javascript'>
function jsload(src){
var a=document.createElement("script");
a.defer="true";a.src=src;
document.getElementsByTagName("head")[0].appendChild(a);
}
var dynloaded=false;
$(function() {
$(window).bind("scroll", function(event) {
if($(window).scrollTop() > 50){
if(dynloaded==false){
// ...
// javascript loading here, ex. jsload('script.js')
dynloaded=true;
}
}
});
});
</script>

The number, marked in red is the scrolled distance from the top of the page, at which the loading of additional javascript code will occur.

Please note that if you want to use this in your blogger template, make sure to escape html tags within the javascript code.

Enjoy. Please leave a comment below for questions and suggestions.

Social Toolbars for Websites

2010-12-30T21:36:00.009+01:00

Apture toolbar with branding, share buttons, and search bar.
Many websites have an interactive toolbar providing social and other instruments situated often on top or on the bottom of the page. Blogger has its Navbar, Wordpress has WordPress Bar, and there are many other toolbars with different functionalities that offer integration with basically any website. This article provides a comparison of different web toolbars.

When I heard Andrew Machado from Apture comment on branding and engagement of their toolbar something resonated in me. I use and like some elements of Apture, but I am not really sure of the toolbar. I looked at different toolbars and thought about which toolbar I wanted to have.

A social toolbar can provide many advantages (taken from conduit.com), such as increased traffic, brand awareness, contact with your community, engaged users, fresh content, effective promotions, and generation of more revenue.

With so many different toolbars available, which one to choose?

Social Toolbars: The Candidates

Competitors are the following:

The social bar from google friend connect,
- video introduction, demo site
- offers log in and commenting
facebook bar, (didn't find any link now)
- offers log in, commenting, and posting on facebook,
- javascript code on github
meebo bar,
- see long presentation,
- Alexa traffic rank of meebo.com is 927. Meebo offers mainly chat solutions. The toolbar sports:
- Sharing buttons,
- Full facebook and twitter integration,
- supports drag sharing (dragging an object triggers a share menu),
- Chat
- no branding,
- no search
addthis sharebar,
- Alexa traffic rank of addthis.com is 166.
- Social bookmark toolbar plus configurable search engine,
- design and positioning of bar can be customized,
- no branding,
- no counters with social services.
wibiya bar,
- Alexa traffic rank of wibiya.com: 3121.
- video review
- highly functional, many applications available,
- full fledged integration of facebook, twitter, and buzz
- branding,
- if you want to integrate anything else: HTML or javascript integration is available at the price of close to 10 dollars per month,
- search allows integration of custom search engine with results as window overlay
apture search bar.
- Alexa traffic rank of apture.com: 12,670.
- Hear Apture's Andrew Machado comment on branding and engagement of their toolbar.
- Branding,
- Social share buttons for facebook and twitter with counters, and email sharing button
- Search as overlay for engagement
- Customization: site search in addition to google, amazon, and video search; however results mostly from external sites
One True Fan
- Alexa traffic rank of onetruefan.com: 77,007
- share buttons
- log in functionality; twitter, facebook member listing
WordPress Bar
- See the rundown in a video
- Share buttons for most important social services.
- opens external links in a frame with the bar on top so that visitors are not lost.
Blogger Navbar.
- What most people want to know about the blogger navigation bar is how to remove it, although there is some customization that you can do with the navbar.
- Share with twitter, facebook, buzz, google reader
- Follow with google friend connect.
- Buttons for next blog and to report abuse

I had problems with meebo integration. It disappeared after few seconds.

One downside to all tested services is that even if the search form is fully configurable and as overlay, it is not as clean as the blogger custom search widget (no advertisements).

Of all the tested toolbars wibiya provided best functionality. Apture was also good in many aspects and the addthis sharebar fared also not too bad in the comparison.

Others: Not Compared Here

Gigya provide APIs and code examples to set up everything for sharing, community, and authentification on a website at around $1,700-$2,100/month plus set up fee. They also provide a very innovative comment plugin. See a video.

Extendy demo and sign up didn’t work when I tried to test it.

The Stumbleupon toolbar specializes on pages shared over stumbleupon. Similarly, for digg, there's also the Diggbar, a website widget, explained in a videocast by Kevin Rose.

Conduit offers customization of a windows application that integrates with a web browser. See video. digg toolbar for web browsers is powered by conduit.

The Optimal Toolbar

This section summarizes my personal opinion on how a blog toolbar should look like.

A blog toolbar should contain the following (ordered by given importance):

branding
a site search widget (optionally other sites, too), should be interactive without leaving the site
it should have social bookmarking tools. Links to social networks, such as twitter and facebook, and other sites. It should also have a "mail this" function.
follow widgets
a) social: twitter follow, facebook follow, google followers, optionally buzz
b) feed subscription button
engagement: something like recent posts, article archive, related posts

I want google custom search, social bookmarks for twittering, facebook like, and sharing, maybe recent comments and posts, and related posts. In the next sections, I give pointers to code that can help you in order to write a custom toolbar.

Custom Toolbar

I put my own toolbar together, but then found these two articles which explain a more elegant way of doing it based on jquery.

JQuery Fubar: how to create a website toolbar from scratch and add widgets to it.
Toolbar with CSS and JQuery (in German)

Share your thoughts with me in the comments sections. This time I am especially interested in this question: What would you put in a social toolbar?

Christmas in Germany

2010-12-25T16:37:00.004+01:00

Christ child descends with the presents. via wikipedia

It's already two years ago that I wrote about Christmas traditions in Catalonia, where one of the eccentricities is that one shepherd, strategically placed at the corner of the barn of the nativity scene, is attending to an urgent bodily function. German Christmas traditions are rather downbeat compared to that, however Western Christmas traditions seem to have spun off from Germany so what better place is there to write about Christmas traditions? If you like songs and good food, you get a good share of both here in Germany where I am celebrating Christmas this year. This post is a short account of Christmas celebration in Germany. It follows a compilation of German Christmas songs. Enjoy reading and listening to the songs.

Christmas Tradition in Germany

Christmas celebrations in Germany begin on Christmas Eve, the 24th of December. The date of 25th of December has been traced back to Rome in 336 CE. While it is not clear why it is celebrated on this day, it has been argued that the date of Christmas was selected to correspond with the winter solstice, the day when Earth's axial tilt is farthest away from the sun. In fact, the 25th of December may have been chosen in account of the Roman Sun God. Another hypothesis is that the choice of day corresponds to 9 months after the day of annunciation.

Before I come to songs, I want to show off some information I found on the German wikipedia article on Christmas. The custom of celebrating Christmas in the family and giving gifts was introduced in 1535 by Martin Luther as alternative to the then prevalent custom of giving presents on the day of Saint Nicholas, in order to steer the interest of children towards Jesus Christ instead of the adoration of saints. In Roman-Catholic families the gift-giving continued over a long time on the same day, December 6th.

Several new customs were taken up, such as, for example, nativity plays (since the 11th century) , the Christmas tree (since the 15th century), which is decorated with lights, candles, glass balls, tinsel, angels or other figures, the Advent Wreath (since 1839), and Santa Claus (since the 20th century), who replaced the Christkind (lit.: Christ Child, see picture on top of this post) as deliverer of of gifts.

Christmas food: goose and dumplings (my photo).

While on the 24th, there is a festive but simple dinner (for example fish with salted potatoes or Potato salad with Sausages), the family dinner in the evening of the 25th, is prepared with a lot of attention to detail. People prepare many different dishes, however often there is duck or goose accompanied with dumplings. After dinner, gifts are presented, usually under the Christmas tree. Families usually visit church in the early or late evening.

German Christmas Songs

In all Christian cultures there is a collection of folk Christmas songs, some of which have been used extensively in liturgies. Curiously, Martin Luther made major contributions to this collection, writing several songs and lyrics himself. As for German Christmas songs in general, Silent Night (in German: "Stille Nacht, heilige Nacht"), first performed in Austria in 1818, is one of the most popular. I selected several popular German Christmas songs, which I now briefly introduce. For each song I put a link to youtube, so you can listen to it. Some songs, especially the religious ones, are more solemn, some are more fun.

"Ihr Kinderlein Kommet" is a Christian Christmas song from the 18th century. Christoph von Schmid, a clergyman, wrote many short stories for children to illustrate how God will let the good prevail. Here comes a short excerpt from the song. I found an English translation at about.com.

