ACM SIGBIO (bio-matrix definition)

Foteos Macrides MACRIDES at WFEB2.BITNET
Sun Jan 5 17:28:00 EST 1992

Tom Schneider said:
> How about posting the further information here?  How about a definition
> of bio-matrix, and some information about what people are doing on
> this topic?

Dan Davison replied:
>There are extensive Biomatrix archives on gene-server at, try
>I used to post a monthly notice but got a lot of flak about the
>monthlyness, so I gave up.

        Since it's been a lot longer than a month, and the volume in this
forum is low, below are the relevant sections of the HELP and INDEX files.


 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES at WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545

[This is a posting of a notice about the BIO-MATRIX project, its aims,
and current activities. It appears irregularly.]

BIO-MATRIX is not a database or a functional tool.  It is a concept,
evangelized by Dr. Harold Morowitz of Yale University.  The concept's
underpinnings are best described in the Final Report of the Workshop
on Matrix Biology.  I will summarize here my interpretation of
the Matrix concept.

The Matrix of Biological Knowledge is a response to the way biologists
reason about their systems.  Physicists have recourse to first
principles and in the last 20 years we've seen implications of quantum
mechanics on the cosmological scale.  The complexity of biological
systems is such that it's going to be a *long* time before one can
reason a Tetrahymena from first principles.  As each scientist thinks
about their particular system, they consciously (and frequently
unconsiously) reason about their system by analogy.  A striking
example of this appeared recently on the cover of Science; the
three-dimensional structure of _ras_ is essentially identical to one
proposed a few years before, based on what was known about a property
of _ras_, that it binds GTP.  By examining an already-determined
tertiary structure of a GTP-binding protein, they were able to make an
accurate prediction of what _ras_ would look like.

        The Matrix concept wants to organize biological knowledge so
that the predictive power of models in different disciplines can be
applied to a different, perhaps new, discipline.  Molecular biologists
have been using such reasoning for years; but what does the hydra
biologist know of the models in toxicology?  Are there any
toxicological model systems that speak to a protoist system?  I don't
know the answer, and I doubt that anyone else does either.

        The Matrix subsitutes reasoning by analogy for reasoning
from first principles.  The proposal is to combine biological
knowledge in three ways; (1) collect data into databases, and have the
agencies that fund research get serious about the proper disposition
of the knowledge they've been funding (such as requiring, as a
condition of grant funding, any resulting data to be submitted to
GenBank for nucleotide information; PIR for protein information; and
Brookhaven for x-ray crystallographic information).  (2) organize the
databases in such a way that access to them is transparent.  You tell
your MacIntosh (sp?) that you want to know all about X; the program
goes and calls MedLine, ToxLine, BRS, and whatever else...including
databases that you may not know exist... and retrieves the information
for you.  This is the knowledge base component of the Matrix (yes,
highly simpilified).  (3) Tools to help get that information even if
you don't know it's there; this is the Information Retrieval component
of the Matrix.

Requests to be added to the direct-distribution mailing list should be
sent to biosci at (BITNET: at CUNYVM)

Submissions for the list are always encouraged, and should be sent to

The BIO-MATRIX archive-server can be contacted from most networks and
can reply to all known networks (no failures yet!).  For info, send
the line
gene-server at (internet),
gene-server%bchs.uh.ed at CUNYVM (bitnet, EARN)
gene-server at uhnix1.UUCP (UUCP)
(JANET and JUNET can reach the server also, but I haven't figured out
the proper path.  Please check with your local mail wizard).


(last change 11/24/91 dbd)
The bio-matrix archives consist of:

87matrix.       (NOTE THE "." IN THE NAME!) 1987 Bio-Matrix posings
88matrix.       (NOTE THE "." IN THE NAME!) 1988 Bio-Matrix postings
matrixreport    (NOTE THE "." IN THE NAME!) 1987 Bio-Matrix Workshop Report
                                                               (draft copy)
limb1           LiMB v. 1.2 part 1
limb2           LiMB v. 1.2 part 2
limb3           LiMB v. 1.2 part 3
limb4           LiMB v. 1.2 part 4
limb5           LiMB v. 1.2 part 5
limb.overview   Introduction to the Listing of Molecular Biology Databases
limb.readme     LiMB README file

matrix-bib.bib Peter Karp's Matrix BibTeX bibliographic db
matrix-bib.txt Text form of matrix-bib.txt  Postscript formatted version of P. Karp's biblograph.
               5/13/91 version

   1071 Aug 10 15:52 README-aarep  L. Hunter's amino acid
  13426 Aug 10 15:52 aa-bitstrings.lisp  datastructures -- see
   8985 Aug 10 15:53 aa-representation   README-aarep for details
 151243 Aug 10 15:52   The CABIOS paper.

aimb-db-form  "-form" is the fill-in registration form
aimb-db.el   elisp code  Larry Hunter (LHC-NLM) listing of AI and molecular
aimb.notice         molecular biology researchers, interests, addresses,
aimb.readme         e-mail, 10/24/91 version, don't know why the dates
aimb.text.11-23-91   are wrong
   6438 Nov 24 21:48 aimb-db.el   Updates to the AI/MB database
  64823 Nov 24 21:48
   1984 Nov 24 21:49 aimb.ftp-sample-session
   3342 Nov 24 21:49 aimb.readme
  82998 Nov 24 21:48 aimb.text.11-18-91
  78802 Oct 24 21:56 aimb.text.11-23-91

These files are retrieved using the "send matrix xxxx" command, where
"xxxx" is the complete name of one of the above files.

More information about the Biomatrx mailing list