Dear participants In the challenge description we wrote that all participants who "outperform simple baseline methods will be invited as Consortium co-authors". We now found it difficult and somewhat arbitrary to choose any specific baseline method that would be used to exclude teams from the consortium. Moreover, we believe that the contributions of all teams were important for the success of the challenge. * We have thus decided to invite all teams with valid final submissions to be part of the consortium and the joint paper. * Teams joining the consortium/paper are expected to be responsive to any questions we might have concerning their method and, if necessary, improve their write-ups according to our feedback. * For now, you don't need to take any action. We are still busy with the analysis of results and have not yet started writing the manuscript. Once we shift to writing mode (likely in February), we will contact you and also share the manuscript draft for your feedback. We wish you a great holiday season, Daniel & Sarvenaz

Created by Daniel Marbach daniel.marbach
PS: Regarding the schedule, our aim is to submit the main challenge paper before summer.
Dear Anaïs We encourage participants to write papers about their methods, results and additional analysis you might have done with the shared data. You have two options, described below. Either way, please contact us by email once you have specific plans to write a manuscript or a draft. We would be happy to give you feedback and coordinate to find the best publication strategy. 1. Submit to our partner F1000 Research as a DREAM companion paper (please contact us for detailed submission instructions). This has the advantage that: * The publication of your paper can be coordinated (at the same time) with the main paper, thus increasing visibility (we can cite you in the main paper) * Your paper will be part of the DREAM channel of F1000 Research, together with other DREAM papers * --You can submit to F1000 Research (*but not to another journal*) *before* the main paper is accepted (F1000 Research will delay publication until that of the main paper)-- ** SUBMISSION TO F1000 RESEARCH CAN ONLY OCCUR ONCE THE MAIN PAPER IS PUBLISHED, SEE [THIS POST](https://www.synapse.org/#!Synapse:syn6156761/discussion/threadId=1504) ** 2. Submit to your preferred journal *AFTER the main challenge paper has been accepted for publication*.   Regarding content, the main challenge paper focuses on the description of the challenge (data, scoring, etc.), the best performing methods, consensus/ensemble predictions across teams, and analysis of strengths and weaknesses of different types of methods (see the [Wisdom of crowds paper](http://compbio.mit.edu/marbach/papers/Marbach2012b.pdf) for an example of a main challenge paper). The companion papers should focus on specific types of methods and detailed discussion of your results. Of course, you can also briefly describe the challenge so that readers understand your results without having to read the main paper first, and you can also include results from the challenge (e.g., to compare your results to that of other teams). But if you have a general analysis of challenge results/module predictions that is not focused on your method or results (e.g., a novel meta predictor combining modules across teams), you should coordinate with us -- companion papers are not supposed to duplicate the overall challenge analysis of the main paper (we could consider to feature such results in the main paper, with a more detailed description in a companion paper, for instance). Best Daniel
Dear Daniel and Sarvenaz, Thanks for the update. One quick question: how do you see the balance between the joint paper and putative F1000 method-specific papers, in terms of both content and schedule ? Anaïs
Some of the teams did not provide a link to their write-ups, we kindly ask them to complete their write-ups and add the link to the following google doc: https://docs.google.com/spreadsheets/d/1WLW2nEgUMoAUlRaOiMsu21EDMPFoGV2uMmVQUVhz4ik/edit#gid=0 Thanks

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