Ihr Kinderlein kommet, o kommet doch all! Zur Krippe her kommet in Bethlehems Stall, und seht, was in dieser hochheiligen Nacht der Vater im Himmel für Freude uns macht.
O seht in der Krippe, im nächtlichen Stall, seht hier bei des Lichtleins hellglänzendem Strahl, in reinlichen Windeln das himmlische Kind, viel schöner und holder als Engel es sind.

O come, little children, O come, one and all, O come to the manger in Bethlehem's stall; And see what our Father on this holy night, Has sent us from Heaven for our pure delight.
O see, in the cradle, this night in the stall, O see how the light dazzles even us all; In pure gleaming white lies this Child, heaven's love, More beaut'ous and holy than angels above.

After Johannes Daniel Falk lost four of his seven children to typhoid fever, he founded an institute for children in need. To these children he dedicated his song "Oh Du Fröhliche" in 1816. As a melody he used the song "O sanctissima, o purissima, dulcis virgo Maria," which is still sung in Italy today.

The following two songs are less religious.

The lyrics of "Fröhliche Weihnacht" were composed by Austust Heinsrich Hoffmann von Fallersleben (1798-1874), who later composed "Lied der Deutschen," the German national anthem.

Karl Wilhelm Ferdinand Enslin (1819-1875) wrote the lyrics for "Kling Glöckchen." He also wrote the children's song "Guter Mond du gehst so stille."

"Vom Himmel hoch, da komm ich her" is one of the most popular songs by Martin Luther. It is said that he composed this song in 1535 for his own children. Later he composed the music. The song is now preceded by a first stanza written in 1555 by clergyman Valentin Triller.

"Alle Jahre wieder" was composed by Wilhelm Hey in 1837. The most common melody is attributed to Friedrich Silcher.

Happy Christmas to everybody! And happy singing! Tell me about your Christmas.

How to Use Flattr, the Microdonation Platform

2010-12-22T15:01:00.018+01:00

Flattr is a relatively new social bookmarking and micropayment (or rather: microdonation) platform. After Paypal, BAC, and Visa and Mastercard bent down to political pressure, Flattr is currently one of the very few options left for people if they want to donate money to wikileaks and consequently Flattr is getting a fair share of exposure. In this post, I explain what flattr is, how you can use it to make money with your content and give some money to people who earn it, and how you can integrate it with your site.

What is Flattr?

I think one of the fastest ways to explain is that Flattr is a social bookmarking site, where you show your appreciation with money. Some internet sites have paypal buttons asking for donations if you like the content. Flattr is similar to that but has some differences. Now again from the beginning.

Flattr was founded in Malmö, Sweden, by Peter Sunde, who was one of the founders of piratebay, together with Linus Olsson, as a way to encourage people to share money aside from content. It can be very hard to earn money with content on the internet just by advertisement and Flattr wants to make it easier for people to give monetary tokens of appreciation and for bloggers and content creators to earn money. How does it work practically?

You start by setting up an account on flattr and transfer some money to it by credit card or paypal. Remember: flattr is about giving and getting, before you can start making money getting flattred you need to add some funds. Withdrawals are supported via Paypal and Moneybookers.

Next you determine the monthly amount you want to spend (minimum 2 euros). Each time you click on a flattr button on a website you give a share of this monthly amount to that website. This can be explained with a cake analogy. Your monthly flat rate, say 2 euros, is the cake. Each time you click on a flattr button this cake is divided into another part. The video introduction of flattr explains this very smoothly.

Flattr was made open to the public only in March 2010, but since then has enjoyed a growth that has given it an Alexa rank of 12,872 (as of today), which means that traffic on flattr is only surpassed by roughly 13,000 other sites globally. For writers and bloggers it is also worth mentioning that Flattr combines elements of social bookmarking and is do–follow site with pagerank 5.

However, you can see that it is still in an early phase of development with its user base consisting disproportionately of young males under the age of 35. It is used currently mainly in Europe, although in the United States it currently ranked 20,451. According to the Alexa entry for flattr, around a third of the visitors to this site come from Germany, where it is ranked 2,007. It is also used by two major German newspapers, TAZ and Freitag.

The growth curve for flattr, again taken from the aforementioned alexa page, shows that from March 2010, the site has been attracting more and more visitors to their website and with a bounce rate of below 60 percent it is an obvious conjecture that flattr has been gaining many users. As of today, more than 300,000 items have been flattred.

The graph below shows Alexa's estimation of Flatt's traffic rank trend.

How to Integrate Flattr on a Website or Blog

In order to get money with flattr you need to put a button on your website. This is relatively easy and here comes the generic code, which you can copy and paste on any website.

<script type='text/javascript'>
/* <![CDATA[ */
(function() {
var s = document.createElement('script'), t = document.getElementsByTagName('script')[0];
s.type = 'text/javascript';
s.async = true;
s.src = 'http://api.flattr.com/js/0.6/load.js?mode=auto&uid=auffarth&langage=en_GB&category=text';
t.parentNode.insertBefore(s, t);
})();
/* ]]> */
</script>
<a class='FlattrButton' href='http://www.myoutsourcedbrain.com/2010/12/how-to-use-flattr-microdonation.html' rev='flattr;button:compact;' style='display:none;'></a>
<noscript>
<a href="http://flattr.com/thing/105273/How-to-Use-Flattr-the-Microdonation-Platform" target="_blank">
<img src="http://api.flattr.com/button/flattr-badge-large.png" alt="Flattr this" title="Flattr this" border="0" /></a></noscript>

I put here a version of the code which is slightly more complex, however works without javascript and gives visitors to your site the possibility to be the first to submit your pages or articles to flattr. This is why I included my flattr user id, the language code, and the category "text." I indicated in red where you would want to make changes.

Most important is to put the address (at href) of your website or page on your website. Category has to be one of images, video, audio, software, and rest. The language has to be specified in the format en_GB (currently only English option available, other language options). If you leave out the rev="flattr;button:compact;" then you will get the bigger default button.

The result would look like this:

Wordpress Integration

See the wordpress flattr plugin.

Blogger Integration

If you are using blogger, you can use the button above for a side–wide flattr button. If you want to show a flattr button with each post, then I have just the right code for you.

Go to blogger.com, go to design, html, choose expand templates, and search for <div class='post-footer-line post-footer-line-2'>. Directly after that you can paste the following code which will put the flattr button below each of your posts:

<script type='text/javascript'>
/* <![CDATA[ */
(function() {
var s = document.createElement('script'), t = document.getElementsByTagName('script')[0];
s.type = 'text/javascript';
s.async = true;
s.src = 'http://api.flattr.com/js/0.6/load.js?mode=auto&uid=auffarth&langage=en_GB&category=text';
t.parentNode.insertBefore(s, t);
})();
/* ]]> */
</script>
<a class='FlattrButton' expr:href='data:post.url' expr:title='data:post.title' rev='flattr;button:compact;' style='display:none;'></a><noscript>
<a href='https://flattr.com/thing/105342/My-Outsourced-Brain' target="_blank"><img src="http://api.flattr.com/button/flattr-badge-large.png" alt="Flattr this" title="Flattr this" border="0" /></a></noscript>

You should change the user-id, category, and language (see comments above). Users who don't have javascript activated would donate not to the article but to the blog in this case. Therefore I submitted myoutsourcedbrain.com to flattr and got an item id.

Other Platforms

See the flattr plugin listing.

"Everywhere"

The firefox plugin Överallt (Swedish for Everywhere) allows you to put your flattr plugin basically anywhere you want by a simple code: [Flattr=auffarth] (auffarth is my id, you would put yours). Anybody who has the firefox plugin installed will see a flattr button and will be able to donate money to you.

What's your opinion on earning and giving away money for writing? Do you think you can trust Flattr? Would you use it?

Data Sharing Between Windows and Linux

2010-12-22T01:05:00.021+01:00

Image via WikipediaIf you use several operating systems on your computer, such as Windows 7 and Ubuntu 10.10, and maybe also MacOS, data sharing between the operating system becomes an important issue. You don't want to have to reboot your computer every time you need some data, do you? I now use double boot with Windows 7 for work-related stuff and Ubuntu Maverick for mostly everything else. I share data between the two operating systems using only a few tricks. Keep reading.
In a recent post, I explained how to setup data sharing between a linux in a virtual machine and Windows host operating system. In this post I want to show how to share data on a double boot configuration between Windows and Linux. Note that similar tricks will work for MacOS as well.
We could use complicated scripts for automatic synchronization, such as subversion, even over some remote servers, however by Occam's razor we go for the easiest solution.
We'll do everything from linux. This because Windows doesn't handle any file systems other than ntfs and fat (not the standard linux filesystems), in turn linux handles a lot of file systems (including the windows filesystems), and Linux allows symbolic links, which is what we will use. If you don't understand what I am talking about, don't worry.
For data sharing between linux and windows to work it is required that you delete some files and copy them some other place. Before deleting any files make backups of them. Don't blame me if you loose your data. Before you execute any commands, make sure you understand what they do. Let's dive in.

