Collaborative Research: ABI Innovation: Biofilm Resource and Information Database (BRaID): A Tool to Fuse Diverse Biofilm Data Types

“生物膜资源和信息数据库”项目是蒙大拿州立大学生物膜工程中心(CBE)、密歇根州立大学吉安福特计算学院和国家基因组资源中心(NCGR)的合作项目。生物膜是微生物群落，对水质、食品生产、能源制造过程以及人和动物健康的各个方面都有重要影响。Braid充当社区资源，同时包含数据和元数据(数据是在哪里或如何收集、处理和解释的)。元数据的一些例子包括：地理位置，如博兹曼水回收设施；微环境，如水化学；环境因素，如温度变化；扰动，如添加腐蚀剂；以及干预，如抗生素治疗。Braid在基础和应用研究中对广泛的利益相关者具有实用价值，因此预计它将增强美国工业、基础研究和国防的竞争力，并有助于人类健康、环境健康和能源生产的进步。外展活动将包括(1)在会议和立法者活动中向当地社区成员和行业利益攸关方传播研究成果；(2)来自高中和部落大学的未被充分代表的美国原住民学生以及密歇根州立大学博兹曼分校的本科生和本科生研究人员参与暑期研究活动；(3)密歇根州立大学本科生和研究生课程的教育活动，以及NCGR的暑期实习、外展和培训活动。人们对微生物生物膜重要性的认识在过去十年中出现了爆炸性增长。在牙菌斑、心脏瓣膜、天然水道、废水处理过程、冷却系统、石油和天然气管道以及持续感染等环境中，各种微生物群落以生物膜的形式生长。生物膜可以对人类健康、工业生产力和自然资源产生重大影响，涉及自然、工程和医疗系统。尽管生物膜很重要，但没有专门用于存储、分析和交流特定生物膜数据的公共门户网站和数据库。部分原因是用于描述生物膜的数据类型非常广泛，包括核苷酸序列、图像、视频、化学(水、表面和细胞外聚合物基质)、修复历史、临床结果和地理空间数据。Braid将通过开发一种数据表示范式来补充现有的微生物数据库，以解决由独特的数据组合引起的挑战所带来的问题，并将为生物膜数据的正式描述和分析实施新的度量和算法。该项目旨在提供主要的资源，使用户能够提出复杂的问题(包括那些目前无法回答的问题)，允许在生物膜之间进行定量比较，支持补救工作，并能够预测结果。该项目的结果可在以下网址查阅：http://ncgr.org/braid.

The "Biofilm Resource and Information Database (BRaID)" project is a collaboration between the Center for Biofilm Engineering (CBE) at Montana State University, Bozeman, MT and the Gianforte School of Computing at MSU and the National Center for Genome Resources (NCGR), Santa Fe, NM. Biofilms are microbial communities that have important impacts on water quality, food production, energy-making processes, and various aspects of human and animal health. BRaID serves as a community resource, containing both data and the metadata (where or how data was collected, processed, and interpreted). Some examples of metadata include: a geographical location, such as the Bozeman Water Reclamation Facility; microenvironments such as water chemistry; environmental factors such as changes in temperature, perturbations such as adding corrosion inhibitors; and interventions such as antibiotic treatments. BRaID has utility to a broad range of stakeholders in basic and applied research, as such it is expected to enhance the competitiveness of US industry, basic research, and defense, as well as assist with advancements in human health, environmental health, and energy production. Outreach activities will include (1) dissemination of research outcomes to local community members and industry stakeholders at conferences and legislator engagements; (2) involvement of underrepresented Native American students from high schools and tribal colleges in summer research activities as well as undergraduate researchers at MSU-Bozeman; and (3) educational activities in undergraduate and graduate courses at MSU, as well as summer internship, outreach and training activities at the NCGR.Awareness of the importance of microbial biofilms - microorganisms growing as aggregates attached to surfaces, interfaces, or each other - has exploded in the past decade. Diverse microbial communities grow as biofilms in such settings as dental plaque, heart valves, natural watercourses, wastewater treatment processes, cooling systems, oil and gas pipelines, and persistent infections. Biofilms can have significant impacts on human health, industrial productivity, and natural resources, spanning natural, engineered, and medical systems. Despite the importance of biofilms, there is no public web portal and database dedicated to storage, analysis, and communication of biofilm-specific data. Part of the reason for this is the sheer breadth of data types used to describe biofilms, including nucleotide sequences, images, video, chemistry (water, surface, and extracellular polymer matrix), remediation history, clinical outcomes, and geospatial data. BRaID will complement existing microbial databases by developing a data representation paradigm that solves the problems posed by the challenge arising from the unique combination of data, and will implement new metrics and algorithms for the formal description and analysis of biofilms data. This project aims to provide the premier resource that offers users the ability to ask complex questions (including those currently impossible to answer), permitting quantitative comparisons among biofilms, supporting remediation efforts, and enabling predictions about outcomes. Results of the project can be found at: http://ncgr.org/braid.