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Archive for August, 2011

GMDS Notes Now Online

GMDS error

THE FOLLOWING research notes have just been uploaded, hopefully to help others understand the work undertaken and what ideas are being tested (generalised to the extent of being applicable to any type of data, including biomedical). The 200+ pages long document which is more complete is still work in progress and it will be published at a later date. Thanks to the ERC for funding this work.

GMDS and PCA Duality (PDF, HTML)
3-D Expression Dissection: An Approach In Brief (PDF, HTML)
Multi-Feature PCA (PDF, HTML)
Exploratory GMDS Integration (PDF, HTML)
GMDS-PCA: Project Plan (PDF, TXT)

Is It Now a Crime to be Poor?

Union Jack

There is an initiative to distract the British public from the real problems, which revolve around a debt crisis. While many of the country’s richest people receive unjust tax exemptions (Vodafone, for example, enjoys a tax dodge of over 7 billion pounds, or 30 times the estimated aggregate cost of all the recent riots and the damages caused throughout), the centralised media seeks to characterise the victims — not tax evaders — as the danger to this country’s future.

Earlier this month, events resulting from genuine grievances were collectively painted only as vandalism and looting, even though that is a gross generalisation – an oversimplification to be exploited by opportunistic politicians . The real issues were left buried under the rug and a mesmerising picture of buildings/buses on fire was implanted in people’s minds in order to make oppressive new legal instruments seem acceptable and even necessary.

These events we are seeing are not unprecedented. The burning of the Reichstag in the 1930s, for example, was used as a pretext in Germany in order to eliminate civil liberties that had been approved in 1919. Based on The Star, a respected daily newspaper, our Prime Minister is now blaming civil rights for the riots, seeking to remove these and by doing this potentially criminalising some forms of union or civil protest.

The argument is not one of left versus right wing, which would be a false dichotomy. It is not about rioters and non-rioters, either. The real issue at hand is class war and the ascent of suppressive policies that limit free speech on the Web and freedom of expression on the streets, however non-violent these may be. Do not fall for the illusion that the lower economic class is the enemy; do not allow draconian new policies to pass, either, mainly because history shows that the decline is democracy is steep and irreversible one it commences.

Riots Are Over, Problems Are Not

Hooligans

Burial of one’s problems is not the solution to these problems. Burial of a state’s problem is not the mass arrest of the symptom of this problem.

Last week there was a lot of unrest in the UK. It was only the rioters whom the media chose to focus on. It was intentional. Allow me to explain.

Grouping or stereotyping the unrest is a way of evoking a sense of urgency in the fight against dissent. All those who point out that there is societal disparity can easily be classified as “part of the problem”, which is no longer a problem of disparity but a problem of looting and vandalism. The media really squeezed the juice out of last week’s events as it showed people gore or fire. People, in turn, are likely to run into the state’s authority for protection — the same authority which often neglects to publish rich offenders (tax evasion and other very costly crimes).

A week after the protests (collectively referred to as “riots” in the media) began, the storm began to quiet down and national debates approached their conclusion. That having been said, there are some lessons we must take from the whole episode:

1. Genuinely non-violent people who merely attend the streets at times of unrest because they are concerned will be associated — deliberately — with a violent crowd. The message to take from this is that the presence of an anarchistic element in the crowd can depress and gag legitimate attempts to make oneself heard. There are proven cases from other countries where agent provocateur and ‘plants’ were used for this.

2. Freedom of speech is only respected as long as it is not dissenting or revolutionary in nature.

3. Class hypocrisy does not enter the debate, at least not in the mainstream, and when people raise the offences of the Prime Minister or even a history of arson conviction for his deputy, those allegations of hypocrisy are faced with resistance going along the lines of, “you help the looters” (or “help the enemy,” which is how people defend unjust wars). It does not matter how much looting occurs at a ‘legalised’ level (like tax avoidance or lies that lead to wars of vested interests), this does not matter when the poor people rebel. This in its own right is indicative of discrimination based on class.