Preliminaries

1. mount the windows partition(s) on boot. Usually in ubuntu you can just click on the windows disk and it will be mounted with permissions as needed. We will just copy permissions and paths and make sure it uses these parameters on every boot. Check in /etc/mtab how the filesystem is mounted (should be last line in that file). Copy that line into /etc/fstab (as sudo). Change the third column (fusebl) in the line to "ntfs".
For example: (> sudo gedit /etc/fstab)
> /dev/sda3 /media/Acer ntfs rw,nosuid,nodev,user,allow_other,blksize=4096,default_permissions 0 0

Applications

Dropbox

In linux the dropbox desktop application automatically appends "/Dropbox" to the end of your path if it is not already that. For Windows it insists on "\My Dropbox" at the end. Therefore you cannot (better: should not) use the dropbox application itself to use the same directory. You should use a symbolic link, so that the directory in linux is virtual and points to the windows directory.
For example:
> ln -s /media/Acer/Users/benjamin/My\ Documents/My\ Dropbox/ Dropbox

Tomboy

Tomboy is a cross-platform note taking application. It is installed by default in Ubuntu.
Make sure you have all your notes under Windows. If your notes are in linux copy all files from ~/.tomboy to %APPDATA%\tomboy\ (check at Tomboy Directories if this information is still current). Then make a symbolic link as before.
Example:
cp -r .local/share/tomboy/* /media/Acer/Users/benjamin/AppData/Roaming/Tomboy/notes/
rm -r .local/share/tomboy
ln -s /media/Acer/Users/benjamin/AppData/Roaming/Tomboy/notes/ .local/share/tomboy
If you are in doubt where your %appdata% folder is, type in the windows command prompt > %appdata%.
I don't bother with Firefox or Chrome bookmarks because you probably already use some programs to synchronize bookmarks across different computers (you do, right?).
Enjoy. Do you need any other application urgently? Please leave a comment below for questions and suggestions.

Private Information Sent By Android and IPhone Apps

2010-12-20T00:54:00.009+01:00

If you own an iphone or an android phone you may know from your own experience that the information transmitted by applications can be disturbing. I think you should know what data applications transmit about you, so that you can make an informed decision on which applications you want to have. I compiled a table of applications and which data they transmit.

Even though free and open-source software (FOSS) has come a long way to make software better and our life easier, not all software can be free as in beer and free as in speech, because developers of software have to make a living from applications. However what is disturbing is if software transmits a lot of information that has potential to violate your privacy.

In the article Your Apps Are Watching You, the Wallstreet Journal investigated the kind of information sent by different applications. Slashdot user scruffy parsed the information and I re-edited it into a table.

The table lists iPhone and Android Applications together with the information they transmit.

Explanation of the table:
Some apps asked the user to provide a username or password to create an account, or to interact with services such as Facebook or Twitter. This is included in the first column.

Some applications can access information from the user's address book, usually with permission. This is the second column.

In the third column, it is indicated whether apps collect age, gender or other demographic information (usually through a form). Phones collect global-positioning-system (GPS) data and can triangulate location based on Wi-Fi or cellular signals.

The fourth column shows whether location information included city, zip code and metropolitan area, as well as latitude and longitude. Phones have several serial-number-like identifiers that are nearly impossible to delete.

The ID passed most commonly was the phone's UDID, followed by an Android ID and numbers placed by the phones manufacturer and the cellular network. This is shown in the fifth column. The phone number was passed infrequently and was primarily sent by the user to app makers or Facebook. This is indicated in the sixth column.

Explanation of values: 0 – does not transmit data, 1 – transmits data to app owners, 2 – Transmits data to third parties.

iPhone Apps

Username, Password	Contacts	Age, Gender	Location	Phone ID	Phone Number
0	0	0	0	2	0	0.03 Seconds Pro
0	0	0	0	2	0	Age My Face
2	2	0	2	2	0	Angry Birds
2	0	0	2	2	0	Angry Birds Lite
1	0	0	2	2	0	Aurora Feint II: Lite
0	0	0	0	2	0	Barcode Scanner (BahnTech)
2	0	0	0	0	2	Bejeweled 2
0	0	0	2	2	0	Best Alarm Clock Free
0	0	0	2	2	0	Bible App (LifeChurch.tv)
0	0	0	0	0	0	Bump
0	0	0	2	2	0	CBS News
0	0	0	0	2	0	0.03 Seconds
0	0	0	2	2	0	Dictionary.com
2	0	0	0	1	0	Doodle Jump
1	0	0	1	1	0	ESPN ScoreCenter
1	1	0	1	0	0	Facebook
0	0	0	0	0	0	Flashlight (John Haney Software)
0	0	0	1	2	0	Fluent News Reader
1	0	1	2	0	1	Foursquare
0	0	0	2	2	0	Fox News
2	0	0	2	0	0	Google Maps
1	0	2	2	2	0	Grindr
2	0	0	1	2	0	Groupon
0	0	0	0	2	0	Hipstamatic
0	0	0	0	2	0	iJewels
0	0	0	0	0	0	iLoveBeer: Zythology
1	0	0	1	2	0	Medscape
1	0	1	2	2	0	MyFitnessPal
1	0	0	1	1	0	Netflix
0	0	0	2	2	0	NYTimes
0	0	0	2	2	0	Ninjump
0	0	2	2	2	0	Pandora
0	0	0	2	2	0	Paper Toss
0	0	0	0	0	0	PerfectPhoto
0	0	0	2	2	0	Pimple Popper Lite
0	0	0	2	2	0	Pumpkin Maker
0	0	0	0	1	0	RedLaser
0	0	0	0	2	0	Ringtone Maker
2	0	0	0	2	0	Ringtone Maker Pro
0	0	0	2	2	0	Shazam
2	0	0	2	2	0	Talking Tom Cat
1	1	2	2	2	1	TextPlus 4
0	0	0	2	2	0	The Moron Test
0	0	0	0	2	0	The Moron Test: Section 1
0	0	0	2	2	0	Tips & Tricks: IPhone Secrets Lite
2	0	0	2	0	0	TweetDeck
0	0	0	0	1	0	WSJ Mobile Reader
0	0	0	2	2	0	The Weather Channel
0	0	0	0	0	1	WhatsApp Messenger
1	0	0	2	2	0	Yelp
1	0	0	0	0	0	YouTube

Android Apps

Username, Password	Age, Gender	Location	Phone ID	Phone Number
0	0	0	2	0	Advanced Task Killer
0	0	0	0	0	Advanced Task Killer Pro
0	0	2	2	0	Alchemy (Andrey Zaikin)
0	0	0	2	0	Backgrounds (Stylem Media)
0	0	2	0	0	Barcode Scanner (Zxing Team)
0	0	2	0	0	Beautiful Widgets
0	0	1	2	0	Bible App (LifeChurch.tv)
1	0	2	2	1	Calorie Counter (FatSecret)
0	1	2	2	0	CardioTrainer
0	0	2	2	0	CBS News
0	0	0	2	0	DailyHoroscope (Comitic)
0	0	0	2	0	Dictionary.com
0	0	1	1	0	ESPN ScoreCenter
1	0	0	0	0	Facebook
0	0	0	0	0	Fishin' 2 Go
1	0	2	0	1	Foursquare
0	0	2	2	0	Fox News
2	0	0	2	0	Fruit Ninja
0	0	1	0	0	Google Maps
1	0	2	2	0	Groupon
0	0	0	2	0	Handcent SMS
0	0	0	2	0	Jewels
0	0	0	0	0	Labyrinth
0	0	0	0	0	Labyrinth Lite
0	0	0	2	0	LauncherPro
2	0	2	2	0	Movies by Flixster
0	0	0	1	0	MyBackup Pro
1	2	0	2	0	MySpace Mobile
0	0	0	2	0	NYTimes
0	2	2	2	0	Pandora
0	0	2	2	0	Paper Toss
0	0	0	0	0	Ringdroid
0	0	0	0	0	Robo Defense
0	0	0	0	0	Robo Defense Free
2	0	2	2	0	Shazam
1	0	0	0	0	ShopSavvy Barcode Scanner
0	0	0	0	0	Solitaire (Ken Magic)
0	0	0	1	0	Talking Tom Cat
2	0	0	2	0	Talking Tom Cat Free
0	0	2	2	2	The Coupons App
0	0	2	2	0	Toss It
2	0	2	2	0	TweetCaster
1	0	2	2	0	US Yellow Pages Search
0	0	2	0	0	Weather & Toggle Widget
0	0	2	0	0	The Weather Channel
0	0	2	0	0	WeatherBug
0	0	2	2	0	WeatherBug Elite
1	0	1	2	0	Yelp
0	0	0	0	0	YouTube
0	0	0	2	0	Zedge Ringtones & Wallpapers

Enjoy. What do you think about the information transmitted? Do you think your privacy is at risk? Please leave a comment below to give us your opinion.

Disqus Comments on this Blog

2010-12-16T23:57:00.012+01:00

In an earlier article on the importance of comments for a blog I summarized studies about blog comments, concluding that blog comments lead to more traffic, better search engine optimization (SEO), apart from being personally rewarding to the blog writer. I worked on many optimizations for this blog to make commenting more attractive. Recently I made a major change on this blog and changed the commenting system. My blog continues to be a "do-follow" blog and I am positive this blog will benefit from the change both in terms of SEO and comment quality. In this post I explain my motivation and reasoning behind this change.

Image credit: My Comment Line, Call me! By greggoconnell.

The best comment systems for blogs in my opinion are echo, disqus, coComment, and Intense Debate. There are many other systems, for example on earlier occasion I showed integration of google wave as a discussion forum, which was also quite feature-rich, however, I think these four are the best for bloggers. They provide integration with the most popular blogging platforms, comfortable editing, moderation and editing of comments, integration with social networks, threaded comments, social reactions (trackbacks), and many other features. All except Echo offer a basic subscription free of charge with an offer of additional paid features as a business model.

In contrast, the blogger commenting system is uncomfortable and clunky, and misses out on many features that other comment systems have, for example, I've written before about a workaround to correct the blogger comment count and if you really want to export all your blog posts as a single file, edit this file, and re-import, is possible to change comments. I think the commenting system in blogger is one of the biggest drawbacks of the blogger platform and this was one of my motivations to review alternative blogging platforms.

Notwithstanding these shortcomings, I was reluctant to replace it with another system because of SEI reasons. The only integration in blogger with third-party commenting systems are based on javascript and this would mean that search engines would not integrate content from comments in their indexes (although there are some solutions to this issue). Also I didn't want to slow down page loading even more javascript on my site and incur a penalty with search engine rankings.

Disqus and Echo, both, for some time now already synchronize comments with blogger which means that you don't loose SEO any more from comments. Comments will be taken into account for search engine indexing. It also means that if you reward commentators with "do-follow" links as I do, you can continue to do so. The reason is that comment synchronization with blogger means that comments are first printed by blogger and then replaced by the other commenting system. This means that in spite using javascript to pull comments from another site at loading time you will probably not loose out on SEO. The synchronization means also that you can continue to use your comment feeds as before with all your existing widgets.

I am concerned a lot about effectiveness in social networking and I've written before about how to add social networking features for blogs and how to install and customize a social networking toolbar. I am therefore very glad that that another advantage of third-party commenting tools is that they integrate with social networks. Readers of this blog will now be able to log in using facebook, twitter, yahoo, disqus, and openid. Facebook, Twitter are two of the most used social networking sites. As of December 2010, Facebook holds a share of 44 percent among services supported by addthis and twitter holds around 9 percent, and login via these two makes it much faster for people to leave a comment. In fact, according to data by gigya, when given a choice of different ID providers for login, 46 percent of users tend to choose facebook, 17 percent google, 14 percent twitter, 13 percent yahoo, 7 percent myspace. With the new login options I think I can offer a better match to what people want. Furthermore comments can now be syndicated over twitter if the commentator wants to.

I am positively surprised at the speed of the loading of comments. People from disqus did a great job in optimizing page loading. I also got rid of some other code, so I am not so much worried about the speed.

Enjoy. Please test out my new comment system below, tell me of your experiences, and give me some feedback.

Attacks on Assange: Shooting the Messenger?

2010-12-14T00:00:00.011+01:00

After wikileaks published the diplomatic dispatches, Politicians and political commentators around the world and from all parts of the political spectrum unsurprisingly use wikileaks to profile themselves for their voters and to get attention. Some reactions are quite shocking to some people not used to American politics. Some public voices call for assassination of Julian Assange, the founder and spokesperson of wikileaks.

Image credit: Robbespierre, released under CC-BY-3.0. Found on wikimedia commons.

Recently, Sara Palin wrote on facebook:

Assange is not a "journalist," any more than the "editor" of al Qaeda's new English-language magazine Inspire is a "journalist." He is an anti-American operative with blood on his hands. His past posting of classified documents revealed the identity of more than 100 Afghan sources to the Taliban. Why was he not pursued with the same urgency we pursue al Qaeda and Taliban leaders?

Julian Assange is a highly controversial person. Vladimir Putin suggested he should be awarded the Nobel peace prize and Assange is leading in opinion polls for the Time person of the year 2010. Currently he is wanted in Sweden for questioning in relation to charges of rape, sexual coercion, and sexual molestation.

Search for "kill assange" on a search engine and you'll find thousands of people advocating black-ops operations or death penalty for assange, among other things to make an example of him and discourage other people to speak out or publish documents critical of the United States.

Sara Palin is not the only public person who uses strong expressions. I compiled some soundbites from U.S. politicians and political commentators that I found on youtube (The Young Turks and Fox Channel). I concentrated on reactions of politicians on wikileaks and assange and leave out demands for capital punishment of Mannings, a former intelligence analyst, who allegedly leaked the documents.

Surprisingly to me, incitement is not illegal in the United States. In turn, laws concerning hate speech outside of obscenity, defamation and incitement to riot are illegal in the United States, because they would violate rights guaranteed in the First Amendment of the Constitution, the same amendment that gives freedom of the press and freedom of speech. Instances of incitement qualify as criminal only if the threat of violence is imminent. This is different from other countries, say Germany, where there are restrictions on free speech; "Sedition" (incitement of hatred against parts of the population) is illegal in Germany.

I came across an article on TechCrunch asking "Why Is America So Furious About Wikileaks?" which I found had an interesting thought. It called these violent reactions to wikileaks or Assange stupid and then went on

The American diplomatic corps actually comes across as smart and competent in the Wikileaked cables. Unfortunately, the politicians they report to seem anything but. The scariest truth that Wikileaks has confirmed is that most of the world's decisionmakers, like most Wall Street 'wizards', are petty, bureaucratic, dogmatic, myopic, and hostile to any innovation, largely because they're not very intelligent. Not that smarts are everything, but it's hard to tackle complex problems when you don't fully understand them. It's easy to forget this in the tech world, which is (relatively speaking) a results-oriented meritocracy... until you step into most governments or megacorporations, and find that suddenly the ambient IQ has dropped 20 points.

In a Huffington Post article, Ron Paul Defends WikiLeaks On House Floor, I found an extract from a speech by Ron Paul, which I want to contrast with above comments.

WikiLeaks release of classified information has generated a lot of attention in the past few weeks. The hysterical reaction makes one wonder if this is not an example of killing the messenger for the bad news. Despite what is claimed, the information that has been so far released, though classified, has caused no known harm to any individual, but it has caused plenty of embarrassment to our government. Losing our grip on our empire is not welcomed by the neoconservatives in charge.
There is now more information confirming that Saudi Arabia is a principal supporter and financier of al Qaeda, and that this should set off alarm bells since we guarantee its Sharia-run government. This emphasizes even more the fact that no al Qaeda existed in Iraq before 9/11, and yet we went to war against Iraq based on the lie that it did. It has been charged by experts that Julian Assange, the internet publisher of this information, has committed a heinous crime, deserving prosecution for treason and execution, or even assassination.
But should we not at least ask how the U.S. government should prosecute an Australian citizen for treason for publishing U.S. secret information that he did not steal? And if WikiLeaks is to be prosecuted for publishing classified documents, why shouldn't the Washington Post, the New York Times, and others also published these documents be prosecuted? Actually, some in Congress are threatening this as well.

What is your opinion? Is Assange a traitor to the United States as some of the above claim? Does he overstep the freedom of free speech? Do the political commentators go to far? Should Assange be prosecuted?

Update: An earlier version of this post said he was wanted for alleged rape and molestation, however it is more accurate to say that he is wanted for questioning.

