Denis C. Bauer

My formal education is over (21. April 2010), life can start now! A big thanks to everyone who helped along the way.

We are organizing a special topics workshop titled “The successes, challenges and prospects for GWAS mega-analyses for complex diseases“, which is part of this years’ International Conference on Systems Biology (ICSB2010).

The program features a fantastic list of high profile researchers from a wide range of disciplines and institutes around the world. The workshop will create a productive environment, where new collaborations are formed and new experimental setups discussed.

Please visit the workshop’s web page for more details of the program and information how to register.

by mithrandir3

Amazon’s e-book reader, Kindle, has just become a whole lot more convenient, not for the owner that is, but for steering the stupid masses towards the good of humanity. By deleting sold e-books from the Kindle devices due to copyright-issues of the digital publishers, Amazon has “generated waves of online pique” according to The New York Times. Although Jeffrey P. Bezos, the founder and CEO of Amazon, apologized later for deleting the illegally sold copies of the e-books in a forums discussion entry and called the ” ‘solution’ to the problem [..] stupid, thoughtless, and painfully out of line with our principles”. It might have been an action free from censorship ambitions, but it shows that the mechanisms are in place to eliminate unwanted books.

Books are “a pleasure to burn. It [is] a special pleasure to see things eaten, to see things blackened and changed.” as Guy Montag, the “fireman” in Farenheit 451, knows. But the act of burning books in reality is generally less pleasurable because widely unaccepted and very unpopular these days. How convenient that the new technology can make books “disappear” clean and easy, without huge arguments by the hysterical book-owner, without even being there. Remotely and and with full refund can books be dropped down the memory hole – book burning v2.0.

But why burn them? Burning implies nasty things about an increasingly censorship-hungry “system” and does not make creative use of the associations we have with books to begin with. Why not instead tweak the content of a book as desired and bring the past up-to-date as suggested by Nineteen Eighty-Four (incidentally one of the books deleted). Books still have a status of trustworthiness, in our minds they are a silent witness of the invariable truth of our collective memory because once published the content did not change. Well, that’s all in the past that is. Nowadays, Amazon updates books without warning to bring them up-to-date to the newest edition. If this new edition removes spelling errors or adjusts the content to a more … can not be controlled. As rrabbit noted, if Amazon wants “Oceania [is] at war with Eurasia: Oceania had always been at war with Eurasia” until tomorrow when Amazon updates the books to say that Oceania had always been at war with Eastasia instead and that Eurasia is our trusted ally — has always been. The need to burn books has ceased to exist (if it ever had in the first place), because undesirable content can be rewritten on-the-fly — embrace book burning v3.0, made possible with Kindle.

But it is not the technology that is evil, the effort of saving trees and gallons of fuel by distributing books online must be applauded and so the aim of providing editing-error free books. Even the act of deleting illegally sold books is not shocking in itself, if Amazon would have knocked on every buyers door and would have swapped the illegal copy with a legal one from a different publisher, no-one would have second guessed Amazon. But it is the combination of technological possibility and questionable intentions or judgements of a company that lets the darkest dystopian fiction seem plausible: who would not start to doubt ones mental health if facts start to dissolve before ones very own eyes.

Amazon has demonstrated of being capable to commit book-burning v2.0 if convenient (letting books disappear). They have the technology in place of burning books v3.0 (updating the content unnoticed). I am not convinced that Amazon has enough integrity to withstand the pressure of a government endorsed censorship to tweak the by then unwanted content. Next time when you hold a Kindle, be prepared to read nothing but government approved propaganda.

While I’m against illegal content on the web, an internet filter is not the solution.

“Risotto? – that takes ages …”. Not so with this nice and easy recipe.

