About BAGIM

BAGIM is an active community of Boston area scientists bringing together people from diverse fields of modeling and informatics to impact life and health sciences. BAGIM strives to create a forum for great scientific discussions covering a wide range of topics including data management, visualization, computational chemistry, drug discovery, protein structure, molecular modeling, structure-based drug design, data mining, software tools, and the sharing of goals and experiences. Our community is made up of participants from academia, government, and industry whose goal is to engage in the discussion of science involving a synthesis of theory and technology. Discussions sponsored by BAGIM are targeted to the needs and interests of informatics scientists, computational chemists, medicinal chemists, and statisticians. BAGIM also provides opportunities for networking within these disciplines as well as an arena for the dissemination of information of specific interest to the membership.

Monday, September 11, 2017

BAGIM Event: Panel on Cloud Computing for Molecular Modeling at NIBR in Cambridge, Monday September 11, 2017

A panel of industry experts will present a discussion on Cloud Computing for Molecular Modeling in the auditorium at NIBR at 250 Mass Avenue in Cambridge, starting at 6pm, following refreshments at 5:30pm. Further networking time with refreshments will follow the discussion. Panel members include:  

• Lucas Nivon, Ph.D. (discussion leader)
Co-founder and CEO, Cyrus Biotechnology 
• Pat Lorton, Ph.D. (panelist)
Chief Technology Officer, Schrodinger
• Essam Metwally, Ph.D. (panelist)
Senior Scientist, Chemical Computing Group
• Craig Bruce, Ph.D. (panelist)
Scientific Software Development Manager, OpenEye Scientific

Molecular Modeling on the Cloud: Implementing complex workflows for all users

Many major advances have been made in the last 10 years in small molecule and protein modeling and design, including the design of novel protein folds and protein-binding activity into inert scaffolds. All of these have required very large amounts of computing and complex workflows with sensitive benchmarking and expert configuration. This complexity, sensitivity and large infrastructure requirements have in many cases limited these tools to very few use cases in an academic environment with access to very large shared compute resources. We propose that the public cloud provides an opportunity to circumvent infrastructure limitations while simultaneously reducing complexity and increasing accessibility.

Here we examine the previously existing infrastructure used to run these types of calculations. We consider the design requirements for a value-focused research organization in a cloud implementation of molecular modeling and design, such as maintenance cost/time, reliability, speed to answers, and correctness of answers. Then we propose various architectural instantiations of a “cloud” modeling suite of software while considering best practices in software-as-a-service tools from other fields (such as email). Finally, we outline one general solution to a cloud architecture that emphasizes these requirements and reduces user complexity. Simplification to users requires shifting complexity to cloud infrastructure and increased software development time.

We focus on one case study of a scientific workflow implementation, detailing architectural/workflow aspects and the scientific benchmarking required.

Special thanks to NIBR for hosting, especially Lewis Whitehead and Erica Gauthier, ACS COMP for sponsoring refreshments

BAGIM is sponsored by Dassault Systemes, DNASTAR, LabAnswer, OpenEye Scientific, Schrodinger, Silicon Therapeutics, Acellera, Acpharis, Cambridge Crystallographic Data Centre, Chemical Computing Group, Dotmatics, Cresset, Cyrus Biotechnology, Optibrium, Team Arrayo, and Scilligence
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