Organisers

Eric Westhof, University Louis Pasteur of Strasbourg and Institut Universitaire de France, France
Elena Rivas, Janelia Farm Research Campus, Ashburn, Virginia, USA

Introduction

Early on in 2001, the relevance of RNA molecules, and the potential that computational methods could have on identifying new RNA families and their function was recognised. As a result, we organised the first workshop on RNA Bioinformatics that took place in the summer of 2003, at the Foundation Center for Science of Benasque (FCCB) in Benasque, Spain.

This will be the third edition of the Benasque RNA meetings. The second workshop took place in the summer of 2006 at the same location. Benasque is a small village in the center of the Pyrenees about 300Km from Barcelona.

There are 2 key ingredients that characterise the Benasque workshops on RNA. First, we try to bring the best scientists with the newest, more advanced, and innovative methods. We do so by identifying not just the established researchers, but also the newer investigators with fresh ideas if not with a large history of research in the field. Second, Benasque is a place to work and collaborate, with facilities that promote interaction, and an inspiring nature around it. We expect to have two seminars a day, and also anticipate an undetermined number of informal and more specific talks that would be arranged on the spot according to the participants’ interests. We want to give researchers the time to explore in groups or individually the fundamental problems of RNA Bioinformatics.

These days it is hard to avoid the relevance of RNA molecules in a cell, from long– known players such as transfer RNA (tRNA) and ribosomal RNA (rRNA) to newer identified families of RNAs such as micro RNAs (miRNAs), riboswitches, or other regulatory RNAs in bacteria such RyhB. These noncoding RNAs (ncRNAs), that is RNA molecules with a proper function of their own, perform many different cellular functions from regulatory to catalytic. One of the most active areas of research since the 2003 Benasque meeting has been that of miRNAs, a very special class of noncoding RNAs of which we have already gathered an important understanding. In the same way that the large family of miRNAs (present in worms, flies, mouse, human, chicken and plants) has remained elusive until the year 2000, it is possible that other families exist (maybe smaller in size, or more restricted in phylogenetic spread) waiting to be discovered.

One key ingredient for identifying new ncRNAs is comparative genomics. Comparative genomics has played a crucial role in the identification of most of the new ncRNAs. Whether the conservation extends to a large clade (as is the case of miRNAs), or is restricted to closely related organisms (as in the case of riboswitches and other regulatory RNAs in bacteria), the amount of comparative sequence data at hand has made the task of identifying new RNAs easier. One of the main current objectives in functional genomics is the identification of the functional sequences by comparative genomics, and the identification of possibly new ncRNAs is of high scientific interest because of the possibilities that new RNAs open of novel regulatory mechanisms.

However, conservation alone is not enough to identify new ncRNAs. There is simply too much conservation in between related genomes to be able to sort out the chaff from the genes just by visual inspection of conserved sequences. Algorithms that would key on some fundamental traits of functional genes can help distinguishing functional genes from non–functional conserved sequences. For ncRNAs genes one of the more important identifying traits is secondary structure. Most of the algorithms for ncRNAs are based on secondary structure in combination with conservation. Algorithms for noncoding RNAs (quite different from those of protein coding genes) have been the subject of research by many groups working in the field. However, there is an important challenge regarding the number of RNA genes that will have to be elucidated in the near future. RNA genefinding methods predict in general many potential candidates for ncRNAs, however these methods tend to have large number of false positives. In addition, experimental confirmation of candidates generated this way tend to give a low yield of confirmed transcript. On the other hand, experimental large scale expression chip experiments are showing that large fractions of a given genome are actually transcribed. Determining the actual amount of function-directed transcription in a cell is an open problem that will benefit from having more reliable computational methods.

At the heart of all algorithms for structural RNAs there is a model for RNA folding. It is imperative that the accuracy of RNA folding increases in order to create more precise algorithms. New developments in this direction together with more crystallographic and electron microscopy data are making this area of research very promising. Another source of opportunity is presented by the new wealth of environmental data (importantly rRNA data). This kind of data is shaping up a faster and more mature type of algorithms for RNA structural alignments that need to become extremely accurate, capable of dealing with large and oftentimes incomplete amounts of data.

