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BIA绑定器:面向生物图像分析社区的原生网络云计算服务。

bia-binder: A web-native cloud compute service for the bioimage analysis community.

作者信息

Russell Craig T, Burel Jean-Marie, Athar Awais, Li Simon, Sarkans Ugis, Swedlow Jason, Brazma Alvis, Hartley Matthew, Uhlmann Virginie

出版信息

ArXiv. 2024 Nov 19:arXiv:2411.12662v1.

Abstract

We introduce bia-binder (BioImage Archive Binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter Notebook coding environments hosted on EMBL-EBI's Embassy Cloud, which provides significant computational resources. The bia-binder architecture is free, open-source and publicly available for deployment. It features fast and direct access to images in the BioImage Archive, the Image Data Resource, and the BioStudies databases. We believe that this service can play a role in mitigating the current inequalities in access to scientific resources across academia. As bia-binder produces permanent links to compiled coding environments, we foresee the service to become widely-used within the community and enable exploratory research. bia-binder is built and deployed using helmsman and helm and released under the MIT licence. It can be accessed at binder.bioimagearchive.org and runs on any standard web browser.

摘要

我们推出了生物图像存档绑定器(BioImage Archive Binder),这是一个开源的、基于云架构且基于网络的编码环境,专为生物图像分析量身定制,所有研究人员均可免费使用。该服务会在欧洲分子生物学实验室欧洲生物信息学研究所(EMBL-EBI)的大使馆云平台上生成易于使用的Jupyter Notebook编码环境,该平台提供了大量计算资源。生物图像存档绑定器的架构是免费、开源且可供公众部署的。它的特点是能够快速直接访问生物图像存档库、图像数据资源库和生物研究数据库中的图像。我们相信,这项服务能够在缓解当前学术界获取科学资源方面存在的不平等现象中发挥作用。由于生物图像存档绑定器会生成指向已编译编码环境的永久链接,我们预计该服务将会在社区中得到广泛应用,并能推动探索性研究。生物图像存档绑定器是使用舵手(helmsman)和舵(helm)构建并部署的,并根据麻省理工学院许可协议发布。可通过binder.bioimagearchive.org访问它,并且它能在任何标准网页浏览器上运行。

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