Press category: Challenges

November 11, 2013

Media Contact:
Janet Janjigian, Carmen Group West
janjigianj@carmengroup.com

Marina del Rey, California- November 11, 2013 – Heritage Provider Network, (HPN) The National Cancer Institute, (NCI) Sage Bionetworks and DREAM announced the best performers in the Heritage-DREAM Breast Cancer Network Inference Challenge. The competition challenged teams to use big data to develop more effective treatments for breast cancer. Six best performing teams were honored with cash prizes at the Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges in Toronto, Ontario on November 8, 2013. Sponsored by HPN and the NCI Division of Cancer Biology, (DCB) the goal of the competition was to challenge data scientists to find ways to increase our understanding of signaling cellular pathways in breast cancer cells that could lead to more effective treatments for breast cancer patients.

Six teams were chosen as best performers within three categories of the challenge. Category questions posed to participants included (1) identifying cellular pathways that transmit extra cellular signals in breast cancer cells (2) predicting the dynamics of the proteins responsible for transmitting extracellular signals in breast cancer cells and (3) how to visualize complex big data sets in biomedical research such as those used in this challenge.

“I am so pleased with this successful collaboration between HPN and the NCI in sponsoring this important competition,” said Dr. Richard Merkin, President and CEO of HPN. “More than two hundred teams completed to better predict the networks and signaling dynamics in breast cancer cells, with one hundred teams making the final submission round. The innovations fostered by this competition will undoubtedly lead to an improved understanding of breast cancer, identify new therapeutic targets and most importantly, will help save lives. Congratulations to the six best performing teams.”

“This was a complex and difficult challenge, dealing with the way breast cancer cells process extracellular information to alter their internal states,” said Gustavo Stolovitzky, co-founder of the Dream Project. “When we formulated the challenge, there was no certainty that there would be any teams that could solve the problem to any degree of significance. We are extremely pleased that several teams managed to find methodologies that yielded pretty accurate solutions.”

“Cancer remains one of the most challenging and devastating diseases afflicting the planet,” said Dan Gallahan, Deputy Director, DCB, National Cancer Institute. “The NCI has worked tirelessly to develop new understandings of cancer with the direct goal of reducing its burden. Besides exploring new scientific discoveries, the NCI is also exploring new methods to uncover those discoveries. Crowd sourcing and challenges represent a new opportunity to go beyond our traditional research paradigm and engage a whole new community in a new way,” he continued. “The DREAM program has been at the forefront of developing these types of research activities for the biomedical community and likewise, HPN has been a generous leader in the support of biomedical research. We would like to thank both these groups for making this important challenge possible and advancing our knowledge of breast cancer. I would also like to personally congratulate the top performers and all participants in the Heritage- DREAM challenge.”

Best performers include Team DC-TDC from the University of California at Santa Cruz, Team NMSUSongLab from New Mexico State University, Team GuanLab from the University of Michigan, Team StochasticChaos from Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center and the University of North Carolina at Chapel Hill, Team CGR from NCI and the Chinese Academy of Medical Sciences in Beijing and Team ABCD from Rice University.

“Team DC-TDC is delighted to have contributed a winning solution by identifying cellular pathways that transmit extra cellular signals in breast cancer cells,” said Josh Stuart, team member. “The DREAM competition is an incredible motivating force and a truly fun experience for all of us. In the end, we came up with a very clever strategy that combines the use of heat diffusion on a “SuperPathway” of known genetic knowledge and a twist on a theory borrowed from economics called Granger Causality. The reward for us is that it pushed us to achieve a new level of creativity in our approaches to reveal cancer processes. As always, we remain hopeful that our efforts as a community of friendly competitors will lead to contributions in fighting this disease.”

The competition will now move into a collaborative phase where teams will be able to share information and work together to find solutions. The deadline for this next phase of the challenge is January 15, 2014.

Press Release

November 8, 2013 In: News Releases

An open Challenge that merges the efforts of the world’s largest cancer genome sequencing consortia, the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) with those of Sage Bionetworks and DREAM.

TORONTO, CANADA – Cancer research leaders from the Ontario Institute for Cancer Research (OICR) and the University of California, Santa Cruz (UCSC), in collaboration with Sage Bionetworks and IBM’s DREAM, will announce tomorrow the opening of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (https://www.synapse.org/#!Challenges:DREAM) at the Sixth Annual RECOMB/ISCB conference (http://www.iscb.org/recomb-regsysgen2013).

Like previous DREAM Challenges in the series, this new Challenge will engage a diverse community of scientists to solve a specific problem in a given time period by placing scientific data, tools, scoreboards and the resulting predictive models into an open Commons.

