The Dialogue for Reverse Engineering Assessments and Methods, has announced its annual competition: DREAM 6.
Dear COPASI users, many of you are interested in parameter estimation therefore may be interested to know that the Dream Project has announced their yearly reverse engineering challenge. They have 3 challenges available that teams can compete for; one of the challenges is to estimate parameters of a gene regulatory network.
This year the Dream Project introduced a novelty: a limited data set is supplied and teams should use their results with that data set to request data from subsequent experiments (but can only ask for a limited set of new experiments). So this does actually mimic how one would carry out parameter estimation in the real world!
The gene regulatory network is supplied in several formats, including SBML, so you can use COPASI directly to compete in this challenge. I think there may be a few entries using COPASI… (and a little bird told me that they may also have used COPASI to generate the data)
The call for DREAM 6 is reproduced below:
Call for Systems Biology Predictions DREAM6: The 6th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS Dear Colleague, We would like to invite you to participate in the following DREAM6 challenges 1. Estimation of Model Parameters Challenge - Infer the kinetic parameters of three gene regulatory networks by iterative optimization and experimental design 2. Alternative Splicing Challenge - Reconstruct the alternatively spliced mRNA transcripts from short-read mRNA-seq data 3. Gene Expression Prediction Challenge - Predict gene expression from promoter sequences in eukaryotes There maybe an additional challenge, to be announced at a later time. To access the data sets, and descriptions of the DREAM6 challenges, please go to http://the-dream-project.org/challenges The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM6 conference. To learn more about the DREAM project and the upcoming DREAM conference, please go to http://the-dream-project.org/ Sincerely, DREAM6 Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Julio Saez Rodriguez, Sys Bio Dept, Harvard University Robert J Prill, IBM Research Pablo Meyer, IBM Research Kely Norel, IBM Research follow the DREAM project on twitter @DR_E_A_M http://twitter.com//DR_E_A_M DREAM is a Dialogue for Reverse Engineering Assessments and Methods. Its main objective is to catalyze the interaction between experiment and theory in the area of rigorous assessment of systems biology prediction methods.