How to Run Ubuntu in Virtual Machine From Windows

2010-12-04T13:02:00.002+01:00

At work I now work a lot with Visual Studio on Windows 7 Professional. While I have to use Windows, I don't want to loose the functionality and power of Linux, so I run a virtual machine with Ubuntu Maverick. Both Windows and Linux run smoothly on my machine and I can share files among them. In this post I give some help for setting this up.

I chose Oracle's VirtualBox (also: VBox) as virtual machine. This decision was motivated mainly by speed. I tried Qemu and it was too slow to be usable. Bochs is also reputed to be slow, I didn't even try it. I found a performance comparison between VMWare, VirtualBox, KVM, and Xen. Most important I found operations per second on guest OS and I/O overhead. The reviewer concludes

To me, it seem that VMware and VirtualBox are the fastest virtual machine across the board. They have good CPU/memory performance, good disk access time and good network layer speed.
KVM is, instead, a mixed beast: it has quite good CPU/memory and network speed, but it fail in the crucial I/O subsystem performance more often than not.
Xen is at the opposite end of the spectrum: it as respectable I/O access time but quite bad CPU/memory performance that, in turn, can badly influence network speed and CPU load also.

Installation of VBox is straightforward. It follows a short howto on sharing folders between a VirtualBox virtual machine with a Windows host and Linux guest OS.

Install VirtualBox guest additions on the linux guest OS:
1. in the running guest OS window, go to devices, install guest add-ons.
2. make the VBox Additions iso available as drive: devices->CD/DVD->VBoxGuestAdditions.iso
3. in the terminal (assuming the iso is automatically mounted as cd, which it is in Ubuntu): i) cd /media/VBOX... (exact name depends on version) ii) sudo sh VBOXLinuxAdditions-x86.run (or the corresponding 64 bit version)
4. maybe you need to restart your guest OS.
Share folder:
1. in the VirtualBox guest OS window menu go to devices->shared folders and choose the host OS folder and a name for it under VirtualBox, say VBoxShare. You can choose permanent and can make it read-only if you want.
2. in the guest OS linux terminal: sudo mkdir /media/WindowsShare; sudo mount -t vboxsf VBoxShare /media/WindowsShare
3. you can put this also in fstab to have the share folder come up automatically on every boot: sudo gedit /etc/fstab
  VBoxShare /media/WindowsShare/ vboxsf defaults 0 0

Enjoy. Please leave a comment below for questions and suggestions.

Create Movie in Matlab

2010-12-03T16:16:00.004+01:00

You spent a long time extracting statistics from data and creating meaningful figures with appropriate line-styles and markers. Now you want to create a video by just concatenating these figures. Some lines of matlab code and you are done.

Just spent too much time to create a movie in matlab. This script takes 10 figures which are already displayed, resizes them to full screen resolution (all figures must have the same resolution) and captures the screen to get a matlab movie. This matlab movie is then converted to an avi.

scrsz = get(0,'ScreenSize');
for i = 1:10
fig=figure(i);
set(fig,'Position',scrsz);
M(i)=getframe(fig);
end
movie2avi(M,'filename.avi', 'compression', 'none');

You may want to substitute filename for something more telling and make number of figures appropriate for your purpose.

Without compression these files are very big. In order to send them to other people by email you might want to compress them. For compression you might have to download codecs or you use a compression utility such as mencoder afterwards:

 > mencoder filename.avi -oac mp3lame -ovc lavc -lavcopts acodec=mp3,1bitrate=128,vcodec=mpeg4,vbitrate=800,vhq,vm4v -o filename_s.aviEdit

If you want to view these movie files, you can use the VLC Media Player, where you activate view->advanced controls and then you have button (rightmost new button) for viewing frame by frame.

Here comes a short function for exporting videos:

function make_video(basename,outfile)
% loads all files that match basename (use wildcards like '*' if you like)
% and write them to a video file.
% The file can be quite big. I recommend you compress it.
% Example:
% make_video('orn_network*.bmp','orn_network.avi');
a=dir(basename);
files = sort_nat({a.name});
scrsz = get(0,'ScreenSize');
for i = 1:numel(files)
fig=figure;A=imread(files{i});image(A);
set(fig,'Position',scrsz);
M(i)=getframe(fig);
close;
end
movie2avi(M,outfile, 'compression', 'none');

Enjoy. Please leave questions and suggestions in the comment section.

You might also be interested in my article on exporting figures from matlab. I also wrote articles about exporting data from matlab and how to get good combinations of linestyles and colors for plots.

Wikileaks - the diplomatic dispatches

2010-11-30T00:20:00.006+01:00

Wikileaks is releasing 251,287 documents of U.S. diplomatic dispatches (as of November 30th, 272 are released). They reveal a lot about American views of the situation in different countries, about world leaders such as Vladimir Putin, Silvio Berlusconi, Cristina Fernandez de Kirchner, and Angela Merkel. Interesting reads provide also U.S. strategies concerning North Korea and Pakistan. This latest release brings up many questions related to national security, to the right for information, and how much the governed should know about their government.

Wikileaks released this year already a movie that shows American soldiers kill civilians, documents related to the war in Afghanistan, and the war in Iraq. Some of the documents may not available on wikileaks currently because of an ongoing DOS attack on wikileaks. The latest release, 7 times the size of the Afghan war diaries, are communications by American diplomats that show the inner workings of American diplomacy.

This latest release and the one before about Afghanistan is deeply embarrassing to American politicians and proves to be very controversial when you talk to people about it. International leaders are furious over the cables, except for Berlusconi, called finicky and inefficient by U.S. diplomats, who reportedly laughed. U.S. president Barack Obama warns that this new release will risk countless lives. Meanwhile Julian Assange, wikileaks spokesperson, comes under increased pressure. He faces rape accusations in Sweden, where he tried to find a safe haven for wikileaks and himself, and the Australian government is investigating him for breaching national security. US Secretary of State Hillary Clinton, who as now became public was asking for biometric details about UN officials, claims it is an attack on the international community.

I think it is worth to remind that in July, it was all over the media that wikileaks endangered individuals by releasing information. Defense Secretary Robert Gates called "the battlefield consequences of the release of these documents are potentially severe and dangerous for our troups, our allies, and Afghan partners and may well damage our relationships and reputation in that key part of the world. [..]" It turned out recently - by admission by Gates himself - that to date no Afghans have been harmed or threatened from it.

The NY Times title: "Leaked Cables Offer Raw Look at U.S. Diplomacy." I want to cite from their article:

Clashes with Europe over human rights: American officials sharply warned Germany in 2007 not to enforce arrest warrants for Central Intelligence Agency officers involved in a bungled operation in which an innocent German citizen with the same name as a suspected militant was mistakenly kidnapped and held for months in Afghanistan. A senior American diplomat told a German official “that our intention was not to threaten Germany, but rather to urge that the German government weigh carefully at every step of the way the implications for relations with the U.S.

I found this report by Democracy Now about wikileaks and this release. It includes an interview with Daniel Ellsberg, who leaked documents about the Vietnam war.

Also worth watching I think is the interview with Assange on TED, under the title "Why the world needs wikileaks?"

What's your opinion? Do you think this information is important to people? Is it dangerous to spread this information? More in general, which information should be made public and for which information is it in the interest of the people that it should remain secret?

Update: Changed wikileaks URL to .ch.

Stockholm Poster

2010-11-10T20:17:00.009+01:00

I created a poster about Stockholm, showing off several of Stockholm's and Sweden's particularities on the background of a historic city panorama. Some other items allude to supercomputing and brain, which can be explained by the poster's original purpose, however fit nicely into the computational neuroscience I am doing in Sweden.

On the top you see a reduced version. You can click on the image to see a bigger flat pdf.

I originally created this poster as a draft for the Twentieth Annual Computational Neuroscience Meeting 2011, or short, CNS 2011. It is going to be held in Stockholm, where I am now residing and working at one of the organizing institutes. As a poster, draft it should invite people to come, however other organizers — although mentioning they found it humorous — thought the poster should be more enticing or promotional of Stockholm and modern science. In the end, I think they found a very good poster, but I am still proud of my poster and don't want to let it waste on my hard disk, so I put it on this blog.

The original version is of A2 format. I created it using inkscape. You can see the sources section to see what are the parts, but take your time first to have a look and take guesses. N.B.: If you look at the original poster, depending on the viewer some elements may not show up. I suppose this has to do with inconsistent renderings of SVG files.