The specific problem the SMC Challenge will address is the need for accurate methods to identify cancer-associated mutations from whole-genome sequencing data. Cancer is a disease of the genome, caused by disruptions in DNA that alter specific gene functions. Although today’s DNA sequencing instruments can amass great quantities of sequence data from a patient’s normal and tumor tissues, the ability to identify DNA mutations and rearrangements accurately on the basis of those data remains elusive; current studies agree in only about 20% of their predictions.

To address this need, the Challenge will post the raw DNA sequencing data of 10 human tumor-normal pairs (5 prostate, 5 pancreatic), comprising approximately 9 terabytes of data to a high-speed distribution server. Contestants will have 6 months to optimize their predictive models. After the Challenge closes in July, 2014, at least 5000 DNA candidate mutations predicted by different participating teams will be prospectively validated on an independent sequencing platform by the Challenge organizers. The accuracy of participants’ predictions will be ranked using the newly generated validation data based on sensitivity, specificity and balanced accuracy amongst other metrics.

To participate in the Challenge that opens tomorrow, individuals will need to register at https://www.synapse.org/#!Challenges:DREAM. In addition, they must be approved by OICR’s ICGC Data Access Compliance Office to acess the data.

As Canadian OICR researcher and Challenge organizer Professor Paul Boutros puts it, “Governments around the world have committed hundreds of millions of dollars to sequence cancer genomes to find new drug targets and to develop treatments that are personalized to each person’s cancer genome. But realizing these goals is currently blocked by scientists’ inability to identify mutations in cancer genomes. It is really tremendous that ICGC and TCGA are coming together with Sage Bionetworks and DREAM to address this problem using a DREAM Challenge that will set a gold standard that groups around the world can use to understand the cancer genome!”

To help realize this Challenge, industrial partners have stepped up. Google is making their Google Cloud Platform available to OICR-approved participants, including free access to the contest data in Google Cloud Storage and discounted Google Compute Engine cycles. Cloud processing will open the door for a whole new set of participants who do not have access to large compute clusters at their own institutions. Hitachi has provided free storage to host the data on a 1PB disk donated for cancer genomics. Annai Systems (http://www.annaisystems.com/) is providing their Annai-GNOS™ data management platform to facilitate upload, hosting and access to the data in the Hitachi store. Annai’s GeneTorrent software will provide high-speed data transfer to the Challenge participants.

Challenge participants will use the Synapse infrastructure (http://www.synapse.org), built by Sage Bionetworks, that allows collaboration by Challenge teams on an open platform. Synapse’s tools and forum will allow Challenge participants to: (1) record what processing and analysis they’ve done on the data; (2) submit their predictive models to a real-time leaderboard for scoring; and (3) share their ideas, model code and analysis results with others in the Challenge.

Publications based on the highest-ranking predictive methods from the Challenge will be considered with Nature Publishing Group. Nature Genetics editor Myles Axton will advise the Challenge on publication strategy and work with Synapse to understand the scientific quality control that can be obtained via competitive collaboration. “The exciting thing about this exercise from an editorial standpoint is that we can analyze just how much the strategies are improved during the contest and how much peer review is then needed to obtain a useful research publication at the end. The beauty of doing this on an open platform is to see the rigor, transparency and detail of each group’s approach and to be able to replay each strategy in a robust way,” Myles says. “This is a good use of editorial time since peer review improves the strategies, it improves the resulting publications and it improves the databases and journals by preparing us for the future of knowledge production. I really hope the winners combine elements of the best strategies into fuller publishable units, in that way they will get the best out of the challenge as well as our involvement with it.”

Explains UC Santa Cruz Professor Josh Stuart, “The timing of this Challenge couldn’t be better. ICGC and TCGA recently announced that they plan to jointly analyze a dataset of approximately 2,000 pairs of tumor-normal whole genomes as part of a 2014-2015 Pan-Cancer effort to elucidate comprehensively the genomic changes present in many forms of cancers. Thus, the winning algorithms selected by this DREAM Challenge will help ICGC/TCGA researchers provide the largest unified view of cancer genome variation to date.”

Cancer researcher Dr. Stephen Friend founded Sage Bionetworks out of a conviction that “…the best approach towards developing robust and accurate predictions such as those needed for mutation calling is to enable an open diverse community where data access is simple and people are incentivized to share. Sage and DREAM have already shown that in the span of several months, DREAM Challenges can attract hundreds of teams who end up submitting thousands of predictive models to a Challenge. Sage and DREAM couldn’t be more delighted to be partnered with the ICGC and TCGA research communities to provide the largest public methodology assessment for the field of somatic mutation identification.”

