Sequencing species.... by the thousands

 When I was giving my first steps in the field of comparative genomics, there was not much to think about when deciding which genomic datasets to use: one would just take them all. With only a few dozens of genomes, mostly of bacteria, one could have everything at hand, in the local disk, just need to update every couple of months by adding one or two more...

 These times have definitely passed, and now the flow of newly sequenced genomes is... well, overwhelming (see figure below, taken from Genomes Online). This is both a blessing and a curse for us doing comparative genomics, since we have an unprecedented amount of data which enables more resolution, but we are increasingly facing novel technical and analyitical challenges.

 Just to give a taste of this avalanche of genomes from different species (projects for sequencing genomes for a given species, such as the 1000 genomes is another story) that is coming, I here list some of the projects I am aware of that aim at sequencing thousands of genomes from a given taxonomic group.

• i5K: 5000 arthropod genomes
• 1000 fungal genomes
• genome 10K: 10000 vertebrate genomes  
• 10000 microbial genome project

As expected, in this kind of projects it is way more easy to come up with a bold number, than to actually define the list of species that are actually going to be sequenced. At least this is what I can tell from my involvement in the i5K initiative, in which prioritisation of species to be sequenced is not simple, since usually one wants to weigh in different criteria (phylogenetic relevance, biological, economical, and clinical importance, etc).   

 I'm sure I missed some, and, in addition, there is a growing flow of genomes that are sequenced by independent groups, including my modest own group. One common weakness of this large, and small-scale initiatives is that they sometimes come with the cost for covering the genome sequencing but do not account for the necessary bioinformatics analyses to actually make sense of the data. With the sequencing costs dropping and the potential analyses becoming more complex, the actual costs of sequencing projects will more and more be on the side of the analysis beyond the assembly and annotation phases. As a result, many bioinformatics groups are streching their resources to contribute to genomics projects without getting any specific funding.

In my opinion the planning of a sequencing project should account for all the downstream phases with their associated costs. With such an approach we may end up having a handful of genomes less, but we will definitely learn more from them. 

Watch the talks from the CRG Symposium: Computational Biology of Molecular Sequences.

 If you missed the opportunity to attend physically our past symposium on "Computational Biology of molecules" (see this past post), you can now watch the videos of the talks (read message below).

*****************

Dear all,

All contents of the 10^th CRG Annual Symposium on Computational Biology of Molecular Sequences, celebrated last 10^th and 11^th of November, are now available online.

Leading scientists in computational biology came together in Barcelona on the occasion of the tenth edition of the CRG Annual Symposium, which focused on computational biology of molecular sequences, organized by the Centre for Genomic Regulation (CRG). The auditorium of the Barcelona Biomedical Research Park (PRBB) hosted the event, celebrated from Thursday 10 to Friday 11 November 2011.

In the microsite you can find the inaugural video of the Symposium, videos of the talks, interviews with some of the speakers, participants and organizers of the event and two summary videos that capture the major points of all sessions. There are also available two articles that summarize the talks and news related to the field of computational biology of sequencing.

We hope that these resources are useful for you!

Click here to visit the 10^th CRG Annual Symposium web.

SESBE: Spanish Society for Evolutionary Biology

 Last week I went to Madrid to attend the 3rd congress of the Spanish Society for Evolutionary Biology (SESBE). This is a relatively new (7 years) society that embraces evolutionary biology as a whole, from palaeontology and systematics, to evolutionary genomics and darwinian medicine. Thus, the meetings are very diverse and one can listen to the most diverse talks, always with the common ground of evolutionary theory as a framework of analysis.

Due to other commitments, I could only stay two days but it was worth and enjoyed most of the talks and, most of all, meeting colleagues around Spain. I would highlight here the talk of Nick Lane, on the evolution of eukaryotes and the role played by mitochondrial endosymbiosis. Nick, who is also a prolific writer of popular science books, gave a very nice talk that seduced the whole audience, including me. I had the opportunity to discuss with him, and it was nice to discuss again on big theories on the evolution of eukaryotes, a big theme that I am passionate.

This year, the SESBE elected a new board, in which I will stand as a secretary. Not that I am very keen on holding such a position, but I was asked and I think one should be prepared to contribute his two cents to noble causes, such as that of this society promoting the study of evolution and its transmission  to society in our country. 