All pictures are free to use (mostly creative commons license) and modify and mostly of high resolution. It used to have conference title (in a Gothic font to match the historic Viking theme) and main organizer's logo on top and logos of other organizing institutes below. If you want to use this poster or parts of it, please do so and let me know, but remember to attribute all sources.

Sources

My sources are (in not particular order):

I want to acknowledge a valuable contribution by Malin Sandström, who not only criticized and brought in ideas, but also put her hand on the poster in Photoshop to make the appearance more lively.

Please leave comments below. Enjoy.

Ubuntu Maverick for PhD Students

2010-11-10T19:04:00.012+01:00

Please see the updated version of this article about installation of software for research in Ubuntu 12.04.

Some time ago I wrote a post about Ubuntu for PhD students, where I gave instructions on how to set up programs and libraries relevant for research on the Ubuntu linux distribution. This was for Ubuntu 8.10, so now I think it's time to update the information for Ubuntu 10.10 (codenamed "maverick"), a distribution which I can warmly recommend, by the way.

Software for research

What does research include? In short maybe this list comprehends some (not all) basic tasks involved: reading articles, doing statistics, illustration, writing articles.

I start by listing again some basic free software tools that I think are essential for research. My list cannot be inclusive and I leave out many more programs or libraries that I think are good but not as essential. Please feel free to suggest other programs in the comment section.

Connectivity

The ssh server.
Google Chromium (Chrome) - because it's very fast and now supports smart bookmarks (at least in linux versions)

Programming

Powerful editors such as vim and emacs,
gnu toolchain,
gnu screen,
subversion (svn), git,
file converter from dos to unix (tofrodos),

Statistical tools

Article writing and reference management

texlive,
many latex packages,
jabref and bibutils for converting to and from other reference formats.

Illustration

graphviz,
ImageMagick,
gnuplot, pdfedit,
inkscape,
Scribus,
gimp,
plugins to play media contents, etc.

Others

perl,
java RE and SDK,
blas
boost libraries

Installation

In the terminal, become superuser (sudo su).
For java, you'll have to do first include a new repository:
> add-apt-repository "deb http://archive.canonical.com/ maverick partner"
For chromium, we include the google repository:
> add-apt-repository "deb http://dl.google.com/linux/deb/ stable main"
> wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -

(If you don't have add-apt-repository installed, you can add the repository manually: echo "deb http://archive.canonical.com/ maverick partner" >> /etc/apt/sources.list)

We update package sources:
> apt-get update
Now let's get on it. Execute this and you will have plenty of time to grab some coffee.
>

apt-get install openssh-server build-essential gcc gcc-doc apt-file gcj gsl-bin gsl-doc-pdf gsl-ref-html libgsl0-dev gsl-bin gsl-doc-pdf libgsl0-dbg libgsl0ldbl glibc-doc libblas-dev maxima maxima-share subversion subversion-tools git screen $(aptitude search R| grep -v ^i | awk '{print $2}' | grep ^r-) octave $(aptitude search texlive | grep -v ^i | awk '{print $2}') untex luatex latex-xft-fonts perl fontforge context-nonfree context-doc-nonfree dvipng imagemagick graphviz gnuplot-x11 gnuplot-doc gnuplot libatlas3gf-base kdevelop kate kile vim-gtk vim vim-addon-manager vim-common vim-doc vim-latexsuite latex2html latex-beamer xpdf writer2latex jabref bibutils hevea hevea-doc wordnet cups-pdf djvulibre-bin djvulibre-plugin pdfedit inkscape scribus pdf2djvu pdf2svg python2.6 ipython python3-dev python3-all python2.6-dev python-scipy unrar tofrodos epiphany-browser epiphany-extensions scribes lyx claws-mail claws-mail-i18n claws-mail-doc claws-mail-tools libqt4-core libqt4-gui flashplugin-nonfree ubuntu-restricted-extras regionset soundconverter gxine libxine1-ffmpeg libstdc++5 libmms0 google-chrome-stable

What I don't cover here is the installation of other programs such as Adobe Acrobat Reader, Skype, mp3 codecs, or samba, which you can click-install in the ubuntu software center (in the GNOME menu, usually at the top, under applications). Neither did I include useful Firefox plugins.
I recommend Mendeley for library management (you can find me there).
You might want to see other of my articles for more tips, such as (for a short selection) smart bookmarks for faster web searches, how to synchronize web browser bookmarks on different work stations, personalize the vim editor, set up a revision control repository, and automatically synchronize data.
You can also see the UbuntuScience community page for some additional information.
Enjoy. Please leave more suggestions below.

Free Text-to-Speech

2010-06-04T21:37:00.005+02:00

Image via Wikipedia

text to speech keyboard

Text-to-speech is great for the lazy, visually impaired, or people with reading disabilities. I think I read much, but I also count myself to the lazy and I like it to be read to. I found how you can select any text, for example in a webpage or a PDF, and let it be spoken using free software. It is relatively easy to set this up and here I show how.

Introduction

I used to have this on my Mac, people even had this on the amiga, and I also know of some firefox add-ons that give this functionality, such as Text to Voice.

Is something like this possible for free, system-wide, on Linux or Windows? Short answer: Yes. Now I explain how with a simple trick you can hear any text that you select, in any program. I concentrate on installation on ubuntu, but similarly this should be possible on other linux distributions, on MacOS, and Windows.

There are several free software projects that produce speech synthesizers. Possibly the two best known free text-to-speech (TTS) systems are espeak and festival. Both come packaged in many linux distributions but can also be installed on other platforms, such as Mac OS or Windows.

TTS with Espeak in Ubuntu

Espeak is a speech synthesizer for English and many other languages. On ubuntu, installation could not be easier: use synaptic or type sudo apt-get install espeak.

Espeak reads text, for example, try: espeak -f sometextfile. You have options to adjust reading speed, pitch, and a choice of different voices in different languages (in ubuntu just look in /usr/share/espeak-data/voices/es-la). Try: echo "hola" | espeak -v es. You can also put these and other options directly into the files in espeak-data directory, thereby creating new voices.

Now how to read text that you select?

I found a nearly complete solution and here I am going to spell it out.

If you use Gnome as window manager, go to system->preferences->keyboard shortcuts
(if you use KDE or other managers, this should be similar), add a new shortcut.

name: read text
command: bash -c "xsel | espeak"

Then define a key combination. I defined windows button-R.

Now you can select text in any application press your keys and hear the text as it is spoken to you.

Refinement

This works already, but you can make some improvements.

I found that filtering out newline symbols was nicer to the ear, because the pauses at the end of each line make it sometimes hard to understand. The command to hear the text without newlines would then be (thanks!):

Change the command in the keyboard shortcuts to this:

bash -c "xsel | sed -e :a -e '$!N;s/\n/ /;ta' | espeak -s 180 -v en-us"

Of course you can put more elaborate filters instead of the sed command. For example you can substitute "i.e." for "this is." For theater plays you could use different voices for each characters.

I also put in some filters. For example I don't want to hear "i.e." spoken as "IdotEdot" but as "this is."

Here comes my filter file, which you can copy. I stored this file as /usr/share/espeak-data/espeak.sed

s/i\.e\./this is/g
s/e\.\g./for example/g
s/et al\./and others/g
s/$[A-Z]$$[A-Z]$/\1 \2/g

If you want to use these filters, your command would look like this:
command: bash -c "xsel | sed -e :a -e '$!N;s/\n/ /;ta' -f /usr/share/espeak-data/espeak.sed | espeak -s 180 -v en-us"

Finally I also defined a key combination, windows button-S to stop the reading.
name: stop text
command: pkill -9 espeak

Note that instead of espeak you can also use the festival speech synthesis system. Install typing sudo apt-get install festival. A simple test: echo hello | festival --tts. I needed to switch to ALSA output for it to work. See configuration options at the archlinux wiki.

Enjoy. Please tell me of any improvement you come up with.

Alternative Blogging Platforms

2010-06-04T21:01:00.001+02:00

A blogging platform is the combination of hosting service and software for the purpose of maintaining a weblog. The most common platforms are blogger.com, always hosted with google (usually with the blogspot.com domain), and the wordpress software, on paid hosting services or using the wordpress.com hosting service. Other popular services are Typepad or liveJournal. In this post I want to show an alternative that can beat these services in price, customization, and loading speed. It involves using free software (as in beer and in spirit) with the google app engine as a hosting service.

Introduction

All blogging platforms have some limitations. Blogger is free and easy to use. Its scripting language, Blogger XML, is very limited, which brings problems for extensions and search engine optimization (SEO). I have the impression that it is also a bit buggy sometimes.

