Computational Core

计算核心

• 批准号: 8374478
• 负责人: MICHAEL ROSBASH
• 金额: $ 8.27万
• 依托单位: BRANDEIS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-30 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8374478
• 关键词: Accounting; Behavior; Belief; Biochemistry; Biology; Cancer Center Support Grant; Collaborations; Computational Biology; Computer Simulation; Computers; Core Facility; Data; Disadvantaged; Faculty; Funding; Grant; Individual; Journals; Laboratories; Long-Term Survivors; Maintenance; Modeling; Names; National Institute of Neurological Disorders and Stroke; Neurobiology; Neurons; Neurosciences; Paper; Physics; Postdoctoral Fellow; Process; Property; Publishing; Recording of previous events; Research; Research Personnel; Running; System; Systems Biology; Technology; Time; Universities; Work; base; computational neuroscience; graduate student; laboratory facility; meetings; operation; response; simulation

Brandeis University has a long history in computational neuroscience. This work has been characterized by the close and intimate relationships between theoretical and computational work, and many of the experimentalists on this grant (Marder, Lisman, Turrigiano, Nelson) have published numerous computational and modeling papers that have illuminated and/or driven many of their experimental findings. At present, we have a strong computational journal club that meets every Monday with attendance of about 20 faculty, postdocs, and graduate students, many of whom work in NINDS-funded labs. For example, Marder now has 4 postdocs and 3 graduate students who are doing exclusively or partially computational work, one of whom is now building models of Birren's neurons Lisman has longstanding computational projects and Paul Miller, a theorist and new hire, is already in collaborative work with Lisman, Fiser, Katz and Turrigiano. We believe that our ability to build and analyze computational models is becoming increasingly important in generating new hypotheses relevant to experimental work. We are now in an era in which reductionist approaches to biology are being supplemented by efforts to account for system behavior in terms of their underlying components. Whether we call this "systems biology" or another name, it remains the case that if one wants to understand the interaction of multiple, non-linear processes, it becomes useful, even necessary, to build models and determine which properties of the system depend on which component interactions. For example, the Birren/Marder computational collaboration arose in response of data generated in the Birren laboratory that were "begging" for a model to help understand these data and make further predictions from them. Therefore, we envision that more and more of our experimental colleagues will find it useful to have both computational expertise on campus, as well as a Core facility that will be available to run simulations, large and small. The addition of a Computational Core will make tangible our firm belief that computational and modeling work will become increasingly important to all of our experimental laboratories, and that these facilities be easily accessible and supported. Initially our computational work was done with lab-based computers, and/or small individual clusters of processors. This has two disadvantages: the relatively small number of processors available to any given investigator, and too much time being spent in maintaining too many small clusters. Consequently, a number of faculty around campus decided, with the advice and help of Dr. Steven Karel, our Biology Computational Expert, and LTS, the university's technology department, to consolidate the various small clusters found in neuroscience, biochemistry, and physics, into one large cluster. We are in the process of doing so, by taking all of our existing machines and then adding to them new hardware; we expect this process to be complete by the end of 2007. This new computational cluster will need oversight and maintenance for most effective management, and it will also need periodic replacements and upgrades. Because computational work is so integral to the experimental components of so many of us, we feel that this cluster will provide a significant asset to the NINDS-funded research we are now doing, and want to add this newly centralized facility to this Core grant. This is expecially important to maintaining consistency in the cluster maintenance and operation.

布兰代斯大学在计算神经科学方面的历史悠久。这项工作的特征是 通过理论和计算工作之间的亲密和亲密关系，许多 这项赠款的实验家（马尔德，利斯曼，塔里吉亚诺，纳尔逊）发表了许多 启动和/或驱动其许多实验的计算和建模论文 发现。目前，我们有一个强大的计算期刊俱乐部，每个星期一都会与 大约有20名教职员工，博士后和研究生的出席人数，其中许多人在Ninds资助 实验室。例如，Marder现在有4位专业的博士后和3名研究生，或者 部分计算工作，其中一项正在建立伯伦神经元的模型。 计算项目和理论家和新员工保罗·米勒（Paul Miller）已经在合作工作 与利斯曼，菲塞尔，卡茨和Turrigiano一起。 我们认为，我们建立和分析计算模型的能力变得越来越重要 在产生与实验工作有关的新假设时。我们现在正处于一个还原主义者的时代 生物学方法正在补充以说明系统行为的努力 基础组件。无论我们称此“系统生物学”或其他名称，仍然是 如果一个人想了解多个非线性过程的相互作用，它将变得有用，即使 需要建立模型并确定系统的哪些属性取决于哪个组件 互动。例如，Birren/Marder计算协作是为了响应数据的响应 在Birren实验室中产生的，该模型“乞求”，以帮助了解这些数据和 从他们那里做出进一步的预测。因此，我们设想越来越多的实验 同事将发现在校园内拥有计算专业知识以及一个核心设施很有用 将可以运行大小的模拟。添加计算核心将使 我们坚定的信念，即计算和建模工作对所有人都将变得越来越重要 我们的实验实验室，并且这些设施很容易获得和支持。 最初，我们的计算工作是通过基于实验室的计算机和/或小的单个集群完成的 处理器。这有两个缺点：任何给定的处理器数量相对较少 调查员，花了太多时间来维持太多小簇。因此， 校园周围的教职员工在我们的生物学史蒂文·卡雷尔（Steven Karel）博士的建议和帮助下决定 计算专家和大学的技术系LTS，以合并各种小型 在神经科学，生物化学和物理学中发现的簇成一个大集群。我们正在 这样做，通过采用我们所有现有的机器，然后将其添加到新硬件中；我们期望这一点 在2007年底之前要完成的过程。这个新的计算集群将需要监督，并且 维护最有效的管理，还需要定期更换和升级。 因为计算工作是我们许多人的实验组成部分不可或缺的，所以我们认为 该集群将为我们现在正在做的Ninds资助的研究提供重要资产，并希望 将这个新的集中式设施添加到该核心赠款中。这对于维护特别重要 集群维护和操作的一致性。