Boot Camp: How to Simulate and Analyze Your Cancer Models with COPASI

(September 29,2014 - October 1,2014 )

Organizers


Stefan Hoops
VBI Research Facility, Virginia Polytechnic Institute and State University
Kathy O Hara
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University
Pedro Pedrosa Mendes
Biochemistry, Virginia Polytechnic Institute and State University

Mathematical models typically start out in simple form. One writes down a few differential equations, estimates the parameters, explores the output, and checks to see if it can predict behavior reasonably well. After that, the process begins to take on a life of its own. Since the model is greatly abstracted and simplified, it captures some aspects of the system, but fails in others, so new variables and more inputs are added. Alternative mechanisms are investigated. At some point, the question arises: How can one tell if this is a good model? The aim of this bootcamp is to provide tools to answer that question. We will frame the question in a way that respects both the biology and the underlying mathematics.Two organizers of the bootcamp, Pedro Mendes and Stefan Hoops, have spent the last twenty years creating a bridge between these paradigms, in the form of a software package called COPASI (COmplex PAthway SImulator).. COPASI is a simulation software that allows one to translate the biochemical interactions between species into dynamical systems represented by the sets of either stochastic or deterministic equations. COPASI developers have created a user-friendly graphical interface, which can help researchers to apply sophisticated analytical tools to their models. This workshop provides an introduction to the ease and power of the software.

Monday, September 29, 2014
Time Session
Tuesday, September 30, 2014
Time Session
Wednesday, October 1, 2014
Time Session
Name Affiliation
Albasini Mourao, Marcio Duarte albasinimourao.1@osu.edu College of Arts and Sciences, Mathematical Biosciences Institute
Blachly, James james.blachly@osumc.edu Internal Medicine, The Ohio State University
Fessel, Kimberly fessel.6@mbi.osu.edu Mathematical Biosceinces Institute, The Ohio State University
Fuertinger, Doris doris.fuertinger@rriny.com N/A, Renal Research Institute
kanji, suman suman.kanji@osumc.edu Radiation Oncology, The Ohio State University
Kim, Jae Kyoung kim.5052@mbi.osu.edu Mathematical Biosciences Institute, The Ohio State University
Lu, Rong lu.550@buckeyemail.osu.edu Biostatistics, The Ohio State University
Meyring-Wosten, Anna anna.meyring-wosten@rriny.com Renal Research Institute, Renal Research Institute
Palanichamy, Kamalakannan pk@osumc.edu Radiation Oncology, The Ohio State University
Rezeai, Mohammad rezaei.4@osu.edu Biophysics Graduate Program, Ohio State University