DREAM Community
October 9, 2014

Stories

DREAM Challenge Community Stories – Our “Wall of DREAMers

We asked DREAM Challenge Community – Participants and Organizer –  to share with us their experiences with the DREAM Challenges over the years.  This “Wall of DREAMers” has pretty cool examples of our DREAM Challenges’ community at work using DREAM Challenges for education and research.

July 4, 2015

Daniel Marbach

Daniel MarbachIn the first edition of the DREAM challenges in 2007, I was a participant and best performer. Subsequently, I designed and led three editions of the DREAM network inference challenge (2008, 2009, 2010). Currently, I’m co-leading the DREAM gene essentiality prediction challenge. My involvement with DREAM has been a central part of my PhD thesis and postdoctoral work. I will continue my engagement with DREAM in the future to help promote open and collaborative science through crowdsourced challenges. Through my involvement with DREAM I changed my research focus from trying to show that my own methods work best, towards unbiased method assessment and creation of useful resources for the community. This work led to several highly cited papers that helped advance my academic career.

October 22, 2014

Kevin Yip

When I participated in the DREAM3 in silico network reconstruction challenge, I had very little experience in reconstructing TF-regulatory networks (I was focusing on protein-protein interaction networks at that time). Given the many sophisticated methods existing at that time, I just hoped to participate and get some experience in this topic. However, perhaps because I was new to this topic, my method was apparently quite different from the other methods, and it seemed to put more emphasis on a new type of features (expression change due to perturbation) than the other methods, which turned out to be very useful. It has helped me to always ask if there are better features to use or better ways to use the existing features before drilling deep into improving subtle details of existing methods. I think this experience has guided my way to dealing with new problems.

October 19, 2014

A DREAM Participant from 2008, 2009, 2010 & 2013

The DREAM challenges have provided a platform to understand network inference algorithm behaviors and experimental data characteristics, unlikely to be as productive if done by individual researchers or labs. This provides an opportunity to evaluate ones work more objectively, in addition to the peer-review system.

DREAM Challenges have greatly influenced the research activities in our lab. We studied the performance of our algorithms in DREAM3,4,5 for their inherent limitations. This led to the design of a novel algorithm in 2010 now called FunChisq that claimed a best performer in DREAM8 network inference challenge. Without DREAM challenges, it would have been unlikely for us to invent the algorithm and even more unlikely to appreciate its power on diverse experimental data.

October 18, 2014

A DREAM Participant from 2010 & 2011

Thanks to the DREAM challenge on PBM data I got acquainted to the data, and more than half of my PhD thesis was on this technology and the field of high-throughput. Through the DREAM challenge I got familiar with protein binding microarrays. Analyzing the data of this technology was more than half of my PhD thesis.

September 13, 2014

Neta Zach

I am the CSO for  Prize4Life.  I first got involved with DREAM challenge in 2011, when we started the planning together the 2012 DREAM Phil Bowen ALS Prediction Prize4Life Challenge. The prize have attracted over 1000 of solvers from all over the world (63 countries) , almost all of them with no prior involvement in ALS research, and generated solutions that can substantially improve the development of novel treatments for ALS. It was truly inspiring- We felt as if for a rare disease like ALS, we really opened the door for a new type of research, that it the first intersection between state of the art computational research and ALS research, the first time such computational tools were widely used for accelerating the development of ALS treatments.

Now we want to create even more exciting solutions, with even more data for the DREAM 10 ALS Stratification Prize4Life Challenge launched on June 23, 2015!.

October 17, 2013

Prostate Cancer Challenge Team Stories

The Prostate Cancer DREAM Challenge has been highlighting the top performing teams at the end of each leaderboard rounds. To learn more about these teams we asked a few questions about their experiences with the DREAM Challenge. These profiles bring names and faces of this part of the DREAM Community to life. (Read more)

Now that the Challenge is over we honor the top performing teams for each sub challenge.  We have profiled each of these teams. Read their stories.