MONOD version $Version$
The Modeler's Notebook and Datastore
(c) 2003 The Molecular Sciences Institute
http://monod.molsci.org
monod@molsci.org

Monod is a web-based environment supporting collaborative work by
scientists studying complex biological systems.


A number of possible development paths are on the table for future
versions of Monod.  Perhaps the largest immediate need is for individual
instances of Monod to be able to communicate with each other (with
appropriate security precautions, of course).  Doing this with a
peer-to-peer architecture would allow the growth of a network of Monod
servers in different labs; a user could then work with an integrated
view of all the data in the Monod network.

We also foresee some level of integration with related products with
complementary functionality, such as simulators and graphical pathway
editors.  This may be done to some extent via OAA and/or SBML.  We feel
that these standards are not yet mature enough, however, to take full
advantage of Monod's features.  In particular, future communication
protocols and languages for integrating biological research software
must include mechanisms for:

* Global object identifiers
* A general ontology, at least to map between different nomenclatures
* Distributed transactions
* Efficient network-wide search mechanisms
* User authentication and permissions control
* Revision control

Lacking open standards that meet these requirements, we can in the
meantime undertake specific integration projects on a case-by-case
basis.  That is, two or more products can be integrated at a lower level
of their respective architectures, e.g. directly in code, rather than
through standardized network protocol.  It may be possible, for
instance, to modify BBN's BioSketchPad to interact with Monod directly
through Enterprise Java Beans.

For further discussion of these matters, please subscribe to the
monod-discuss mailing list, by sending a message to
monod-discuss-subscribe@molsci.org.