For the Risotto:
100 g chicken diced
3 mushrooms diced
salt and pepper
3/4 cup (risotto) rice
2 cups chicken stock
1 tbs margarine
1 tbs parmesan
2 ts capers

Brown Chicken and mushrooms in the same pot as you are going to make the whole risotto in, add salt and pepper. Add additional oil and fry the rice until it is translucent. Add some stock and stir until the stock is absorbed by the rice. Add some more stock and stir until it is absorbed. Repeat this until you used all the stock and the rice is cooked (20 min) – you don’t need to stir so much towards the end – just let it gently bubble. It should be still quite moist so that now when you add the margarine and the parmesan it becomes viscid. Add capers, chicken and mushroom and serve.

You can also add anchovies and parsley towards the end.

This is the perfect soup for times when you fancy a clear noodle soup without the usual greens.

For the Dumplings
200g Prawns (shelled and chopped)
150g Chicken mince
5-6 slices of dried shitake mushrooms (chopped)
2 garlic cloves (chopped)
1 tbs fresh ginger (chopped)
1.5 ts sesame oil
2 shallots (chopped)
1 ts salt
20 wonton wrappers*

For the Soup
Chicken stock
3 cups chicken stock
1 cup water
2 tbl soy sauce (kikoman)
1 chili (chopped)

For the sides
0.5 chili (chopped)
1 charlot (chopped)
(1 citron slice)

Mix dumpling ingredients and fill wonton wrappers. Bring stock and water to boil, add chili and wontons and boil for another 10 minutes or until the wontons float to the surface. Serve with sides.

*wonton wrapper can be substituted with homemade pasta dough.

Note, this recipe is adapted from the Woolworth magazine.

Wine Selector sent us this excellent wine from SA (Limestone coast):

This year’s Pattern Recognition in Bioinformatics (PRIB 2008) was organized by the Monash University and was therefore held in Melbourne. It was a very interesting conference with a great sessions and a good organization. On-top of that, our paper even won the best paper award. The slides from my talk are online on slideshare.

We came across this excellent wine from Victory (but not the Yarra Valley):

Developing code should involve a robust and rigorous testing step. Unit testing is commonly used but there is a different more flexible way introduced by Bertrand Meyer called “Design by Contract” (wikipedia), where the server ensures that the invoked stated is correct if the client provides correct data. Whether the “contract” is fulfilled by both parties can be tested by assert statements in the code, however this may cause a log of clutter. A nicer way is to write the tests in the “documentation” part. Several packages provide such an environment for Java. Here I looked at Contract4J.

If you know how, it is real easy to set up your “design by contract” environment in Eclipse. The following step-by-step instruction is for Eclipse 3.2 and Java 5.0.

1) Download AspectJ

in eclipse go to Help->Software Updates->Find and Install->Search for new Features to Install->Add remote location…
here you have to add the URL for the AspectJ version matching your Eclipse version – search for the URL here:
http://www.eclipse.org/ajdt/downloads/
Continue to install AspectJ by following the wizard prompts.

2) Download Contract4J

https://sourceforge.net/project/showfiles.php?group_id=130191
in the archive should be Contract4J.jar and lib/*.jar

3) Get an AspectJ Project

Create a new *AspectJ* Project by doing
File -> New -> Others.. -> AspectJProject

or

Convert your current project to an AspectJ project by right clicking on the project and -> Convert to AspectJ Project

4) Link in depended libraries

At project properties :
1) Add Contract4J.jar to AspectJ Aspect Path Libraries (or AspectJ Build InPath in Eclipse 3.4)
2) Add Contract4J.jar to the Build Path
3) Add other dependent libraries (from the lib/ folder in the zip) to the build Path

5) Write code

E.g. a counter.

Where the member variable is tested to have a range between 1 and 4.

6) Execute Program

Run as -> AspectJ / Java Application

The output for e.g. the counter should be like this:

Current count 1
Current count 2
Current count 3
Current count 4
[FATAL] DefaultContractEnforcer: *** Contract Failure (Counter.java:22): Invar test “count>=0 && count <5″ for “Counter” failed. Count must be between 0 and 5 [failure cause = null]
…

Which indicates that the counter is outside the valid range and therefore that the contract is violated.