SPAdes Assembler, Python in Bio, US Effect, Return of Lysenko and Other Stories

SPAdes Assembler, Python in Bio, US Effect, Return of Lysenko and Other Stories

SPAdes Assembler

SPAdes assembler is starting to get some love from bioinformaticians, thanks to its success in GAGE-B. Australian bioinformatician Torsten Seemann covered it in his blog and explained the difference between Velvet and SPAdes.

How Spades differs from Velvet

Despite these alternatives, Velvet has still thrived due to it having a strong user community, and still giving good, usable assemblies. But there is always room for improvement and new ideas, and I believe an excellent option for bacterial assemblies currently is SPAdes. It recently ranked very well in the GAGE-B assessment and in this post I will explain its relationship to Velvet in broad terms.

Phil Ashton, who writes an informative blog, also covered SPAdes two month’s back.

Assembly optimisation impact of error correction and a new assembler, SPAdes

In addition to being a great assembler, the other aspect of SPAdes worth mentioning is the SPAdes papers. All three of them (main paper, rectangular graph paper and Son Pham’s pathset graph paper) are very informative on the algorithmic aspects of dBG. Last year we wrote a number of commentaries on SPAdes, but they are no substitute for going through the papers themselves.

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

Starting to Understand the SPAdes Papers

Rectangular Graph Algorithm

Going Through the SPAdes Code (Rectangular Graph)


Python for Biologists


This is the index page for everything to do with the Python for Biologists course a free introductory programming course for biologists, suitable for complete beginners. You can scroll down to start reading the course content right away as a set of web pages. You can also get the course as a free ebook in PDF format enter your email address to get a copy of the ebook and exercises (and occasional notifications when the book is updated).

Also check Jason Chin’s “Write A Genome Assembler with blasr and (I)Python

I am not sure it is right thing to do some coding in a vacation. (See this tweet, not sure if I would agree.) Anyway, before the vacation, I decided to organize whole bunch of random papers I collected in the last few years in my laptop. I eventually felt that I should read some of some theoretical papers about genome assembly again. I grabbed Gene Meyer’s paper, and started to think about the problem about constructing unitigs (high-confident contigs). Before I tried to read the paper in detail, I just felt maybe that it was useful to write some quick code to check out what real data looked like. I started writing some code visualizing the local overlapping and generating the global overlapping graph. It was pretty straight forward and quite inspiring from the visualization. The visualization motived me to write more ad-hoc code in IPython to go beyond generating simple visualization during the vacation. I started to implement a very simple greedy algorithm to connect the input DNA fragments. Eventually, I found I can atucally get the whole genome assembly right!! This Notebook shows the work step by step toward a simple genome assembler for long read data using IPython and Python.


Return of Lysenko?

In a commentary titled Genome Biology: Not Drowning but Waving published in Cell, UK scientist Adrian Bird wrote about various unscientific ideas and inflated claims permeating through biology (h/t: @genologos). Those are ENCODE, GWAS, long noncoding RNAs expressed in 85% of genome and epigenetics, and we discussed why those are epitomes of bad science. Dr. Bird linked epigenetics to Lamarckian evolution and we found that idea thought- provoking.

Unlike the longstanding debates about the nature of genes and the concept of junk DNA, controversy regarding the impact of epigenetics is relatively recent. Among several current perceptions of epigenetics (Bird, 2007), the most radical is that epigenetic information can be transmitted across animal generations. Add to this scenario the widespread assumption that epigenetic marking is often directed by the environment and we have the essential ingredients of Lamarckian evolution, or inheritance of acquired characteristics. An oft-quoted example of intergenerational transmission of an environmentally determined trait is altered mortality among the descendants of people who experienced the Swedish famines (Pembrey et al., 2006). But while it is conceivable that transmission between generations of chemical marks on the genome underlies this effect, it is dif?cult to exclude the possibility that effects of the trauma were transmitted culturally across generations who grew up in familial contact.

Few days back, while learning about Russian history, we reread the story of Lysenkoism built on Lamarckian evolutionary ideas.

Lysenkoism (Russian: ?????????????), or Lysenko-Michurinism was the centralized political control exercised over genetics and agriculture by Trofim Lysenko and his followers. Lysenko was the director of the Soviet Union’s Lenin All-Union Academy of Agricultural Sciences. Lysenkoism began in the late 1920s and formally ended in 1964.

Lysenkoism was built on theories of the heritability of acquired characteristics that Lysenko named “Michurinism”.[1] These theories depart from accepted evolutionary theory and Mendelian inheritance.

Lysenkoism is used metaphorically to describe the manipulation or distortion of the scientific process as a way to reach a predetermined conclusion as dictated by an ideological bias, often related to social or political objectives.

