CARMEN e-Science Portal

CARMEN 电子科学门户

• 批准号: BB/I001042/1
• 负责人: Colin Ingram
• 金额: $ 25.85万
• 依托单位: Newcastle University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI001042%2F1
• 关键词: CARMEN; Science; Portal

The study of the brain and of nervous systems is one of the priority areas for biological research in the UK and internationally. Neuroscience research commonly employs techniques that generate large data files (called time-series data) that record the activity of one or many nerve cells as well as other accompanying data, such as physiological measures, behaviour, or a stimulus that is used to activate the system. This mass of data requires detailed analysis in order to extract the important information and to look for patterns which can provide insight into the way the brain functions. CARMEN (an acronym for Code Analysis, Repository and Modelling for e-Neuroscience) harnesses the power of the web in order to enable researchers to accomplish this analysis and at the same time provide a way to share data, either within private user groups or openly within the science community. Starting in October 2006 a collaborative effort between computer scientists and neuroscientists at 11 UK universities has developed the first version of this resource. Using remote access through a web portal users can upload their data files to the CARMEN platform. At the same time the system allows information about the experiment and the data files (metadata) to be gathered so that others can understand the experiment. Users can also upload software tools that can be used to analyse the data or use tools provided by others in the community. We are also developing ways that the upload can happen whilst the experiment is being performed in order that collaborators can perform recording and analysis at the same time (real time distributed collaboration). Importantly, CARMEN has been developed so that this sharing of the resource is not restricted by the format of the files used to capture the data or the way in which the analysis methods have been written (interoperability). There is also a security structure that allows users to initially work on the files privately but, once the data have been published the data files can be made public so that others can use them. In this way CARMEN can both curate experimental data and provide a resource for secondary analysis or combination of data from different laboratories. This ability to reuse data adds significantly to their value, particularly for experiments that are complex to perform or which employ rare tissue. The current project will maintain and develop the CARMEN portal for a further four years. Importantly the project will support the transition from the initial development stage to a wider community engagement. This will involve Help Desk support for new users, troubleshooting of system problems, and further development of the web portal in response to user feedback. In addition, we will undertake development of new functions to allow specific data types to be uploaded, shared and analysed. In this respect we will focus effort on two main areas: (i) electroencephalogram (EEG) recordings and the brain responses to stimuli (event-related potentials), and (ii) neural activity data that can be extracted from video images. In the latter case this will enable CARMEN to be used for recordings that employ the latest generation of optical recording techniques. Finally, we will develop ways to link into other bioinformatics projects in order that details of brain structure, gene expresion, etc. might be stored and analysed at the same time. This last effort will be assisted by our involvement with the International Neuroinformatics Coordinating Facility (INCF) which was recently established to support links between databases and informatics resources in neuroscience. CARMEN is a unique facility that has addressed the specific issues of storing and analysing neurophysiological data on the web in order to facilitate collaboration and data sharing. With future development of the computing power of the web (cloud computing) it is likely that this will increasingly become the accepted method of research.

大脑和神经系统的研究是英国和国际生物学研究的优先领域之一。神经科学研究通常采用生成大型数据文件（称为时间序列数据）的技术，这些数据文件记录一个或多个神经细胞的活动以及其他伴随数据，例如生理测量、行为或用于激活系统的刺激。大量数据需要进行详细分析，以提取重要信息并寻找可以深入了解大脑功能的模式。 CARMEN（电子神经科学代码分析、存储库和建模的缩写）利用网络的力量，使研究人员能够完成这种分析，同时提供一种在私人用户组内或在科学界内公开共享数据的方法。从 2006 年 10 月开始，英国 11 所大学的计算机科学家和神经科学家合作开发了该资源的第一个版本。通过门户网站进行远程访问，用户可以将其数据文件上传到 CARMEN 平台。同时，系统允许收集有关实验和数据文件（元数据）的信息，以便其他人可以理解该实验。用户还可以上传可用于分析数据的软件工具或使用社区中其他人提供的工具。我们还在开发在进行实验的同时进行上传的方法，以便协作者可以同时进行记录和分析（实时分布式协作）。重要的是，CARMEN 的开发使得这种资源共享不受用于捕获数据的文件格式或分析方法的编写方式（互操作性）的限制。还有一个安全结构，允许用户最初私下处理文件，但一旦数据发布，数据文件就可以公开，以便其他人可以使用它们。通过这种方式，CARMEN 既可以整理实验数据，又可以为二次分析或来自不同实验室的数据组合提供资源。这种重复使用数据的能力显着增加了数据的价值，特别是对于执行复杂或使用稀有组织的实验。当前的项目将在未来四年内维护和开发 CARMEN 门户。重要的是，该项目将支持从最初的开发阶段过渡到更广泛的社区参与。这将涉及对新用户的帮助台支持、系统问题的故障排除以及根据用户反馈进一步开发门户网站。此外，我们将开发新功能，以允许上传、共享和分析特定数据类型。在这方面，我们将重点关注两个主要领域：（i）脑电图（EEG）记录和大脑对刺激（事件相关电位）的反应，以及（ii）可以从视频图像中提取的神经活动数据。在后一种情况下，这将使 CARMEN 能够用于采用最新一代光学记录技术的记录。最后，我们将开发连接其他生物信息学项目的方法，以便同时存储和分析大脑结构、基因表达等细节。我们参与国际神经信息学协调机构（INCF）将有助于这最后一项努力，该机构最近成立是为了支持神经科学数据库和信息学资源之间的联系。 CARMEN 是一个独特的设施，它解决了在网络上存储和分析神经生理学数据的具体问题，以促进协作和数据共享。随着网络计算能力（云计算）的未来发展，这很可能将日益成为公认的研究方法。

项目成果

Age-dependent homeostatic plasticity of GABAergic signaling in developing retinal networks.

• DOI: 10.1523/jneurosci.3112-11.2011
• 发表时间: 2011-08-24
• 期刊: The Journal of neuroscience : the official journal of the Society for Neuroscience
• 作者: Hennig MH;Grady J;van Coppenhagen J;Sernagor E
• 通讯作者: Sernagor E

Non-parametric physiological classification of retinal ganglion cells in the mouse retina

小鼠视网膜视网膜神经节细胞的非参数生理学分类

• DOI: 10.1101/407635
• 发表时间: 2018
• 作者: Jouty J

Spike Detection for Large Neural Populations Using High Density Multielectrode Arrays.

• DOI: 10.3389/fninf.2015.00028
• 发表时间: 2015
• 期刊: Frontiers in neuroinformatics
• 影响因子: 3.5
• 作者: Muthmann JO;Amin H;Sernagor E;Maccione A;Panas D;Berdondini L;Bhalla US;Hennig MH
• 通讯作者: Hennig MH

Pan-retinal characterisation of Light Responses from Ganglion Cells in the Developing Mouse Retina.

• DOI: 10.1038/srep42330
• 发表时间: 2017-02-10
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Hilgen G;Pirmoradian S;Pamplona D;Kornprobst P;Cessac B;Hennig MH;Sernagor E
• 通讯作者: Sernagor E

Following the ontogeny of retinal waves: pan-retinal recordings of population dynamics in the neonatal mouse.

• DOI: 10.1113/jphysiol.2013.262840
• 发表时间: 2014-04-01
• 期刊: The Journal of physiology
• 作者: Maccione A;Hennig MH;Gandolfo M;Muthmann O;van Coppenhagen J;Eglen SJ;Berdondini L;Sernagor E
• 通讯作者: Sernagor E