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Thanks for the biomodels updates, they are very welcome.

I would like to make one comment on the paragraph on Heinrich and MCA. The
paragraph suggests breakthroughs in MCA in the late 1980s. Perhaps the
paragraph is referring to work done by Heinrich in the late 1980s?
Significant take up of MCA however began with work by Hans Westerhoff and
Bert Groen in the very early 1980s when they measured the control
coefficients in oxidative phosphorylation and showed that that wasn't a rate
limiting step in ox phos but that control as shared (J Biol Chem. 1982).

Herbert Sauro
University of Washington
Seattle

-----Original Message-----
From: biomodels-bounces at ebi.ac.uk on behalf of Nicolas Le Novere
Sent: Tue 6/5/2007 3:53 AM
To: biomodels at ebi.ac.uk; sbml-discuss at caltech.edu; sysbio at
caltech.edu; cellml-discussion at cellml.org
Cc:
Subject: [Biomodels] Eight release of BioModels Database

Hinxton, tuesday June 5th 2007.

Dear colleagues,

We are pleased to announce the eigth release of BioModels Database, in
memoriam Reinhart Heinrich.
(A summary of Reinhart Heinrich contribution to Systems Biology can be
found at the end of this announcement).

This new release sees the the addition of 34 models, 27 entering the
curated branch. That brings the public version of BioModels Database
to 7684 reactions. As usual, a significant portion of the annotation
of existing models has also been uptated. The database now features
5330 cross-references.

BioModels Dababase can now be accessed programmatically through
WebServices. You can currently get all the models, or query the
database by publications or person in order to obtain a relevant
subset of models. We welcome any suggestion for new services.

A new search system has been implemented to explore the content of the
SBML elements <name> and <notes>, using text indices generated by
Lucene. This replacement of the ancient system, an XML database using
Xindice, is faster and more robust.

Thanks to our collaboration with the group of Jacky Snoep, most of the
models in the curated branch can now be simulated online using JWS
Online.

Finally, with this release BioModels Database switch to the new EBI
website look and feel. In particular, the generic search form on the
top of each page allow-you to search all the resources of the EBIat
once (including BioModels DB).

For more details on this release, please consult:
http://www.ebi.ac.uk/biomodels/release_05June2007.html

BioModels Database is developed by the teams of Nicolas Le Nov??re
(EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA)
in collaboration with Upinder Bhalla (DOQCS, National Center for
Biological Sciences, India), Herbert Sauro (Keck Graduate Institute,
USA), Hiroaki Kitano (Systems Biology Institute, Japan), Hans
Westerhoff and Jacky Snoep (JWS Online, Stellenbosch (ZA) and
Manchester (UK) Universities), as part of the BioModels.net
initiative. BioModels Database development has benefitted from funds
of the European Molecular Biology Laboratory (Le Nov??re team), the
National Institute of General Medical Sciences (SBML team), and the
DARPA (Sauro team).

A big thank-you to all our collaborators and submitters!

--
The BioModels Database team

"Systems biology studies the cellular networks and their regulation
by combining various types of experimental investigation with
mathematical description and analysis. Though it appears to be a
rather new scientific field, it is based to a large extent on
theoretical work done in the last century.

Among the pioneers of a theoretical analysis of biochemical networks
was Reinhart Heinrich (1946-2006). Together with Tom Rapoport (and
independently of Henrik Kacser and Jim Burns at the same time) he
introduced the concept of metabolic control analysis in the early
1970s. This concept was initially largely ignored, but had a
breakthrough in the late 1980s. It changed many concepts of
biochemists about regulation in metabolic systems, especially the
idea of a rate-limiting step. The investigations were part of a
broader project to understand erythrocyte metabolism in sufficient
detail to simulate their behaviour accurately. Later, Reinhart
contributed substantially to the advance of the field by studying
optimality in biochemical networks, metabolic oscillations, membrane
processes, and quantitative properties of signalling processes as
well as a number of different theoretical problems associated to the
dynamical behaviour and to the biophysical properties of cellular
reaction networks. eside the intellectual originality, the
accurateness and thoroughness of his studies shall remind us that
comprehensive and fast accumulation of data is just one side of the
coin in scientific research, but that careful analysis based on sound
theoretical concepts is necessary to turn the collection of data into
knowledge.

[Heinrich R, Rapoport TA (1974) A linear steady-state treatment of
enzymatic chains. General properties, control and effector
strength. Eur. J. Biochem. 42: 89-95 - MedLine]

Edda Klipp - Berlin, 30 May 2007"

Several models of Reinhart Heinrich are present in BioModels Database,
such as BIOMD0000000039 (calcium oscillations), BIOMD0000000084 (ERK
cascade), BIOMD0000000090 (respiratory oscillations), BIOMD0000000104
(metabolic pathways and gene regulation).



--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nlenovere at hotmail.com
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• [cellml-discussion] [Biomodels] Eight release of BioModels Database, Herbert Sauro, 06/06/2007

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