In 1928, Trofim Lysenko, a previously unknown agronomist, claimed to have developed an agricultural technique, termed vernalization, which tripled or quadrupled crop yield by exposing wheat seed to high humidity and low temperature. While cold and moisture exposure are a normal part of the life cycle of fall-seeded winter cereals, the vernalization technique claimed to increase yields by increasing the intensity of exposure, in some cases planting soaked seeds directly into the snow cover of frozen fields. In reality, the technique was neither new (it had been known since 1854, and was extensively studied during the previous twenty years), nor did it produce the yields he promised, although some increase in production did occur.

This part about Lysenkoism is the most interesting. Lysenkoism was established through mass media and propaganda.

Isaak Izrailevich Prezent, a main Lysenko theorist, presented Lysenko in Soviet mass-media as a genius who had developed a new, revolutionary agricultural technique. In this period, Soviet propaganda often focused on inspirational stories of peasants who, through their own canny ability and intelligence, came up with solutions to practical problems. Lysenko’s widespread popularity provided him a platform to denounce theoretical genetics and to promote his own agricultural practices. He was, in turn, supported by the Soviet propaganda machine, which overstated his successes and omitted mention of his failures. This was accompanied by fake experimental data supporting Lysenkoism from scientists seeking favor and the destruction of counter-evidence to Lysenko’s theories. Instead of performing controlled experiments, Lysenko claimed that vernalization increased wheat yields by 15%, solely based upon questionnaires taken of farmers.

Professsor Bird wrote other articles criticizing epigenetics -

Perceptions of epigenetics

Geneticists study the gene; however, for epigeneticists, there is no obvious epigene. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics. It encompasses some of the most exciting contemporary biology and is portrayed by the popular press as a revolutionary new science an antidote to the idea that we are hard-wired by our genes. So what is epigenetics?

Other respected biologists like Eric Davidson and Mark Ptashne expressed similar opinions, and you can find the links in the following commentary (check epigenetics section).

Epigenetics in Stem Cells Is It a Significant Paradigm Shift in Biology?


US Effect

That brings us to the fourth part of today’s commentary - US effect. It is mentioned only in a news article in Guardian, but in no US-based mass media.

Research finds ‘US effect’ exaggerates results in human behaviour studies

Pressure on scientists to come up with exciting results could soon spread to other developed countries, researchers warn

Scientists who study human behaviour are more likely than average to report exaggerated or eye-catching results if they are based in the United States, according to an analysis of more than 1,000 research papers in psychiatry and genetics. This bias could be due to the research culture in the US, authors of the analysis said, which tends to preferentially reward scientists for the novelty and immediate impact of a piece of work over the quality or its long- term contribution to the field.

Daniele Fanelli, University of Edinburgh, one of the authors of the latest analysis, said that there was intense competition in the US for research funds and, subsequently, pressure to report novel findings in prestigious, high- impact scientific journals.

The original study is published in PNAS. John P. A. Ioannidis wrote a number of other papers on similar theme, and we recommend them all.

US studies may overestimate effect sizes in softer research

What do we get, when we combine the core themes of ‘US effect’ and ‘Return of Lysenko?’ ? Funding pressure from the government is forcing researchers to BS more, and their BS earns more reward in terms of government funding, if they cover dubious topics such as epigenetics. Are we trying to reach Lysenko through a different route?


On Joke Papers, Hoaxes, and Pirates

Good commentary by Iddo

Joke papers have been known to sneak into otherwise serious publications. Notably, in the Sokal Affair, Alan Sokal, a physicist, published a nonsense paper in Social Text, a leading journal in cultural studies. After it was published, Sokal revealed this paper to be a parody, kicking off a culture war between the editors of Social Text who claimed they accepted the paper on Sokals authority, and Sokal & others who said that this was exactly the problem: papers should be subject to review, rather than being accepted on authority. The Sokal affair highlighted the cultural differences between certain sections of the social sciences and the natural sciences, specifically about how academic merit should be established.

Another well-publicized hoax publication occurred when a group of MIT students wrote SciGEN, a program that generates random computer-science papers. One such paper was accepted to the WMSCI conference in 2005, in a non peer- reviewed track. Once the organizers learned theyve been had, they disinvited the authors, which did not stop them from going to the conference venue anyway, and holding their own session at the conference hotel.

Speaking of jokes, fictions and non-fictions, here is a quick story. Schools are starting all over USA and yesterday we attended a short session with our local elementary school teacher to know what our kids would learn over the year. She mentioned that she would teach the kids some fictional writing, and that reminded us of a Nature paper.

These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.

She also mentioned that she would teach non-fictional writing, which reminded us of an article from The Onion. It described the truth very well, and would surely pass as non-fiction writing.

Let Me Explain Why Miley Cyrus VMA Performance Was Our Top Story This Morning

Written by M. //