Those who write more objectively or at least attempt to assess the arguments of both sides are not apologists for looters. They are apologists for truth.

I was actually there at the City Centre for over an hour just before the Manchester riots broke out. I wanted to see for myself what it was all about, not through the lens of corporate media but from the point of view of a bystander. My friends and I left the area just minutes before a shop was put up in flames. The following day it was unsafe to return to the same place, maybe even forbidden. There was no distinct racial characteristic when it to the people who were there to cause trouble (the racists are just being opportunists here). It seems like more an economic commonality. Poor people are not happy in this country and maybe their grievances are somewhat legitimate.

An hour ago at the streets around here (Manchester City Centre), a couple of young people, maybe about 14 years of age, approached me in an attempt to sell me a bike. I wasn’t sure if it was stolen or maybe they were just so poor that they needed to sell their bike. Either way, this is a symptom of a real problem. The older generation in this country collected massive debt at the expense of the young people, who are there to suffer the consequences for many decades to come. I occasionally hear similar frustration from friends of mine. We live in a bubble economy.

The Sunny Days of GNU/Linux

Summer

We are fortunate enough to live at a time when many (if not most) phones run Linux and the overwhelming majority of Web servers do too. Those who say that GNU/Linux is “not ready for the desktop” hardly exist anymore. So for those who insist on running it on their desktop/s, there is rarely a major barrier. Videos work just fine (increasingly with HTML5 and free codecs, not Flash), a lot of applications are Web based, and some of the world’s best Web browsers are available for GNU/Linux, so how can one complain? Among developers and producers, there is no real pitfall associated with GNU/Linux (those that are brought up can easily be defended against, e.g. “fragmentation”).

Earlier this week I had the pleasure of installing the latest Debian GNU/Linux on my home server. I used an SD card mounted onto a USB converter to pass a small ISO image which in turn bootstrapped the system, brought up the network card, and fetch all the remaining packages over the Internet. This made a multi-functional server with KDE4 and GNOME on top of it for some administration. It all started with an SD card and the installation was simple enough for most people to walk through. When even Debian becomes an easy distribution to install it ought to become clear that GNU/Linux continues to mature not only in that little corner called “Ubuntu”. The same components are shared and reused to make the optimal system.

Despite technical competition and also illegal, anti-competitive practices, GNU/Linux now thrives, so all that Apple or Microsoft can do is build a cartel around software patents. They currently go after Android more than they go after GNU/Linux. But Google is wealthy enough to counter this, e.g. with the purchase of patents. It means that, in the long run, the patent angle is not enough to impede GNU/Linux or Java/Linux adoption.

To a lot of us who are staunch advocates of GNU/Linux and proponents of software freedom, the reality of this irreversibility is a true pleasure. It means that we can sit back and watch Linux take over more and more aspects of our lives, slowly demonstrating the merits of software which is free. Apache does something similar, but fewer people out there are aware of what it is. Little by little we’ll be seeing more Free software in more places. Just like Wikipedia, it spreads too fast to ignore.

2011 has been an important year for Linux. This kernel turns 20 this year (depending on which milestone is celebrated). Let us celebrate.

Review of Puppy Linux on an Old Server

Puppies

Puppy has become familiar to many as a Live CD option for aging PCs that sit on people’s desktops at home, maybe even at some offices. Puppy recently became more of a derivative of Ubuntu (arguably, depending on the definition of “derivative”), but its legacy and/or its strength was mostly associated with its version that I used. It contains JVM and it can also use other lightweight desktop environments.

For this review, I have used Puppy for a period of 5 days, first as a desktop (ish) on a server machine and then, briefly, as a development environment (it did not get very far). The way I will structure this review will be compartmentalised and it will focus on items that are more or less unique to Puppy. For example, I will ignore GRUB.

