GenomPort, a panoramic journey across the chromosomes of the human genome

Dr. Xavier Messeguer and Bernat Gel are part of ALGGEN, a subgroup of the Algorithms, Biocomputing, Complexity and Formal Methods Group, ALBCOM. Dr. Messeguer team focuses on bioinformatics and genetics research. ALGGEN has led more than fifty degree projects in Computer Engineering and several PhD Thesis during the last six years.  Dr. Messeguer likes working in collaboration with other centres, such as the Scientific Park of Barcelona, the Biomedicine Research Park, Barcelona University, Pompeu Fabra University or the Vall d'Hebron Hospital, among others. Usually, a biology and genetics research group would felt blocked by a computing problem. This is then when they get into contact with researchers at ALGGEN. They typically require their help to develop software that fits their necessities. ALGGEN research is based on computational methods to help biological research develop faster. This is also the case for GenomPort, the environment for exploration and research of the human genome for which they have been awarded.



Dr. Josep Fransesc Abril, from Barcelona University, proposed to ALGGEN the idea of developing a genomic visualizer using  similar tools to the ones Google uses in their extremely popular Google Map or Google Earth applications. The PhD student Bernat Gel chose this challenge as the subject for his PhD research under Dr. Messeguer supervision, little after Dr. Abril's proposal.

Until now, all the genomic initiatives showed a genome by parts. Therefore, it was very hard to get a global idea of it or to access to all the information related to it.  One of the main successes of the project GenomPort is to be able to represent all the genome in a easy to use way. Data actualization speed on screen has been one of the challenges they have had to face. This project does not represent a biological improvement, but, instead, it is a huge improvement in the speed of genetic information visualization, the integration of genomic information and the connection with a friendly easy to understand, adaptable user interface.

This project works with enormous databases and strives to reach optimal visualization. In fact, you will be able to consult anything about genes with the help of GenomPort. The system responds to different information levels depending on the user's request. Working this way, you can get a faster graphic answer.  So, it manages different levels of content and detail, with different layers and zoom levels in order to be understandable both to a secondary student and to a genetics PhD student.

Another important aspect of the project is its presentation technology. You can see the prototype of the project to get a better idea of it. There you can experiment by yourself: http://gralggen.lsi.upc.edu/recerca/genexp/. GenomPort could be called the new Genomic Google Map. It is freely accessible and is high quality software.

Finally, GenomPort opens up the possibility to pharmaceutical or biochemical companies to announce their products on the genetic section they are interested in. With this proposal, GenomPort becomes a tool with several application domains. First, it is a very useful tool for biologists, as a human genome library online; secondly, it is a computer challenge due to all the issues related to fast representations and friendly interfaces and, finally, it allows the creation of a social network around the human genome formed by laypeople interested in the relation of their health to their genetic structure. It is also a tool for company marketing.

At the moment, the team lead by Dr. Xavier Messeguer has chosen to work on its project by researching about how to attain a high level of depth and detail. They have developed it at the maximum level of detail and information for just a few chromosomes. They would like to get more financing, support and recognition in order to be able to go on with the project on a broader level, eventually giving the same level of detail for all chromosomes.

Fortunately this support has not taken long to arrive. On the last 23rd of May, GenomPort won the BDigital Global Congress prize, which meant some financial support for the project. On the other hand, it also got the support of CitiLab Cornellà which helps researchers and collaborates on the construction of a cyber-infrastructure project related to creating communities of citizens interested in being better informed about health issues and in giving support to other -possibly ill- citizens and the research groups that work on the corresponding diseases.

Although GenomPort is just at its beginning, we are sure that it will be a revolution for the genetic field and a big success at many levels. The research group ALGGEN is now an expert group in the development of software related to genetics. You can see that this in their past projects like PROMO which works with transcription factors or MGCAT, a program to visualize genomes ...etc.


ilapuente@lsi.upc.edu