December 3 and 4, 2007

New York Academy of Sciences

New York, NY

Registration to the DREAM2 conference is open. Registration is processed by the NY Academy of Sciences.

The program of the 2nd DREAM COnference features an exciting group of Invited Speakers, the presentation of papers accepted by our Program Committee, and the presentation of the best network predictions from our data challenges.

Hotel rates in Manhattan are extremely variable, going from expensive to very expensive. To get an idea of the range in prices, please take a look at the following list of hotels and rates. Note that the list contains some hotels in Brooklyn and some in Jersey City (the latter just one train station accross the the Hudson River away from the NYAS). We are providing this list only as a reference. There may be many other more convenient and less expensive hotels not included in this list. Unfortunately we couldn't find hotels that give special conference rates. If you need to know how to get from your hotel to the DREAM2 conference at the NYAS you can use the New York City Transit Trip Planner, or the New York City subway map.

Call for Oral Presentations, Papers and Posters

We are requesting papers and posters for the DREAM2 conference Submit Papers

Download the instructions for paper submissions. Papers and posters submission site Papers will be reviewed by members of the Program Committee A subset of papers papers will be fast-tracked to Molecular Systems Biology Accepted papers will be published in the Annals of the NYAS

Call for Predictions of Networks from Data

The DREAM2 Network Inference Challenge Download Challenges Upload Predictions ( PREDICTION UPLOADING AVAILABLE THROUGHOUT OCT 22 )

A list of proteins some of which interact A synthetic biology circuit transfected to an in-vivo organism The targets of a TF, to be inferred from gene expression data The GRN of a model organism to be inferred from gene expression data An in-silico generated network with simulated "gene expression data"

Important Dates

Regular Paper Submissions

Submission Deadline Extension

The new deadline for paper and poster submission is Monday October 8th.

Week of July 23:	First call for papers and poster abstracts.
Oct 1:	Papers and poster abstract OLD submission deadline.
Oct 8:	Papers and poster abstract NEW submission deadline.
Nov 1:	Paper acceptance decisions issued. Early registration deadline.
Dec 3-4:	Conference dates.
Jan 18, 2008:	Revised papers due to Molecular Systems Biology. If the authors participated in the challenge, the revisions may include the results of the challenge.
Feb 1, 2008:	Final decision for publication in Molecular Systems Biology.
Feb 1, 2008:	Revised papers due for those papers invited to publish in the Proceedings of the DREAM2 (Annals of the NYAS). If the authors participated in the challenge, the revisions may include a section with the results of the challenge.

Predictions Submissions

Challenge Submission Deadline Extension

The new deadline for submissions of challenge predictions is Monday October 22nd.

Week of July 23:	Call for participation in the challenge. Challenges posted.
Oct 15:	OLD Submission deadline.
Oct 22:	NEW Submission deadline.
Nov 1:	Deadline for early registration to conference.
Nov 15:	Notifications to predictors of their scores and ranks.
Dec 3-4:	Conference Dates.
Feb 1, 2008:	Deadline for submission of best predictions as papers to be included as contributions in the Proceedings of the 2nd DREAM Conference (Annals of the NYAS.)

Invited Speakers

Andrea Califano. Tim Gardner, Ravi Iyengar, Fritz Roth, Chris Sander, Ron Shamir, Ilya Shmulevich, Mike Snyder, Peter Sorger, Dennis Vitkup, Ioannis Xenarios.

Program Committee

Andre Levchenko, Avi Ma'ayan, Brandilyn Stigler, Christina Leslie, Eduardo Sontag, Fritz Roth, Harel Weinstein, Igor Jurisica, Ilya Shmulevich, Ioannis Xenarios, Ivet Bahar, Jean-Loup M. Faulon, Jesper Tegner, Jim Collins, Kathleen Marchal, Luis Mendoza, Madan Babu Mohan, Mark Gerstein, Monah Singh, Rune Linding, Satoru Miyano, Seungchan Kim, T Ravasi, Ted Perkins, Tim Elston, Vesteinn Thorsson, Winfried Just, Yannis Kevrekidis, Yuval Kluger, Alex Hartemink, Pablo Iglesias, Adam Margolin, Edward R. Dougherty, Frank Doyle, Gyan Bhanot, Joaquin Dopazo, Michael Samoilov, Pascal Kahlem, Mike Mackey, Denis Thieffry, John Moult, Jeremy Rice, John Wagner, Jose Vilar, Gary Bader, Ilya Nemenman, Leon Glass, Yuhai Tu.

DREAM2 Sponsors

Conference Registration

Data for Reverse Engineering

One of the main thrusts of DREAM is to make available data to contribute to the Reverse Engineering efforts. There is no censensus as to what the best data modality is to infer cellular pathways from high throughput data. Therefore we expect that the novel uses of old data such as gene expression, as well as the use of newer data such as ChIP-chip, or phosphoproteomics, will be good drivers to the field. The objective of this site is to provide links to other sites with available datased aimed at reverse engineering cellular networks, as well as to provide data that came for our own DREAM challenges. As usual, you can add you comments and suggestions in the DREAM Discussion Forum

Data and Gold Standards from the DREAM2 Conference network inference challenges

Important Notice

Datasets of Challenges 1 and 3 cannot be used for external publication without explicit permission from the data owners. For the other datasets, please refer to the original data providers and the DREAM project in your publication.

Step 1. Register your team to download the data. Once you have registered to receive the data, a password will be sent to the e-mail address you provided in the registration.

Step 2. Download the datasets. You will need to use the password provided in Step 1 above.

• Challenge 1: BCL6-Targets Challenges. Data Description. Data Download. Gold-standard Download.
• Challenge 2: The Protein-Protein Subnetwork Challenge. Data Description. Data download. Gold-standard Download.
• Challenge 3: The Five-Gene-Network Challenges. Data Description.Data Download. Gold-standard Download.
• Challenge 4: The In-Silico-Network Challenges. Data Description. Data Download. Gold-standard Download.
• Challenge 5: The Genome-Scale Network Challenge. Data Description. Data download. Gold-standard Download.

Test your predictions for the DREAM2 Conference network inference challenges

As the Gold Standard for Challenge 1 (the BCL6 target challenge) has not yet been released, we created at web tool to facilitate the testing of the predictions for Challenge 1. However, to avoid the releasing the whole set of targets before the data owners could publish their data, we are only allowed to provide results for 5 predictions per team. (Better than nothing...)

You can use a web tool to easily test your predictions for Challenges 3, 4 and/or 5. (Courtesy of Alberto De la Fuente and his team at the CRS4 Bioinformatics Research & Development Lab. )

 

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