Puppy, by default, runs in a mode similar to root and it appears to be quite strictly a single-user OS. It comes preinstalled with a lot of valuable and lightweight applications. It also has Firefox, which is probably the exception when it comes to this defensible ‘weight’ criterion. Chromium is made available through the repositories and it works very well. I tried it and it was perfect. Puppy comes with a variety of themes (about half a dozen) and more can be added in a user-friendly way which, as I unfortunately found out, can lead to a system dependency Hell (it is not entirely clear what caused this). In order to effectively assess Puppy, there ought to be a separation between the boot process, which is fast but lacks polish, the desktop environment, and the applications, some of which are unique to Puppy. The menu which contains these applications is divided into sections that group related items. The problem is, this menu is cumbersome to edit, it is not clear how to create shortcuts on one’s desktop or task bar, and sometimes it is hard to find the category under which is application of interest was placed. Even finding a terminal window application took me minutes of manual searching (no simpler mechanism is available). Configuring the behaviour of the environment is in general very cumbersome compared to newer and heavier desktop environments. This may not be a huge deal when striving to just use this environment to merely host Firefox or OpenOffice.org. It does, however, give little justification to using Puppy on a machine with decent specifications (such as the one I tested Puppy on).

Puppy is generally easy to use and it contains many technical tools in the appropriate menus. It comes preloaded with OpenSSH and other front ends to such “Swiss army knives” that would help advanced users and make it almost suitable for some servers. The problem is, when something is missing (GCC for example), it leaves the user dependent on package managers that do not always succeed at installing desired applications, especially KDE applications and even GNOME applications. The package manager in this release of Puppy offers a gateway into Ubuntu repositories, but there is no guarantee that these would work. And worse — under some of the Puppy packages there are items that explicitly say that they are broken or may break something else. Why even include them? The last thing a user would want is a hosed system; it’s better not to have some software (or having to compile it from source) than to not have the operating system (e.g. in case it gets rendered unbootable). If a package is known to be sensitive and prone to issues, then Barry should probably omit it altogether, leaving the user with something which is not self-nuking. But anyway, I digress.

Here are some of the nice things that I can say about Puppy. Apart from booting fast it is also fast enough while in use, although it may depend greatly on the hardware used and it might scale a lot worse with old processors and deprivation of RAM. This would require another test on a different machine. The selection of themes that Puppy comes with by default is quite pleasing considering the fact that there are no X Composite effects. The task bar (includes more than just user tasks/windows) is not cluttered and the menu cannot baffle any user. Even the names of applications are usually self-explanatory,which is important.

Screenshots would have complemented this review had I still been able to start X. The thing is, Puppy was a challenge to set up properly on a widescreen display. It offered some low-level tools for X configuration and display setup, but these never achieved the required display mode, even after 2 hours of persistent attempts (I have a lot of experience with X, so the fault is not purely mine). In command line mode, Puppy has a lot of the tools one might expect to find (editors, file system repair, rsynch and so on). It would probably benefit from a better terminal application which is visually richer and more customisable (the one it currently has offers no customisation at all and it is rather rudimentary). For those who are into the command-line oriented work, Puppy is not a good choice and perhaps it is possible to install a better terminal to make up for it in the future (or at present from the repositories). Good terminal emulators need not take up much space, so this is an area worthy of expansion in the future.

One thing that occurred to me is that the GUI is not always consistent and does not behave in the best of ways. For example, when installing packages, they get installed upon a single click on the package name and it is not possible to tick several for simultaneous or queued installation. Then installation gets very verbose and distracting. Another example is, when trying to change the number of virtual desktops (for pager size) there is a request for keyboard input of a number between 1 and 8, using a textbox without limitation on length. Why not use a slider or a set of buttons to restrict and validate the user’s input? This might be a JVM-only issue, but either way, even Fluxbox does not have such issues (Fluxbox runs on my old laptop). Openbox and IceWM I have not used for a long time, but they too did not have such fragmented and unexpected settings structure. These are both available for Puppy, but I did not get around to testing them.