If in our previous research proposal for the workshop about the same subject that took place in July 2006, we were describing the situation as “a unique situation to tackle many question relevant to the field of functional and regulatory RNAs”, now we can say we are actually in the middle of exploiting our resources both in terms of genomic sequence and software tools. We are entering a new challenge to try to identify the function of those ncRNAs. For that task, we now need to refine our algorithms so that we can do structure prediction reliably; homology researches for ncRNAs that take into account the structure and are fast enough to search whole databases, and alignment algorithms for RNA structures that permit for instance the alignment of thousand of ribosomal RNA molecules obtained from environmental sampling. We will discuss in depth these challenges in the 2009 meeting.

Programme

The workshop will have a duration of two weeks. We expect to have an average of two formal seminars a day, distributed in a total of 10 working days. In addition to the formal seminars delivered by the invited scientists, we expect to have more informal talks that will spring out of the interest of the workshop participants.

Because the participants are theoreticians in the field of RNA bioinformatics, the dynamics of the workshop will be such that a substantial amount of time will be free for participants to be able to perform actual collaborative work and exchange of ideas.

This informal arrangement has worked well in the previous two meetings. At the 2003 workshop, there was no preorganisation of talks, they all spawned out of the common interests of the participants. Below there is a list of the talks that took place at that workshop. Other more informal talks were also scheduled in between. Some of them were of general interests, other consisted on small meetings amongst people interested on for instance discussing with details of a particular software package with the authors of the programme.

A list of the major talks that took place in the 2003 and 2006 workshop can be
found at http://sophia.ecm.ub.es/main/sessions.htm#2003, and
http://sophia.ecm.ub.es/main/sessions.htm#2006.

In this upcoming workshop we plan to discuss the following topics:

• RNA structure prediction
• RNA genefinding and genome annotation
• RNA homology search
• RNA–based phylogenetic methods
• Structural RNA alignments
• Specific computational tools for well–characterised RNA–gene families
• Computational tools for RNA–DNA and RNA–RNA and RNA–protein interactions
• RNA localisation
• RNA databases

Venue

The workshop will take place at the Benasque Center for Science in Benasque (Huesca, Spain) in the Spanish Pyrenees. Benasque is a small village in the center of the Pyrenees about 300Km from Barcelona. See http://benasque.ecm.ub.es/ for more information about the place, the organisation behind it, and their support to this workshop.

The Benasque Center for Physics was founded in 1994 as an initiative of three theoretical Spanish physicists (Pedro Pascual, Universidad de Barcelona, Manuel Asorey, Universidad de Zaragoza, and Jose Ignacio Latorre, Universidad de Barcelona) working together with the city of Benasque to create a summer institute for advanced research. Paraphrasing the Center’s own views, the Benasque Institute was designed in close (albeit modest) homology to the Aspen Center for Physics which is one of the centers leader in attracting researchers with the highest qualifications, and promoting collaborations amongst them. Since 1995 the center has been performing at least two workshops every summer in the field of Physics. Up to the year 2005, the center has had 1329 participants, coming from 44 different countries, which includes 23 European countries.

The location of the center and the philosophy of the local organisers provide a unique environment for interactions between researchers in a relaxing and free atmosphere. Since 2007 the Center has gone through a new expansion by constructing a new building at the same location where the old building existed.

In order to expand the scientific reach of the center, in 1999 a foundation was created, the center was renamed Benasque Center for Science, and the scope of scientific meetings to be held in Benasque was broadened.

Connections with Benasque are best handled from Barcelona. The local organisation will provide a private bus service from Barcelona to Benasque the day before the meeting starts (July 25th), and from Benasque to Barcelona the day the meeting ends (August 9th). Barcelona has a major international airport with several daily connections to the US.

The Benasque Center for Science is organised as a place to work. To such effect, all participants are offered an individual desk, a computer account, and connections for laptops. These facilities are located in the former elementary school of the village. A completely new building at the same location in the center of town will be available for the summer of 2009. In addition, the Casa de la Cultura, an independent building adjacent to the former schools is also used during the workshops. The Casa de la Cultura holds the secretarial facilities. The larger plenary seminars are also held in the Casa de la Cultura.

Benasque is a small town in which you can reach any destination by a short walk. All researchers have a key to the computer room, and can go to the center at any time of day or night at their convenience. This gives participants all the independence and the chances to organise meetings at their convenience. The town of Benasque has also to offer a large number of restaurants for the social activities of the participants.

The local organisation provides us with personnel to take care of almost all administrative chores associated with the workshop. There is also a system manager in charge during the duration of the workshop. Ten workstations are provided, and renewed yearly by Silicon Graphics to the exclusive use of the workshop participants.

Registration

Registration is now closed.