Data-Focused Cloud Applications


September 12-13 

Day 1 | Day 2

Thursday, September 13

Pharma and Clinical Applications in the Cloud 

8:30 Chairperson’s Remarks

Marc Olesen, President & COO, DNAnexus

8:35 Data Driven Drug Discovery

Nigel DuffyNigel Duffy, Ph.D., Chief Technology Officer, Numerate Inc. 

Machine learning and cloud computing can transform drug design. Our goal is to leverage all available data during the drug design process to accurately model key drug properties. At Numerate we use machine learning to predict the properties of small molecules and cloud computing to search large sets of compounds to identify potential drugs. The potential is enormous, but significant challenges remain. I will describe Numerate’s platform and some of the results we have achieved to date.

9:05 Facilitating Research on Heart Disease through SaaS

Raimond WinslowRaimond Winslow, Ph.D., The Raj and Neera Singh Professor of Biomedical Engineering; Director, The Institute for Computational Medicine, The Johns Hopkins University School of Medicine and Whiting School of Engineering

The goal of the CardioVascular Research Grid Project is to provide researchers intuitive, easy to use tools for storing, accessing, and analyzing their research data. These tools are available on the Amazon EC2 and/or computing and storage resources at Johns Hopkins University, and are accessed through the users browser. The tools include the eXtensible Neuroimaging Archive Toolkit (XNAT - for managing multimodal image data), the ECGrid Toolkit (for managing and analyzing ECG data), OpenClinica (for managing clinical and demographic data), and Galaxy (a reproducible research tool and workflow system). We will describe the capabilities of these tools, how they are accessed via a browser, and the research projects that are using them.

9:35 Facilitating a Community-Inspired Genomics Data and Analysis Center       DNAnexus 

Marc OlesenMarc Olesen, President & COO, DNAnexus

Large-scale genomics data analysis can be challenging, as it requires vast storage and compute infrastructure, and access to the perfect analysis tool to answer a specific scientific question. This talk will focus on DNAnexus’ cloud-based instant genomics data and analysi s center and how it will address these challenges to make any DNA data analysis a success.

10:05 Coffee Break

10:30 Competitive Data Science: All Your Base Are Belong to Us

David ThompsonDavid Thompson, Ph.D., Social Media Strategist, Boehringer Ingelheim

On March 16, 2012 Boehringer Ingelheim, in partnership with data science company Kaggle, launched a crowd-sourcing competition to predict a biological endpoint. At the time of writing this abstract, almost 6 weeks into the competition, there are 399 teams, comprised of 523 players who have made 3379 entries; 174 of which are ‘better’ or more predictive than the best initial benchmark. During this presentation we will describe the provenance of this project, the complete and full structure of the underlying data set and competition, and some thoughts as to the broader utility of such ‘gamification’ approaches to the field of modeling in the pharmaceutical industry.

11:00 Trust, Assurance & Compliance Readiness – The Key to Establishing the Trusted Cloud Ecosystem

Becky SwainBecky Swain, CISSP, CIPP/IT, CIPP/US, CISA, Founding Member, Cloud Security Alliance
Michelle Nix, Relationship Leader of Information Risk Management, PayPal

With new technology innovations in Health IT, especially leveraging cloud computing platforms and mobile devices, it is even more critical for health care providers and their IT solution providers to provide adequate assurances that healthcare services are built to protect the patient on a safe platform for innovation. The Cloud Security Alliance (CSA) believes that trust, assurance and compliance readiness are the key to establishing a trusted cloud ecosystem for the healthcare industry. In this talk, the CSA will provide an overview of their Governance Risk & Compliance (GRC) Stack and the CSA STAR (Security, Trust & Assurance Registry) as well as other research initiatives, all serving as the basis of emerging security and assurance standards and supply chain risk management best practices for cloud computing.

11:30 Panel Discussion: Putting Proprietary Data on the Cloud? - Legal, Cultural, and Technical Barriers

Moderator: Marc Olesen, President & COO, DNAnexus


Nigel Duffy, Ph.D., Chief Technology Officer, Numerate Inc.

