Metagenome Sequence Simulators

Richter DC, Ott F, Auch AF, Schmid R, & Huson DH (2008). MetaSim: a sequencing simulator for genomics and metagenomics. PloS one, 3 (10) PMID: 18841204


An article from the Huson's Group at Tübingen University has just came out in the Open Access (and scientific publishing innovator) journal PLoS ONE, describing MetaSim, a software to produce artificial or syntetic or in silico metagenomes out of a selection of completely sequenced genomes.

This is just "heaven-sent" for me since I've been working on a set of syntetic metagenomes for the past two months, and will be happy to use this software first hand like... today. It seems that the software not only lets you choose the source genomes from a phylogenetic tree (figures reproduced here from the original article al PLoS ONE thanks to the Creative Commons License), but also choose from three different type of sequencing technology output (Sanger, 454 and Illumina) and generate theorethical metagenome.

This is the continuation of a very important change in genomic sciences, moving from experiments far too expensive or long to be replicated and hence out of hard statistical comparision, to null-model based in silico genomic analysis.

The first effort to analyze the true scope of metagenomic analysis was presented by Kostas Mavrommatis and others from the Genome Biology group at JGI (unfortunately published in an non-OA journal), where they produced three simulated metagenomes of contrasting complexity to asses assembly, gene prediction and annotation (SPOILER: the best combination assesed was Arachne assembler with Fgenesb predictor and PhyloPhytia for binning, and BLAST "performed poorly" as usual). This work also produced a database for the Fidelity of Analysis of Metagenomic Samples (FAMeS), a great effort to standarize metagenomic analysis software. A great alternative is ProxyGene annotation, as reported by the Markowitz group.

Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, & Kyrpides NC (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature methods, 4 (6), 495-500 PMID: 17468765

I'll play a little with the software and post some of my impressions here... and maybe in the original PLoS ONE webpage since it is totally open to post-publication review!!!!

You can download MetaSim at Huson's Labpage!!!

Novel Justice on HIV from Nobel Prize

Well I might be a bit late for this post but... The Nobel Prize for Physiology or Medicine 2008 went viral and was granted this Monday to three scientists from the viral research line: 1/2 prize was granted to Harald zur Hausen, for discovering human papilloma virus as a cause of cervical cancer; and another 1/2 (that is, 1/4 each) to Françoise Barré-Sinoussi and Luc Montagnier, for the discovery of the HIV virus.

Now, it's great that the Nobel recognizes the outstanding labor of researchers around the world. And I won't go into how this turns into courthish or royalty-like in science. The really GREAT thing is that this could be read like the final word on the "controversy" around who really had the credit for the discovery.

That is, Montagnier's lab had already reported in Science (with Barré-Sinoussi as a first author) the isolation and initial characterization as a T-lymphotrophic retrovirus from a single AIDS patient. They also linked it (or the family it belonged to) to AIDS.

Robert Gallo (the discoverer of the first human retrovirus in 1980) had been searching for the viral causative agent of AIDS for a while, and wanted to link it to his already discovered HTLV virus. He had already assigned multiple functions to this virus and wanted it to be also the cause of AIDS. He actually reported the dicovery of his so-called HTLV-III virus as the causative agent of AIDS in a Science special issue. He basically reports the methodology to study HTLV-III viruses, the presence of the virus in AIDS patients, and the presence of antibodies against the virus in AIDS patients.

So, what's the problem with this? Well, it started when Gallo asked Montagnier some samples and data. Then, during Gallo's press conference, he used an image from Montagnier's virus. Just after the press conference, he filed a US patent on the detection tests. The French complained (!) and led to a large and mediatic dispute that was partially settled when Reagan and Chirac agreed on sharing the credit AND the money...

In 1993, an article by Sheng-Yung Chang and collaborators analized the archived samples from both l'Institut Pasteur and the Laboratory for Tumor Cell Biology, and found that out of six HIV variants found in Gallo's lab, none of them was similar to the one he isolated. In contrast, they were identical to the french isolate. And though they politely described it as "a contamination", it seemed quite clear (at least to me) that Gallo couldn't find the virus he wanted to find in his own samples, and so took the french virus and turned out to be the one he was looking for.

Recently in 2002, they tried to settle things up (and clean a stain in the history of science on the "mine's bigger" credit) by a collaborative publication by both Gallo and Montagnier. I don't think the peace-making settlement received as much attention as the dispute, as usual.

So, 25 years and an international agreement later, the French are acknowledged by the elite of the scientific community as the discoverers. On interview, Montagnier and Barré-Sinoussi credit Gallo. Diplomatically, Gallo congratulated the french.

Hope all the people in Africa benefit from this tangled web of credits and money.

(And before anyone makes an attack on this... 1) Without Dr. Gallo's research, no HIV virus could have been linked to AIDS; 2) HIV isolation and discovery's credit goes without doubt to Montagnier's; 3) As persons, I equally dislike both scientists, specially after quarreling about who would earn the most out of people's diseases).

Atheists of the world, come out of the closet!!!!

Here's a talk that Richard Dawkins gave a while ago (2002) during a TED conference. It is mainly about defending atheism. You can download it at the TED talks site. A wonderful quote:

"...teach your children evolution in biology class and they'll soon move on to drugs ... and sexual perversion..."

I would also love to recommend his new book, God's Delusion (check the wiki), where he makes his point on not being ashamed about being an atheist while also pointing out all the horrors fueled by religions (YES, with "s" of "plural). I might not totally agree with the rationale, but I definitively agree with the general idea. And... you gotta love the guy!

Hope there's some discussion on this...