DREAM 6 competition challenges announced (parameter estimation)

mendes: 2011-06-03 03:00:00 +0000

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 COPASIā€¦ (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   

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/  


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  

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.