Raimond Winslow, Ph.D., The Raj and Neera Singh Professor of Biomedical Engineering; Director, The Institute for Computational Medicine, The Johns Hopkins University School of Medicine and Whiting School of Engineering

David Thompson, Ph.D., Social Media Strategist, Boehringer Ingelheim

Becky Swain, CISSP, CIPP/IT, CIPP/US, CISA, Founding Member, Cloud Security Alliance

Jason Silva, CEO, Sidus Data

12:00 pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

Going Mobile and Beyond 

1:25 Chairperson’s Remarks

Rick Morrison, CEO, Comprehend Systems

1:30 From Your Heart to the Cloud- How Smartphones will Enable Lifetime Personal Health Monitoring

David AlbertDavid E. Albert, M.D., Founder and CMO, AliveCor

Over 50% of mobile phones in the US today are smartphones. These amazing devices contain multiple sensors which can tell your location, speed and environment. Personal biometric devices are being developed which work with these smartphones to enable health monitoring including blood pressure, blood glucose and even your electrocardiogram (ECG). AliveCor has developed a smartphone ECG device which enables immediate assessment of cardiac rhythm and wireless transmission to the cloud for storage and review. This technology will allow long-term analysis of personal cardiac health status, improving care and reducing the burden of cost.

2:00 Why Future Medicines Will Need to be Discovered in the Cloud

Steven MuskalSteven Muskal, Ph.D., CEO, Eidogen-Sertanty, Inc.

Pharmaceutical companies continue to spend over a decade and billions of dollars to discover and develop a single medicine. Exacerbating this is the small and decreasing number of worldwide drug-discovery workers with the appropriate training, capacity, and funding/employment. Meanwhile in other fields, product innovation and entrepreneurial stewardship are exploding across the planet in epic proportions, leveraging an expanding, highly networked, and more productive workforce. Cloud and mobile computing has been a great enabler of this age of connection and innovation, fostering an unprecedented “global conversation” and capability. The stage is now set to reinvigorate a failing pharmaceutical discovery paradigm and its shrinking workforce. Unless drug-hunters join this conversation and learn to embrace mobile and cloud-based computing strategies, their extinction may become inevitable.

2:30MediSapiens This Cloud Has a Silver Lining - Solving Drug Discovery's Challenges with Web-Based Personalized Genomics
Tommi Pisto, Ph.D., CEO, MediSapiens Ltd

2:45 Refreshment Break

3:00 RCSB PDB Mobile: A Mobile Client for PDB Data in a Mobile Era

Gregory QuinnGregory B. Quinn, Ph.D., Mobile Development Lead, RCSB Protein Data Bank, San Diego Supercomputer Center 

The RCSB PDB website is a crucially important point of access for researchers, scholars and the general public to data stored in the Protein Data Bank, a repository of experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As all of us become accustomed to using connected mobile devices such as smart phones and tablets, the importance of efficient mobile access to scientific data is becoming more relevant. With RCSB PDB Mobile we have introduced a new mobile portal for PDB data users to access this  resource, initially for the iOS platform, later on for Android and potentially other platforms. Using this application, users can perform many functions including searching the entire catalog of structure data and visualize structures using the built-in molecular viewer developed by one of our collaborators.

3:30 Using Siri, Pipeline Pilot, and AWS as a Voice Interface to Computer-Aided Science on the Cloud

William Van EttenWilliam Van Etten, Ph.D., Founding Partner and Principal Investigator, BioTeam

You've seen the ads... Martin Scorsese navigating a busy day, Samuel Jackson preparing for date night, and John Malkovich pondering the meaning of life. When will we see scientists conducting computer aided experiments by voice as we saw on Star Trek? We think very soon.
Toward this goal, BioTeam has enabled a speech interface to computer aided science on the cloud. Using Siri as the speech interface, Accelrys' Pipeline Pilot as the scientific workflow vocabulary, and Amazon's AWS as the compute engine, we conduct computationally intensive scientific data analysis tasks by voice.

4:00 The Sky’s the Limit: Improving Efficiency and Interoperability across Trials with a New Era of Technology

Rick MorrisonRick Morrison, CEO, Comprehend Systems

The clinical industry has heavily invested in new technologies over the past decade but hasn’t fully realized the promised value. The next five years will bring unprecedented advances in clinical technology, leading to large improvements in both efficiency and interoperability. This talk will discuss some of those changes, including advances in databases, cloud computing, connecting data, and extracting information.


4:30 Close of Data-Focused Cloud Applications Meeting

Day 1 | Day 2

Premier Sponsors

Annai Systems


Cycle Computing



Official Media Partner

Bio-IT World 

View All Sponsors 

View Media Partners 

Cloud Usage Study 

* IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide.