Computational Biology in Argentina

Abstract

Computational biology is an interdisciplinary science bred from fields as disparate as mathematics, chemistry, statistics, physics, biology, and computer science. Although the exact definition of computational biology is far from being precise and unambiguous, it is a fact that hundreds of scientists around the world have been increasingly using skills from the above-mentioned fields to approach different biological questions. It is not our aim to elucidate here the definition of computational biology and its differences from related fields such as bioinformatics. However, to review the state of this discipline in Argentina, we need at least a working definition. In this sense, any interdisciplinary research in which the main interest is in studying biological problems and where the working hypothesis can be tested by means of simulation and computational modeling will be considered as belonging to the computational biology field or at least as employing a computational biology approach. It is interesting to note that computational biology research can be implemented in two different ways depending on how the “interdisciplinary” nature of this field is assembled. On one hand, a scientist with formal training in a given field (for example, a molecular biologist) could acquire other skills (such as programming or mathematical training) in his attempt to answer a given biological question. Alternatively, working teams made up of members specializing in different fields may work together to reach a scientific explanation of a problem. We think that the first approach is more common among the scientific community because it depends entirely on the scientist's desire to discover an explanation for their problems and on their capacity to explore different areas of science. The second approach is generally dependent on the availability of research and development programs, funded by public or private resources, that favor collaborations between different research institutions to form multidisciplinary teams. We will see that the first approach is more common in Argentina. This paper summarizes the state of the art of computational biology in Argentina. Our aim is to offer as broad a view as possible of the different groups of scientists and their main research interests. Also, we present a brief review of educational, research, and development policies related to the field. We hope that this review may encourage overseas researchers to contact and collaborate with Argentinean teams, as well as organizing and facilitating the exchange of information between researchers in our country. However, this review will probably be far from complete, due to the lack of centralized information on computational biology, and for this reason we apologize for any potential omissions. (For author information, see Box 1.) Box 1. Authors' Biographies Gustavo Parisi, Ph.D., is the Structural Bioinformatics Group leader and professor at the Universidad Nacional de Quilmes, Buenos Aires, Argentina. He is also a researcher at the Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET). For his Ph.D. thesis, he developed a model of protein molecular evolution which takes into account protein structure to simulate sequence divergence. His principal research interest is focused on the introduction of evolutionary information in the development of bioinformatics tools to study protein structure. Virginia Gonzalez, a graduate student in biotechnology, is part of the Structural Bioinformatics Group at the Universidad Nacional de Quilmes, Buenos Aires, Argentina. She is a member of the DNALinux developer team and is currently working on her doctorate in Sequential, Structural, and Dynamic Characterization of Allergenic Proteins. She is also part of the Latin America Solanaceae Genome Project (LAT-SOL) working on the sequence annotation of the tomato mitochondrial genome. Sebastian Bassi worked for five years as a genome database curator at Advanta Seeds, a plant biotechnology company. He was in charge of the molecular marker database for all crops in the enterprise. He is the leader of the DNALinux bioinformatics distribution and has developed several Web-based utilities for bioinformatics analysis. He is part of the developer team for Biopython (http://www.biopython.org/), and is currently writing a book on Python for Bioinformatics and doing bioinformatics support for the tomato mitochondrial genome sequencing project, which is part of the Latin America Solanaceae Genome Project (LAT-SOL).