Russia - Best Assembler, Best French Actor and now Freest Country !!
World has turned upside down compared to twenty years back. Earlier this year, Putin gave passport to famous French actor Grard Depardieu, who left France for good calling it a Bolshevic country.
French Icon Gets Star Treatmentand Job Offerin Russia
Six months later, he let in the most courageous American Snowden.
Edward Snowden leaves airport after Russia grants asylum, says “the law is winning”
Apart from those political decisions, in computing, the Russians put their brain together to create the coolest bioinformatics site Rosalind, while US government managed to get us NSA :)
To celebrate these achievements, we will run a special day for our readers and contributors from Saint Petersburg. The following commentaries cover their various achievements reported over the last year in our blog.
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly
Jigsaw puzzles were originally constructed by painting a picture on a rectangular piece of wood and further cutting it into smaller pieces with a jigsaw. The Jigsaw Puzzle Problem is to find an arrangement of these pieces that fills up the rectangle in such a way that neighboring pieces have matching boundaries with respect to color and texture. While the general Jigsaw Puzzle Problem is NP-complete [6], we discuss its simpler version (called Rectangle Puzzle Problem) and study the rectangle graphs, recently introduced by Bankevich et al., 2012 [3], for assembling such puzzles. We establish the connection between Rectangle Puzzle Problem and the problem of assembling genomes from read-pairs, and further extend the analysis in [3] to real challenges encountered in applications of rectangle graphs in genome assembly. We demonstrate that addressing these challenges results in an assembler SPAdes+ that improves on existing assembly algorithms in the case of bacterial genomes (including particularly difficult case of genome assemblies from single cells).
Starting to Understand the Spades Paper
Two red blocks are identical, but blue, yellow and green segments are all different. Also, we know the pieces and their distances, but we do not have them assembled as nicely as above. How do we assemble them?
Let us try one strategy, where we start picking pairs of positions 50 nucleotide apart and form circles. In most cases, both ends of pairs will fall on the same colored segments, but in some cases, they will be fall on different segments. We also know that 1,1->1,51? will be followed by 1,2->1,52? and so on. So, we have some way of connecting the pieces in a long chain, but there are too many circles.
Rosalind Project at Algorithmic Biology Laboratory, St. Petersburg
Rosalind Will Get Even More Marvelous
By the way, were slowing down with the current Rosalind engine development to create a new collaborative platform for online education, which will include all current features and more, also itll be scaled to other disciplines (such as algorithms and coding for scientists). New platform will be even more marvelous than Rosalind, so stay tuned :)
In indeed got more marvelous.
SPAdes and MaSuRCA Assemblers Performed Best in GAGE-B Evaluation
Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs
Keep up the good work !!
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[Edit. We are in trouble !! Our readers are complaining (by private email) that Russia should not be called ‘the freest country’, Grard Depardieu should not be called the best French actor (Alain Delon was better) and Rosalind is partly funded by NIH. Please see additional comments.
A reader pointed out that USA is still lot better than Russia despite recent changes. Let us cover Russia first and then USA.
How free is Russia? There are three aspects.
(a) Freedom of speech
but then again, neither Snowden, nor Bradley Manning have freedom of speech in USA and many others (government-funded professors) do not say many things in public out of fear. What is different?
(b) Freedom from taxes
Tax code of Russia is far better than USA. So, people are free from arbitrary seizure and loss of property in that respect.
(c) Freedom of political refugees, as defined by UN convention related to refugees. We do not know how well that works in Russia except for the recent advertised case.
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How good is USA in comparison? Based on our observation, USA looks good, because the American crooks are never advertised. You will enjoy the following story, because it includes all usual suspects - American academia from top university, Russia and corruption.
Why Larry Summers lost the presidency of Harvard
So why did Summers lose his job at Harvard? It was because of his protecting a buddy, a fellow economist at Harvard named Andrei Shleifer.
Andrei Shleifer managed to get put in charge of helping Russia privatize stuff in the mid 1990?s. His mission was to make things more useful and transparent to the infant capitalist system. Through his wife and friends, Shleifer instead orchestrated a boondoggle on Russia. He invested money through his wife and helped his friend Jonathan Hay and his lover and friends invest theirs, and set up the very first mutual fund as well as thwarting the efforts of other people to set up their own funds. All of these things were strictly against the conflict of interest policy they were working under.
Shleifer got in trouble, and the U.S Government sued and won against Harvard and Shleifer. From the article:
….
The article gets Summers fired
An anonymous person got a bunch of copies of the II article and stuck one in every Harvard facultys mailbox the morning of the no-confidence vote that got Summers ousted.
And just in case youre wondering, heres the website of Sheifer, still on faculty of Harvard.
What happened to the Summers thug? He is heading to become US treasury secretary.
(How to understand the career trajectory of Larry Summers)
BTW, the math babe site linked above is fantastic and posts many interesting math-related discussions.
How much is the Stacks Project graph like a random graph?
Analyzing the complexity of the Stacks Project graphs