Wordpress presents a more professional look than blogger. It offers to download and self-host the wordpress software (which is free software), with many possibilities for extension with plugins to help presentation and SEO.

Both blogger and wordpress.com are very fast to load from everywhere on the world, because they use a content delivery system. The same is not automatically given with self-hosted blogs, where the download speed depends on the distance of the reader to the hosting server.

Blogging Software for the Google App Engine

Now, it would be great to have a blogging platform, which is freely extensible (free and open software) like wordpress, fast to load using a content delivery system, and free of costs. There is more and more blogging software emerging that can be hosted on google app engine (GAE). This fulfills the three criteria: it is free and open software, it is fast to load (because of GAE), and it is free of costs (if you don't get millions of visitors at least).

I took a look at blogging software for GAE. Some of them are still in early stages of development, others are more mature. There are huge differences with respect to feature sets. I made a wishlist of features that I want a blogging software to have. My list is based on the post Show me your open source Django blog application.

(Elegant) user interface for managing the blog.
WYSIWYG post editor.
Publishes (RSS and/or Atom) feeds.
Allows importing and exporting of posts.
Post authoring in teams.
Compatibility with most browsers (Firefox, Safari, Konqueror, Internet Explorer 7 and 8).
Documentation of the software.
Native comment system (non-javascript, because of SEO).
Support for remote publishing (for example via scribefire, windows live writer or the metaweblog api).
Project actively developed.
Importer from Blogger.
Importer from Wordpress.

List of Blogging Software

I compiled a list of python software that runs on GAE. I found it remarkable that many of the projects are written by Chinese developers, presumingly because of access restrictions to more common blogging platforms (such as blogspot.com) from within the Chinese mainland. A very influential blog software is bloog; many projects have been based on its code. Again: the projects are in different states of maturation. Setting up a blog on GAE requires at least some knowledge of programming. I put down the list without many comments. There's no special order, although I put my personal favorites as the first.

Software	Demo
Tom Strummer Bloog	demo
cpedia	Ping Chen's blog
i-here	demo
Pyweblog	demo
appengineblogsoftware	Developer Advocate
vasao	veltema.jp
JoeyB	demo
Pinax Combo	no demo yet(?)
Project Picky	demo
Micoblog	demo
toon blog	demo

This blogging software does not run on GAE, but I still list it because it is great (free) software as you can see in the demos.

Software	Demo
Django Techblog"	demo

byteflow	demo 1 demo 2
Mighty Lemon	demo
Kukkaisvoima	demo
Frog	demo

Enjoy. Please leave a comment below for questions and suggestions.

Digg 5 Years Old

2010-01-29T00:52:00.013+01:00

I just received a mail by digg.com celebrating their 5th anniversary and I thought it was worth commemorating this event with a post. Digg is one of the biggest social bookmarking websites. Inspired by slashdot, Kevin Rose, then 27 years old, founded digg on December 4th, 2004. Since then the site overtook slashdot in popularity and spawned itself many imitations. In this post there is more on digg.

Digg is a do-follow social bookmarking site with pagerank 7, very popular with news submitters. At alexa rank 99 (as of Jan 2010) it is one of the biggest social bookmarking sites by traffic volume (compare other social bookmarking sites by traffic, do-follow status, and pagerank).

People from digg created a promotional video about their anniversary, which you find below.

I looked up the search volume trend at google trend where I found the number given in the video of about 30,000 monthly visitors roughly confirmed. According to google websites trends, digg.com had about about 1.4 million unique daily visitors. At the same link address you'll see that digg's growth seemed to stagnate in 2009.

Search volume for search volume for the term digg.

Scale is based on the average worldwide traffic of digg in all years. Learn more

digg

1.00

reddit

0.18

slashdot

0.62

stumbleupon

0.22

Rank by

	Digg.comNewsBusters - May 2 2007
	Digg and MicrosoftTechnology News Daily - Jul 26 2007
	Google + Digg?InformationWeek - Jul 23 2008
	VCs shovel another $28.7 million into DiggBusinessWeek - Sep 24 2008
	Digg Ads: Digg or Bury Ads to express your opinionOzel Web Tasar $(C)% (Bm - Jun 4 2009
	Reddit Runs Elaborate Secret Santa ExchangeNewsNet5.com - Dec 17 2009
	More news results »

The graph shows that search volume for digg (in light blue) increases very much until 2007. In fact you can see that the term digg passes slashdot (yellow) in popularity in the beginning of 2006. The letter A marks the digg revolt. This was when Digg, prompted by legal threats, took down a news with more than 10,000 votes about the decryption of HD-DVDs. Because of massive protests they put the news on-line again. Since then, since May 2007, search volume for digg has been going down slowly but steadily, while competitors such as reddit (in red), and stumbleupon (green) have been catching up.

Many people go to webpages searching for the name of the webpage, so search volume for the name of the webpage could be indicative of its visitor statistics. On the other side, many regular visitors may have bookmarked the page or may have learned it URL (it's short enough), so search statistics alone may just as well be misleading.

However, looking at Alexa pageview statistics for 2009 for digg.com sems to confirm the impression that digg does not grow that much anymore. See alexa statistics for digg.com in the image below.

Unfortunately Alexa.com and compete.com do provide statistics only for time periods until two years and a half.

Is digg being overtaken by other sites? What is your impression of digg.com or other social bookmarking sites for that matter?

If you liked this article you might be interested in other articles on My Outsourced Brain. Some time ago I summarized information from several scientific studies about how and when to submit articles to digg, you might want to check it out. If you want to put a digg widget on your blog, you could be interested in my post about social voting widgets.

Widgets for Most Popular Articles on Twitter, Digg, Delicious, Propeller, and Reddit

2010-01-15T01:38:00.008+01:00

One of the most appealing elements on a webpage are "popular posts". There are several possibilities to get popular posts, e.g. by number of comments or visitor statistics. In this post I present 5 widgets that display your highest voted posts from social websites. These widgets can serve to increase visitor involvement and as navigational element. Some of these widgets display a vote or bookmark button and can help you to attract more visitors by social recommendations.

I thought why not install a widget that displays popularity in terms of votes, motivates people to vote, and thereby attract more visitors, while at the same time serving as navigational elements.

I was searching several of the most popular social websites to find possibilities to get such widgets. I found such widgets for Twitter, Digg, Reddit, Delicious, and Propeller.

Here you find demos: Twitter Demo, Digg Demo, Reddit Demo, Delicious Demo, Propeller Demo

For each widget I will show a javascript code which you can simply copy and paste with very few changes that I indicate. You can do so without any knowledge of HTML or javascript. In blogger you can create a new HTML widget in layout, paste the code, and there you go with a new widget.

Digg - Most Dugg

Reddit Most Popular

Propeller Most Popular

For this widget I had to create a yahoo pipe.
<script type="text/javascript">
function pipeCallback(obj) {
document.write("<ul>");
var i;
for (i = 0; i < obj.count ; i++)
{
var href = "'" + obj.value.items[i].link + "'";
var item = "<li>" + "<a href=" + href + ">" + obj.value.items[i].title + "</a> </li>";
document.write(item);
}
document.write("</ul>");
}
</script>
<script src= "http://pipes.yahoo.com/pipes/pipe.run?_render=json&_callback=pipeCallback&
_id=6e954c49f0ea1f933e9faf78321799a1&userid=username&num=5" type="text/javascript"></script>

Again you should put in your username, this time at propeller, and you can change the number of posts displayed.

Delicious Recent Bookmarks

Delicious provides a linkroll, which sorts your bookmarks alphabetically or by date.
<script type="text/javascript" src="http://feeds.delicious.com/v2/js/username?title=Most Popular on Delicious&icon=m&count=5&sort=date&tags&extended&name&showadd"></script>

Put in your username and there you see it on your blog.

Twitter - Most Tweeted Posts

This is the longest code, fear not. At the end are the options you'll have to change, indicated in bold.

