Evolution, Bioinformatics and Evolutionary Bioinformatics Online

E volutionary Bioinformatics Online enjoyed a busy and productive fi rst year in 2005, capped off by being accepted by the Literature Selection and Technical Review Committee at the National Library of Medicine in the US, for inclusion in PubMed Central. This means that EBO will be indexed online in this internationally preeminent archive. A brief history. Evolutionary Bioinformatics Online was established as the offi cial journal of The Bioinformatics Institute, a joint-venture between the University of Auckland, situated in New Zealand's largest city, and AgResearch, New Zealand's largest Crown Research Institute. Allen Rodrigo, Professor of Computational Biology and Bioinformatics, is the Institute's Director, and it was at his initiative that the journal was established. Rodrigo, The Institute, and I all work with Libertas Academica, a publishing fi rm committed to high editorial standards and open access publishing methodologies, to produce the journal. We are fortunate for the help of an impressive editorial board (http://www.la-press.com/ EBO-edboard.htm), and our acceptance into PubMed Central in our fi rst year refl ects the board's reputation and high standard of submissions accepted for publication. The contents of our Volume 1 gives some views of where our fi eld is now: papers on phylogenetics, genetic databases and software for managing and exploiting them, gene regulation, and proteomics. These papers show how evolutionary biologists are working with researchers in these areas to begin to produce working pictures of how genomes and gene-regulation evolve. This situation will only grow more complex as more and more species are characterised at the whole-genome level. New architectures and technologies for building very large trees — grid computing, supertrees, and parallel algorithms for tree building – will be needed, as will software for conducting comparisons among them. Looking ahead what topics might come to dominate future volumes of the journal? My sense is that from the beginning just described, a big challenge for evolutionary bioinformatics is to begin to unravel the evolution of phenotypes. This means understanding networks of genes, their topological properties, how the networks evolve, how their genes are regulated and, fi nally, how these wired-up and regulated networks produce the phenotypes we see. This is the real evo-devo (evolutionary developmental biology) we have been waiting for. It will depend on good phylogenies, good models of sequence and protein evolution and on the efforts of the armies of people annotating genes, and studying their expression with such technologies as …