Press Release

November 7, 2013

Press Release | Fri Apr 19, 2013 5:15pm EDT

DREAM and Sage Bionetworks Announce Big Data Challenges to Impact Biomedical and Clinical Research

DREAM8 Challenges Tackle Tough Problems from Toxicology to Cancer

DREAM and Sage Bionetworks today announced that they will run four Big Data open science Challenges between now and the fall. These open computational Challenges are a new method in biomedicine to rapidly share and evolve predictive models for important questions and were featured at today’s session of the Sage Bionetworks Commons Congress taking place in San Francisco.

Challenges have been used successfully in other research fields, and in the past 6 years the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project has run 24 successful Challenges in Systems Biology. Due to efforts like DREAM, the “Challenge” concept has reached a status of legitimacy and maturity: the NIH and private companies are investing in the Challenge model to solve complex problems. In February 2013, and based on the success of collaborating to run the 2012 Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge, Sage Bionetworks merged its open science efforts with those of DREAM.

This year’s so-called DREAM8 Challenges mark the eighth year that DREAM founder Dr. Gustavo Stolovitzky has been working with his distributed group of systems biology scientists to engage wider and more diverse communities of scientists to competitively solve important problems in biomedicine. Says Stolovitzky about this year’s Challenges, “The Challenge infrastructure, computational model archive and data governance systems that Sage Bionetworks has established allows the DREAM Challenges to shift in exciting new ways. In DREAM8 and future Challenges, we will use the solutions from some Challenges to serve as seeds for subsequent Challenges and for basic and clinical validation of the models that show outstanding performance. And we are already planting the seeds for Challenges that start with citizens and patients donating their data so that we can run Challenges that answer questions that are directly relevant to their disease progression and treatment options.”

The first four DREAM8 Challenges announced today will launch later this spring and be open for participation by anyone interested (signup is open at DREAM8@sagebase.org). The model submission phase will close in the fall and the Challenge winners will be announced at the DREAM8 Conference taking place in early November. Sage Bionetworks and DREAM expect to launch another round of DREAM8 Challenges in the fall. Brief information about each of the announced DREAM8 Challenges is provided below:

1. Heritage-DREAM Breast Cancer Challenge (read HPN press release:http://www.prnewswire.com/news-releases/heritage-dream-national-cancer-institute-breast-cancer-network-inference-prize-announced-203812141.html)

a. Data provided by Oregon Health Sciences University (OHSU) and the MD Anderson Cancer Center

b. Sponsored by the Heritage Provider Network (HPN) and the National Cancer Institute (NCI), Division of Cancer Biology

c. Challenge Focus: To use proteomics data to build network models that represent the active pathways in breast cancer cells and to predict their responses to different drug treatments.

2. NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge

a. Data provided by National Institute for Environmental Health Sciences (NIEHS), the National Center for Advancing Translational Sciences (NCATS), and the University of North Carolina at Chapel Hill (UNC).

b. Challenge Focus:

i. To use genetics, genomic and toxicity data to predict individual response to exposure to common environmental and pharmaceutical chemicals.

ii. To predict variation in toxicities across populations exposed to compounds based on the chemical information of the toxic agent and population genetics information.

3. National Brain Tumor Society-DREAM Breast Cancer Prediction Challenge (read NBTS press release: http://www.braintumor.org/news/latest-nbts-news/announcing-the-national-brain.html)

a. Sponsored by the National Brain Tumor Society.

b. Jointly led by experts from the National Brain Tumor Society (NTBS), Columbia University and DREAM/Sage Bionetworks.

c. Challenge Focus: to predict the specific drugs that will elicit the strongest therapeutic response in mice transplanted with human brain tumors, based on their genomic characterization.

4. DREAM Whole Cell Parameter Estimation Challenge

a. Data and models provided by Stanford University

b. Sponsored by IBM

c. Challenge Focus: to predict kinetic parameters of a whole-cell computational model of the human pathogen Mycoplasma genitalium, using algorithms that use experiments as part of the parameter inference process.

Click here to be contacted when the DREAM8 Challenges open for competition.

Read more about the DREAM8 Challenges here.

Press Release

April 19, 2013

Competition aims to develop more efficient treatment strategies for breast cancer patients

San Francisco, California-April 19, 2013- Heritage Provider Network (HPN), The National Cancer Institute, Sage Bionetworks and DREAM today announced the Heritage-DREAM Breast Cancer Network Inference Challenge. The prize contest uses big data to develop more effective treatments for breast cancer, and was featured at the Sage Bionetworks Commons Congress in San Francisco, California(http://sagebio2018.wpengine.com/wp-content/uploads/2013/04/DREAM8_Press_Release.pdf)

http://www.youtube.com/user/HPNHealth

Sponsored by HPN and the NCI Division of Cancer Biology, the goal of the prize is to challenge data scientists to find ways to quickly and effectively increase our understanding of signaling cellular pathways in breast cancer.