<style type="text/css">
/* ul list */
ul.pot{
padding:0;
margin:0;
}
ul.pot li{
border-bottom:silver 1px solid;
float:left;
margin:1px 0 1px 0;
padding:2px;
list-style-type:none;
/* height:50px; */
width:100%;
overflow:hidden;
}
/* link span */
ul.pot span.pot-url{
display:block;
font-weight:bold;
}
ul.pot span.pot-url a{
text-decoration:none;
}
ul.pot span.pot-url a:hover{
text-decoration:underline;
}

/* tweet content */
ul.pot span.pot-tweet{
color:#333
}

/* link meta : tweets, score,.. line */
ul.pot span.pot-meta {
color:#006699;
display:block;
font-size:90%;
margin:3px 0 0;
}
ul.pot span.pot-meta a{
color:#006699;
text-decoration:none;
}
ul.pot span.pot-meta a:hover{
text-decoration:underline;
}
/* tweeter username span */
ul.pot span.pot-tweeter{
padding:0 2px;
}
/* tweets count span */
ul.pot span.pot-tweets{
padding:0 2px;
}
/* score span */
ul.pot span.pot-score{
padding:0 2px;
}

/* customize @user links */
ul.pot a.pot-at { }
/* customize #hashtags links */
ul.pot a.pot-hashtag { }
</style>



<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.3.2/jquery.min.js" type="text/javascript"></script>
<script src="http://popular-on-twitter.googlecode.com/files/jquery.popular-on-twitter-1.0.min.js" type="text/javascript"></script>



<div class="popular-on-twitter" options="{
site:'blogurl'
,show_n:0
,n:5
,animate:'height'
,tweeter_text:''
,show_tweet:1
}">loading..</div>


Here you should change blogurl to your websites web address without the http://www. part (e.g. myoutsourcedbrain.com). The parameter n indicates the number of posts you want to have displayed (here 5).

See the widget's google code project page for an explanation of more options.

Credit for this widget goes to Moretechtips, where the widget was shown in the post Popular-on-Twitter Widget: Topsy-enabled jQuery Plugin.

Enjoy. Please leave a comment below for questions and suggestions.

Thanks to December's Top Visitors

2010-01-11T01:09:00.001+01:00

My Outsourced Brain again has made a great improvement in visitor statistics last month. Most importantly it had an increase of about 300 percent in visitors, many new comments, the recent google pagerank update gave it three upgrades to currently 3, and it is now at 120,000 Alexa rank (3 month statistics). Thanks to everybody who visits and comments here, especially to people from entrecard who drop here as often as possible. I encourage you to leave suggestions on topics you are interested in and I try to cover them. If you like our posts, please consider getting updates via feed, e-mail, or twitter.

In this post I am listing top visitors and top commentators of December.

Here come December's top ten droppers:

Serian Man

Some thoughts on teaching and the exploration of the land of the hornbills, my beloved Sarawak, on the island of Borneo.
Picture to People

Researches about Computer Graphics.
New free software for graphics.
Hot free graphic effects.
The Cooling Stream

rambling thoughts and reflections on life issues and faith.
First Door on the Left

Democrat surviving in Texas. Barely.
(Entrecard ads are always displayed above the first fold!)
Opportunities Knock

This is a blog about taking back control of your personal financial future. We talk about opportunities in the stock market and in life.We believe that anyone can and should create their own wealth.
Crimsonsparkle.net

The view from my window.
Mutual Love

Sharing tender loving care and make this world a better place to stay.
On A Lighter Note

Daily life, photography, finance, and travel.
Lakbay Philippines

Lakbay Philippines! A blog about the best places the Philippines has to boast, from the famous to the not-so-famous-yet-equally-great spots.
Also contains satire and humour about the current showbiz, er, politics of the Philippines.
Nolitz hunting

Watch hunting videos from all video sharing websites in one place and keep track of the best published video on the net.

Thanks also to the top commentators. Here comes a top five list of commentators from December until today:

I plan to repeat these rankings for top droppers and commentators each month.

We would be happy to welcome you again this month. Enjoy.

Onlywire Article Submission

2010-01-07T20:32:00.007+01:00

In my last post I listed 72 social websites by usefulness for traffic or search engine optimization. The more sites you submit your articles to the better. The problem is that submitting articles to many social networking sites takes a lot of time, however there are many mass submission services that offer to make article submission easier for you. One of these services is Onlywire. In this post I describe my experiences with the onlywire semi-automatic mass submission service.

Semi-Automatic Social Network Aggregation

You have this great article and you want to submit it to a social bookmark aggregator to promote it. By social bookmark aggregator I mean any popular website that allows public sharing of bookmarks (called social bookmarking sites or social networking sites), b) promotes article by collective voting (social news aggregators). Examples for social bookmark aggregators are facebook, delicious, and digg.

To submit your article to a social bookmark aggregator you can use buttons for individual services or a social bookmarking toolbar, which integrates many networks. However with so many choices of social websites it is great to get some help from social network automation services, or mass submission services. Mass submission services can make the task of submitting to social networks much easier. You have to prepare most of the information only once: url (page address), post title, tags, and description. This information is then transmitted to each social networking service.

There are two kinds of mass submission services: mostly-manual or semi-automatic ones. With a mostly-manual submission service you connect with each social website as usual and manually complete the submission process. The submission automation services fills out some form fields for you but you are required to complete and review fields and press the submit button.

With a semi-automatic mass submission service, you are spared the completion step. The submission service automatically enters your url, post title, tags into forms at different social websites. This means your article is submitted to different social websites at the press of a single button.

Mostly-manual services include socialposter, socializer, and getbookmark. I tried out socialposter which offers submission help for 72 popular bookmark aggregators and which works great, but still requires many manual steps.

As for semi-automatic submission, apart from several commercial software products there is the onlywire automatic social mass submission service. In the following I will write about my experience with onlywire.

Onlywire

To use onlywire, you first need to get a free account at onlywire and then provide usernames and passwords for up to 32 different social networking sites. I don't like to give away my passwords to third-parties but I went along with it anyway. It took me some time to create new accounts at several of these networks. Some logins work at first try others didn't (e.g. delicious). Annoyingly, onlywire sends spam by default any time you change accounts as a way of self-promotion.

After this setup, you are ready to go and enter the specifics of your submissions, i.e., again: url, post title, description, and tags. I didn't like about the tags that they are space-separated which prevented me from entering more complex terms such as "search engine optimization."

After a pressing a submit button, you might have to wait up to 5 to 10 minutes to get a list with feedback for the submission. For each social network you see one of three values: success, failure, or finalization. Finalization means that a manual step is required.

I submitted about 45 articles using onlywire. This table sums up my experiences:

Social Networking Service	Onlywire Report	Remarks
Digg	SUCCESS	works. Finalization step only requires choosing of category and entering a capcha.
Stumbleupon	SUCCESS	works
Simpy	SUCCESS	works
Propeller	FAILURE	Most submissions work, however the article description is not entered correctly.
Plaxo	FAILURE
Newsvine	FAILURE	account disabled
Fark	FAILURE	works partly
BookmarkSync	SUCCESS	links are private by default (not visible to others). How make them public?
Bibsonomy	SUCCESS	works
Spurl	SUCCESS	works
Reddit	FINALIZE	Finalization doesn't work. Returns some javascript feed error.
Plurk	SUCCESS	works
Multiply	SUCCESS	Doesn't work at all, not submitted
Mixx	FINALIZE	requires insertion of all data again
Mister Wong	SUCCESS	works
LinkaGoGo	SUCCESS	works
Jumptags	FAILURE	works
Hi5	SUCCESS	not submitted
Faves	SUCCESS	works for around a third, you have to vote your own article to get to 2 votes
Diigo	SUCCESS	works half of the time, submitted as private, marking as public requires editing of each post entry
Delicious	FAILURE	login doesn't work
Connotea	FINALIZE	requires entry of all data again
Blinklist	SUCCESS	doesn't work
Bebo	SUCCESS	works (social network)

"Works partly" means that only some of the submissions show up in the network. "Not submitted" means that article submissions do not appear in the network. This means that either submission didn't work or they could have been deleted.

Note that some social news sites have declared war on onlywire and will treat onlywire submissions as spam. This could mean that if you have used onlywire your article submissions could be treated as spam and be deleted right away. At netvibes my account was terminated because of violations of codes of conduct.

My new delicious login, which uses a yahoo cookie, didn't work with onlywire.

My jumptags account was confirmed by jumptags admins after 3 days much later as all other services, so I only submitted very few articles.

Conclusions

Submissions are very fast, however do not work reliably for all networks. In such cases you could use a mostly-manual submission service, such as socialposter, or to visit important social networks individually.

The success of article submissions was very variable. From the automatic submissions I have gotten several visitors from propeller, and no visitors from other sites. From stumbleupon I got from today around 3800 visitors within the last 7 days for mostly two articles, Firefox in Parallel - A Pre-Release Version and Can the Second Law of Thermodynamics be Violated?.

I think this kind of traffic is a great success and I hope the created links will help the blog to further increase from now (since December 31st) pagerank 3.

Enjoy. What are your experiences with social network submission or submission automation?