Data Sharing Working Group

From IMAG_Wiki

Data Sharing Working Group

Working Group leads: Jim Bassingthwaighte; Roger Mark; George Moody

Goals and Objectives

Recognizing that the interpretation of DATA and the integration of knowledge about real biological systems is the prime purpose of the IMAG working groups and the consortium as a whole, this working group is dedicated to the purpose of encouraging the development, use, and maintenance of repositories of experimental data. In particular, the goal is to facilitate the free exchange of data. The philosophical view is that good data are the basic treasures of science; such treasures should be made freely available.

"The Working Group is concerned with archiving data in forms convenient to potential users, and in developing archives that will have permanence. The PhysioNet archive, at www.physionet.org/, is a prime example; it originated for archiving electrocardiographic time series data, and has developed a large set of tools for analyzing such data. Recent efforts include the addition of data from intensive care units, very large sets of clinical physiological and pathological data."

We would like to list other archives, and therefore appreciate input from the biological science community on other archives for biological data.

"A further goal is to foster the accompaniment of models with data. Multiscale models may in fact become the entry points into data bases of physiological information, model parameters, rate constants, physical and chemical attributes of cell components and tissues, anatomic measures, kinetic rates and physico-chemical equilibria, etc. Models accompanied by the data providing evidence of validity will serve as milestones of scientific progress."

Announcements:

Jim Bassingthwaighte 7feb12: Donna R. Lochner (Associate Director, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health U.S. Food and Drug Administration 301-796-6309) announces: "FDA/ PhUSE computational science conference"

This conference, co-sponsored by FDA and the Pharmaceutical Users Software Exchange, may be of interest to some in IMAG. It seems to be geared towards manipulation of large clinical data sets for development of new drugs. Perhaps folks in the Data Sharing Working Group and maybe others would find the conference working groups of interest: "http://www.phuse.eu/css" "http://www.phuse.eu/Working-Groups.aspx"

Participants

Name	Project	Email
James Bassingthwaighte, M.D., Ph.D.	Sortware Integration between JSim and Systems Biology Workbench, Adaptive Multi-Scale Model Simulation, Reduction and Integration for Cardiac Muscle Physiology	jbb2@u.washington.edu
Daniel Beard, Ph.D.	Multi-Scale Modeling of the Heart in Metabolic Syndrome and Cardiovascular Disease, Mechanisms of Metabolic Dysfunction in Heart Disease	dbeard@mcw.edu
Roger Mark, M.D., Ph.D.	Physionet	rgmark@mit.edu
Andrew McCulloch, Ph.D.	Multi-Scale Modeling of the Mouse Heart: From Genotype to Phenotype http://cmrg.ucsd.edu, Multi-Scale Modeling of the Failing Heart for Cardiac Rysynchronization Therapy	amcculloch@ucsd.edu
George Moody	Physionet	george@MIT.edu
Bridget Wilson, Ph.D.	Mapping and Modeling ErbB Receptor Membrane Topography	bwilson@salud.unm.edu

Presentations

Thursday January 19, 2012 12-1pm EDT - Working Group Leads will moderate a discussion

TITLE: Project files: Reproducible Scientific Units.

ABSTRACT -

"In this we would address the essential close relationships amongst hypotheses (models), data, model verification (for mathematical accuracy), validity testing of model against data, parameter estimation and confidence ranges, and open sourcing of models, data, and data analyses for widespread dissemination. The JSim project file, by including data storage, the platform for model design, the technologies for the modeling analysis of data and the displays of results, is an exemplary unit for the exchange of reproducible science."

SLIDES

Friday February 25, 2011 3-4pm EDT - Working Group Leads will moderate a discussion

TITLE: Data Sharing within the MSM Community - Is it Desirable? Feasible?

ABSTRACT - Discussion Guide