“This is our first prize challenge to foster innovations in breast cancer research,” said Dr. Richard Merkin, President and CEO of Heritage Provider Network. “Hopefully, our understanding of how these signaling pathways are deregulated in cancer cells will lead to a better understanding of how cancer cells are wired,” he continued. “Currently, we don’t have the maps needed to guide our efforts. This challenge can provide those key maps, allowing effective treatment therapies to be accelerated, savings lives and millions of dollars.”

“It is a privilege to be able to count the Heritage Provider Network as a partner in this important effort to unravel the networks that are deregulated in breast cancer. The challenge format will help discover new biology in an accelerated way, as dozens of participants working on the same data for 4 months can achieve what a single group would achieve in many years,” said Gustavo Stolovitzky, co-founder of The DREAM Project.

“Cancer remains one of the most daunting and important challenges for the medical research community. While tremendous progress has been made in its understanding and management, the personal and societal losses remain huge. Biomedical research remains the key to future progress and cures for all diseases including cancer,” said Dan Gallahan, Deputy Director, DCB, National Cancer Institute. “The NCI remains committed to supporting that research but recognizes the need for new approaches and innovations in how that research is advanced. That is why we are very pleased to have participated in the development of this Heritage-DREAM Breast Cancer Network Inference Challenge.

This challenge utilizes the power of crowdsourcing to address some of the fundamental issues of how breast cancer cells function, allowing for more directed and precise treatment. Crowdsourcing has proven to be an important mechanism to broaden the community of researchers focused on cancer related issues,” Gallahan continued. “Heritage Provider Network (HPN) is an early adopter of challenges, having already engaged in some of the most ambitious challenges to date. We are very pleased and grateful for the insight and support by HPN and its CEO, Dr. Richard Merkin, in this important endeavor. We look forward to future interactions as we continue the struggle against cancer.”

Sage Bionetworks and DREAM are running the prize challenge.

The Heritage DREAM Breast Cancer Network Inference Challenge is one of a number of competitions Dr. Merkin is sponsoring in HPN’s ongoing efforts to spur innovations that improve quality and reduce inefficiencies in healthcare.

Press Release

Press Release | Tue Feb 19, 2013 3:01am EST

SEATTLE--(Business Wire)--
Sage Bionetworks, a non-profit organization, announced today that it will merge
its efforts with that of the DREAM Project to run open science computational
challenges, which foster the broader collaboration of the research community and
provide a meaningful impact to both discovery and clinical research. 

This collaboration will pair Sage Bionetworks` Synapse, an open compute platform
that allows data to be shared and worked on collaboratively by teams of teams,
with the experience that the DREAM Project brings from running 24 successful
computational challenges over the last five years. 

Sage Bionetworks and DREAM are convinced that open computational challenges
represent an innovative new method to rapidly share and evolve predictive
disease models that would otherwise take years to produce using the usual siloed
research paradigms. Their merger provides a collaborative framework that will
bring the ideals of open science one step closer to reality. 

"The traditional ways of doing science has researchers too focused on being the
first to publish," remarked Dr. Gustavo Stolovitzky, Founder of the DREAM
Project. "This has given rise to a culture of secrecy about scientific results
and data. By refocusing our efforts on creating a collaborative research
environment, we at DREAM and Sage Bionetworks can foster a complementary way of
doing science, which will accelerate the pace of discovery with the goal of
contributing to a faster reduction of suffering due to disease. This seems to me
like an ethical imperative." 

Sage Bionetworks and DREAM`s merger builds off of the success of their recent
2012 Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge that for the first
time, allowed participants to share code in the context of a computational
biology challenge. Participating teams were asked to submit their computational
model to Synapse as open source code made viewable to all participants: their
models were assessed against a hidden dataset and their scores were reported on
a real-time leaderboard. The combination of immediate feedback and code sharing
allowed participants to improve their leaderboard ranking by adjusting their own
models or by borrowing the code of others to forge new models. 

Synapse is built to meet the needs of the data scientists that participate in
DREAM`s challenges. It provides an open repository of analysis-ready data that
scientific teams can work on in an open, online form accessible by all through a
collaborative web portal. 

The merger will allow Sage Bionetworks and DREAM to run several challenges
similar to the Breast Cancer Prognosis Challenge every year. Dr. Stephen Friend,
President and Founder of Sage Bionetworks, remarked, "With the growing
affordability of genomic data and wide availability of cloud-based computing, we
know it is timely for us to join our efforts to scale and dream beyond the great
things that DREAM has already enabled. We want to evolve challenges so that
solutions from the last phase become the starting point for a new step towards
meaningful validation, and where newly created datasets might allow the
answering of important clinical questions. These are the approaches that will
bring about the promises of Precision Medicine."

Press Release