I-Corps: Enterprise Rosetta Protein Modelling and Design Software on the Cloud

Rosetta是综合性能最好的分子建模和设计软件工具包，在预测新的蛋白质结构和设计用于工业和医疗应用的新蛋白质方面都是一流的。Rosetta目前被授权给企业使用，并获得了一定的吸引力，但最主要的三个痛点是：难以使用，几乎不提供用户支持，需要大量的计算资源。该项目旨在构建企业版的Rosetta分子建模和设计软件包，并将加速制药和生物技术公司对小分子和生物药物的开发，并允许这些公司通过计算蛋白质设计创建全新的生物药物、诊断和生物工具。该提案将通过一个干净的3D图形用户界面（GUI）、工作流流水线和云计算引擎来解决这些问题。这个被提议的软件，赛勒斯，是对罗塞塔的包装。它提供GUI前端、标准用户过程的自动化和云计算。GUI是全新的，并且将构建在web浏览器中，以实现与云的最大兼容性和接口的易用性。过程的自动化和标准化包括对现有协议进行基准测试和编写脚本，以删除人工交互步骤，并纳入专家知识。Cyrus的云实现将使用最前沿的开源工具（如Redis和OpenStack）从头开始构建，以提供功率(1000？5个cpu)和易用性（为最终用户提供云资源的图形界面）。

Rosetta is the best-overall-performance molecular modeling and design software toolkit, and is best-in-class both for predicting new protein structures and for designing new proteins for industrial and medical applications. Rosetta is currently licensed to enterprise and has gained some traction, but the top 3 identified pain points are: Difficult to use, offers almost no user support and requires immense amounts of computational resources. This project aims to build an enterprise version of the Rosetta molecular modeling and design software package, and will accelerate the development of small-molecule and biological drugs in Pharma and Biotech firms, and allow for the creation of entirely new biological drugs, diagnostics, and biological tools at those firms through computational protein design.This proposal will solve these problems with a clean 3D Graphical User Interface (GUI), workflow pipelining, and a cloud compute engine. The proposed software, Cyrus, is a wrapper around Rosetta. It provides a GUI front-end, automation of standard user procedures and compute on the cloud. The GUI is all-new, and will be built inside a web browser for maximum compatibility and ease of interface with the cloud. Automation and standardization of procedures consists of benchmarking and scripting of existing protocols to remove human interaction steps, and incorporate expert know-how. The cloud Implementation of Cyrus will be built from scratch using cutting edge open source tools such as Redis and OpenStack to provide power (1000?s of CPUs) and ease of use (graphic interface with cloud resources for the end user).