WELCOME

Welcome to the new software package.  The Enterprise Biology Software Project has reached its first ten-year milepost and the report uses this occasion to look back and then ahead. 

Two overarching themes - complexity and phenotypes – have become central to the ongoing effort.  Although we already know many details about how the genome codes for the parts making up the phenotype, we are only beginning to understand the extent to which the phenotype defines and is defined by complexity. 

Conventional wisdom often assumes that understanding the genome will allow us to understand biology and to revolutionize modern medicine.  Surprisingly little attention, however, is being given to understanding the underlying principles of phenotypes or to those of biological complexity.  Numerous articles - even in the popular press - repeatedly remind us that the benefits of the Human Genome Project continue to fall far short of expectations.  Indeed, the major diseases do not appear to be in decline.  On the contrary, many are reporting considerable gains in recent years.  Is this telling us that we are missing something important? 

What we need, perhaps, is a new role model, one with real-world skills and many years of experience.  Take biology, for instance.  It runs its business with great success as a grand enterprise, paying very careful attention to what happens in its genome and in all the hierarchical parts of its phenotype (i.e., its phenome).  If biology has learned how to solve its problems by taking the trouble to work out the complex relationships of genome to phenome, how can we justify devoting so much of our time and effort to just the genome?  Have we somehow forgotten that the genome is just the opening chapter of a story that is - for the most part - about phenotypes. 

Biology has figured out how to turn something simple – genes – into something complex – phenotypes.  It performs this astonishing task because it can build, maintain, and relentlessly fine-tune a massive information infrastructure.  If our goal is to become as clever as biology, then how can we do it without a comparable infrastructure?  Is this the key point that we seem to be missing?  The current report finds such questions engaging and considers what we might learn from phenotypes by merely simplifying their complexity.

The software package offers:

• A progress report.

• A complete copy of the Information Infrastructure.

• A new digital libraries for organism codes based on triplets.

• Worked examples.

• Recommendations

• Updates to programs and databases.