Now we come to remarking on Puppy as a server. In short, it is not. Puppy’s task bar gives way to the stereotype that it’s a browser-based distribution, as it links only to two browsers, Puppy’s browser and Firefox. If this machine is to be used as a monitoring server, than maybe with a browser up and some terminals it is suitable for the task. But otherwise, given the lack of necessary applications (preinstalled or in the repository), aspirations to run Puppy on a server are a dream pipe. I gave up on this pretty fast, before I even managed to compile a mail server package (too many dependencies and packages were missing).

I wish there was more to tell and I wish I could recommend Puppy for anything other than very old computers, but based on 5 days of use, Puppy is a niche product and it does what it’s intended to do pretty pretty well. A friend warned me over at Identi.ca about dependency nightmare and he was right. It was only days later that I started to experience those myself. At first I failed to install some KDE/Qt applications, but later it was the addition of many more packages that should be ‘safe’ that led to the “nightmare” I had been warned about.

Puppy is available for free download from its well-established Web site. it packs a lot of power in very small size and it is available for use in live mode too, meaning that one can try without committing by full installation. This is probably one of the strengths of this GNULlinux distribution.

Thank you, Puppy. And thank you, Barry, for Puppy.

Wikileaks Makes the World More Civilised

Wikileaks cite

Earlier on in the day, Wikileaks’ official account echoed my tweet to over a million followers, which is rare (I have posted over 50,000 tweets and never was I mentioned by Wikileaks). For whatever reason, people still associate Wikileaks with crime, even though its only connection to crime is that it helps expose crime. In this world and in this strange age of oppression, exposing crime is criminal if the criminals are very rich. If they are poor people who commit petty crimes, nobody seems to care — neither about them nor those who expose them.

Whether people realise it or not, there is a coordinated campaign to slander Wikileaks and put down those who support it. Evidence was leaked that millions of dollar were going to be invested in the defamation of Wikileaks simply because ad hominem attacks are the last resort for those whom Wikileaks exposes, e.g. Bank of America.

To a certain degree, Wikileaks has been de-funded and driven ‘underground’. Its founder is treated like a criminal even though he is not and the organisation is being deprived of donations. Is this justice?

Some people would hastily state that leaking is a crime, but actually, most crimes are exposed and the criminals caught after a sort of leak — either by the police or a member of the public (civilian). The difference is, Wikileaks exposes some bigwigs who can afford PR operations that falsely characterise Wikileaks as the problem. It’s a deflection tactic. They actually do use those tactics a lot (look up “HBGary”).

In some sense, Wikileaks suffers a similar reputation problem to that of the British public, whose gripes are collectively referred to as “vandalism” and “looting” as it helps trivialisse real grievances. At Wikileaks, praises and awards are received when they expose criminality in rogue African nations, but when the same type of scrutiny is applied to people in the West, suddenly Wikileaks is an “evil plot” that must be shut down. In the UK, when millionaires that include MPs steal from the public, it’s alright, but when misguided individuals steal smaller amounts of money/assets, then it’s a punishable crime that warrants expanding the police’s scale and powers. In both cases, the allegation that the police serves rich people (oppresses the poor and protects the rich) is only further validated. To an extent, the same applies to the court systems, which are themselves run and managed by rich people. See what Julian Assange is being subjected to.

Wikileaks — unlike looters — can be defended without risk of being associated with criminality. The only ‘crime’ of Wikileaks is that it exposes criminals. By doing so, it removes uncivilised people from society. Some leave in disgrace.

Speaking for myself, as someone who wrote about corporate crime over at Techrights, I sure empathise with Wikileaks. It is common for those who expose criminals to be portrayed as criminals and in some cases “poisonous” (a projection from the accused).

Oppose Attempts to Censor the British Public

For those who have not heard, the government looks into censorship of the Web as miserable and counter-productive means for suppressing real grievances. The Prime Minister surely learned nothing from Egypt, which had this famous cartoon produced. I decided to do some GIMPing of the original to show the equivalence.

UK censorship

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