XI Jornadas de Bioinformatica in Barcelona (23-25 January)

  A short note to spread the word on the joint Spanish and Portuguese Meeting on Bioinformatics.  This is a yearly meeting that is gaining momentum every year, and it is a great opportunity to meet most groups doing bioinformatics in the region. Talks are in English and everybody is welcome to attend.

 As other years, this meeting has associated a regional (Spain, Portugal and North Africa) ISCB student symposium. This year this symposium is co-organized by, Salvador Capella-Gutierrez, one of the members of my lab. 

 If you plan to submit a communication, there is time till the end of November.

 See you there.

ALPHY 2012: French-Spanish meeting on Bioinformatics and Evolutionary Genomics (March 19 -21, Banyuls-sur-Mer)

 I am glad to announce ALPHY 2012, which for the first time is jointly co-organized by French and Spanish researchers. I was very glad to be invited by my French colleagues to sit at the organizing committe. I think it is a great opportunity to join two communities with ample experience in phylogenetics-related research.

ALPHY is an annual meeting, organized in France since 1995, dedicated to the field of Bioinformatics and Comparative Genomics (ALPHY = ALignments and PHYlogeny). The main goal of this meeting is to promote informal exchanges in this highly multidisciplinary field, and to encourage young scientists to present their work. The official invitation follows, plus a very tempting picture of the location.

This year, ALPHY is co-organized by Spanish and French scientists, in the nice city of Banyuls. There will be two invited speakers (Henrik Kaessmann and Jose Castresana), and the program will be open to contributions for 20’ talks.
The registration to the meeting is free, but mandatory. Please use the link (top left of this page) to register. If you wish to present your work, submit your abstract in the registration form.
Important dates:

• Deadline for abstract submission: January 10 2012
• Deadline for registration : February 1st 2012

Hasta pronto – A bientôt – fins aviat - see you in Banyuls!

Sad news from CIPF: the rise and fall of the "flagship" of valencian research

For those who don't know. I am originally from Valencia. There, one of the deepest traditions and the main festivity are the so-called "Falles", which in part consist of building huge temporary cardboard sculptures which are exposed for little more than a week and then burned in a big fire. For some people is hard to understand how so much time and money is invested in something that is then left to the flames.

Apparently, something similar is happening with a research centre!!!

 The "Centro de Investigación Príncipe Felipe" was created in 2005 by the local Valencian government with the idea of making it the "flagship" of research in the region. It came with a strong investment from the regional and central governments and soon attracted many scientists. I was one of the seduced scientists, who originally from Valencia, and at that time in the Netherlands was enthusiastic about a move aiming to put biomedical research in Valencia at the forefront.

 Five years after its creation, the cuts started. Crisis had hit Spanish economy and many local governments had big debts, particularly that of Valencia who has been famous for investing in huge events such as the America's cup or the formula 1 competition. When things went complicated, research was seen as one of the most superfluous thing in which a government could invest, and thus cuts were announced. This year the centre is firing 40% of the personnel, including PhD candidates at the middle of their PhD. I guess many of the remaining researchers will leave this downsized center for a better live elsewhere. The flagship is now sinking, "burned" after so much investment and efforts, the comparison to our "Falles" is unavoidable.

The whole story is reported by Nature and by many articles in the Spanish press. As Juli Peretó reports, the local government is letting CIPF fall, while keeping investing on other type of events, such as an international Golf tournament in Castelló, or increasing the funds for a motorbike circuit. This is most ironic, and deeply sad.

 I just wish the best for my many ex-colleagues that are still at CIPF and hope this is not the kind of science policy that the future government of Spain (according to polls is likely to be the same conservative party that is now governing in Valencia) is planning.

Educational video on the Tree of Life

In the blog of Jun-Hoe Lee, a former visiting student in my lab, I found this interesting video from Yale university on the Tree of Life and the efforts to reconstruct it.

  

I think it is a good piece for popular communication of science and conveys pretty reasonably well the problem. Of course, there are simplifications and some important aspects such as that of horizontal transfer of genes, symbioses, and their effects on the tree are not covered, but it provides an attractive and educational introduction to the problem of assembling the tree of life.