News Article

Numerate Collaborates with Sage Bionetworks and IBM to Help Researchers Create Better Models of the Cell
Date: Aug 14, 2013
Author: Numerate
Source: Company Data ( click here to go to the source)

Featured firm in this article: Numerate Inc of San Francisco, CA

SAN BRUNO, CA -- August 14, 2013 -- Numerate, a pioneer in computational drug design, announced today that it has provided its cloud-based BitMill data analytics platform to support the DREAM Whole Cell Parameter Estimation Challenge, organized by Sage Bionetworks and sponsored by IBM.

The DREAM (Dialogue on Reverse Engineering Assessment and Methods) Whole Cell Parameter Estimation project is one of four big data open computational challenges taking place through the fall of 2013. These crowd-sourcing efforts offer a new approach to advancing biomedicine by enabling the rapid sharing and improvement of predictive models to better understand complex processes in systems biology. The ultimate goal is to foster collaborations among researchers that will result in new solutions to critical problems in science and medicine. To date, over 100 academic research teams have registered to participate in the Whole Cell Challenge.

"The Whole Cell Parameter Challenge is fostering important research about cellular processes, which will likely help us to better understand key diseases, identify new drug targets, and predict the side effects of potential drugs," said Brandon Allgood, co-founder and Chief Technology Officer of Numerate. "Predictive modeling like this requires a highly adept big data tool -- and with the budgetary and time constraints of the medical research community -- our cloud-based BitMill service provides the scalability and ease of use required, and is an ideal way for researchers to test various algorithms and conduct necessary analysis to formulate conclusions. In this challenge, modelers are being presented with a substantial leap in computational demands as they are working with a model that is orders of magnitude more complex than in previous DREAM runs. We are pleased to offer a tool that can provide the needed computational power, and are excited to see what the research reveals."

BitMill: The Elasticity and Scalability of the Cloud with Minimal IT Requirements

Numerate's BitMill platform is a cloud-based big data analytics service for scientists and life sciences companies that provides massive scalability of familiar software tools. The current focus for BitMill is next generation sequencing (NGS) analysis. By leveraging the power of the cloud, BitMill delivers performance and cost efficiency in an easy-to-use package:

Performance -- The NGS tools offered by BitMill have been integrated into a highly parallelized and distributed computing infrastructure, allowing fast delivery of results while handling large amounts of data.
Cost -- By taking advantage of the scale and centralized nature of the cloud, the cost of processing is much lower than running software locally, and the pay-as-you-go payment model means users pay only for resources they use.
Ease-of-use -- BitMill delivers high-performance computational capabilities with a lower barrier to entry.
Numerate's BitMill is currently a beta service based on its Numatix cloud platform. This platform has been continuously developed and deployed to run Numerate's drug design projects, both internally and in collaboration with several major pharmaceutical companies, over the past 10 years. The BitMill service is a dataflow execution solution that allows users to run data analysis pipelines at large-scale in the cloud and can cost-effectively process extremely large sets of data in hours or minutes. Numerate uses the platform in combination with proprietary machine learning and screening technologies to fuel its drug design programs.

"We are excited to collaborate with IBM and Sage Bionetworks to make this challenge possible," said Guido Lanza, Chief Executive Officer of Numerate. "It has always been a goal of ours to apply our underlying analytics technology to a wider set of problems and make it available to the external community of scientists and researchers. Numerate is dedicated to empowering scientists to tackle tough problems like the Whole Cell Challenge."

The DREAM Whole Cell Parameter Estimation Challenge launched on June 21, 2013, and will run through September 20, 2013, when the winning team will be invited to present their approach at the 6th Annual RECOMB/ISCB conference on Regulatory and Systems Genomics in Toronto, Canada. In addition the winning team will be invited to submit a manuscript describing their methodology to PLoS Computational Biology, the leading computational biology journal. For more information about the challenge, visit!Synapse:syn1876068.

About the DREAM Project

The Dialogue on Reverse Engineering Assessment and Methods Project (DREAM Project), founded in 2006 by Andrea Califano (Columbia University) and Gustavo Stolovitzky (IBM), was originally conceived as an initiative to advance the nascent field of network biology through the organization of Challenges on network reconstruction and pathway inference. Since the first set of network inference challenges of 2007 (DREAM2) the concept of using collaborative-competitions as a vehicle to carry on a meaningful dialogue in the computational biology community has evolved significantly. In 2012, the last DREAM7 project featured four powerful challenges of which one was on network biology and the other three dealt with three important problems in translational medicine. With the experience gathered by the launching of 24 successful challenges over the past five years, the "Challenge" concept has reached a status of legitimacy and maturity. The DREAM Challenges have brought rigor in the process of verification of computational methods, have enabled the democratization of different kinds of biological data, and have facilitated the collaboration of dozens of research teams. This success has triggered considerable interest by different government institutions and private organizations in working with DREAM to engage distributed teams to solve tough computational problems in biomedical research.

About Sage Bionetworks

Sage Bionetworks ( is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at