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<h1>FIG: The Fellowship for Interpretation of Genomes</h1>

FIG is a nonprofit organization devoted to providing support for those analyzing genomes.
Sequencing of genomes is laying the foundation for advances in
science that will dramatically reshape our society.  These advances
will initially occur in medicine, agriculture, and chemical
production, but in the long term the impact will be pervasive.  The
computer revolution started by impacting payrolls, but eventually
allowed man to travel to the moon.  Similarly, the biological
revolution is beginning by reshaping the life sciences, but this will
surely not be the the whole story or even the most significant
The interpretation of genomes will constitute the most exciting and
most significant science of the century.  By rapidly advancing our
understanding of life, how it arose, and how it continues to change,
we will acquire the tools that will allow us to better understand and
improve our existence.  Understanding will begin with relatively
simple forms of life -- unicellular organisms.  While the central
mechanisms of life are shared by both these organisms and the most
complex animals and plants, they also contain a remarkable diversity.
They have an immense amount to teach us about life itself, and we will
need to master these lessons before full understanding of complex
genomes will be achievable.
The Fellowship for Interpretation of Genomes will focus on
organizing the data needed to support interpretation of genomes,
providing the infrastructure needed by the world community in its
efforts to achieve understanding.  In addition, we will ourselves pick
specific, critical problems and attempt to actively participate in the
unravelling of the secrets within these amazing entities.  It is only
by merging the work of building infrastructure with the applications
that use it that we will more deeply understand what is needed at each
FIG was started in May, 2003.  The founders were Michael Fonstein,
Yakov Kogan, Andrei Osterman, Ross Overbeek, and Veronika Vonstein.
An early position paper began with the following comments:

<b> The FIG Architecture: the Seed</b><br><br><i>

We begin with the "seed" of FIG.  The seed contains the essential,
basic elements that are needed to sustain a scalable integration of
thousands of genomes.  The later parts of this document will attempt
to offer precise notions of what makes up the seed of FIG.  I will
cover the basic types of objects, make comments on what extensions
will be needed to support hundreds of thousands of genomes, and offer
an implementation plan.
However, before we go into such detail, some broad notions should be
discussed.  The idea of integrating hundreds of thousands of genomes
needs some clarification.  Indeed, what is meant by integrating a
bunch of genomes, no matter what the number.  In my mind, the notion
of integration is essentially "maintenance of notions of neighborhood,
allowing forms of access that can be used to easily explore
connections and comparisons between data from numerous genomes".  This
may be viewed as a complicated way to say "a framework to support
comparative analysis".  To be a shade more precise:
       Genes from a single genomes are often "functionally related" in
       that the participate in implementing a single pathway or
       subsystem.  For any single gene, the "functional neighborhood"
       of that gene is the set of genes that are functionally related
       to the gene.  To support access relating to this notion of
       neighborhood requires an encoding of the cellular machinery
       (e.g., pathways).

       Genes that occur close to each other on a chromosome may be
       thought of as "postionally related".  The set of genes that are
       positionally related to a given gene amounts to the "positional
       neighborhood" of the gene.  One of the huge payouts of
       integrations to data has been based on a correlation between
       the neighborhoods imposed by "functionally related" and
       "positionally related" in the case of prokaryotic genomes.
       Genes from one or more genomes that share a common ancestor are
       called "homologous".  Homology induces yet another notion of
       neigborhood.   One can build more restricted neighborhoods upon
       this basic concept.  Thus, I tend to think of a protein family
       as a set of homologous genes that have a common function (a
       very imprecise notion, I grant).  Maintenance of protein
       families will, of course, be an absolutely essential part of
       effectively integrating many thousands of genomes.
       Sets of very closely related genomes may be viewed as a
       neighborhood (i.e., the neighborhood of a genome becomes a set
       of closely related genomes).  One can layer a notion of
       "variation", including SNPs, on the notion of closely related
       genomes, and then whole frameworks for exploring minor
       variations become possible.
The power in an integration arises from mixing the different notions
of neighborhood.  The tools for supporting effective use of a variety
of comparative notions constitute the computational framework for
comparative analysis, which is often abbreviated to the notion of
FIG will offer the key services required to architect and implement a
comparative framwork for interpreting genomes.
We will add more detail as the story of FIG emerges.

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