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.

布兰迪斯大学在计算神经科学方面有着悠久的历史。这项工作的特点是 理论和计算工作之间的密切和亲密的关系，以及许多 这项资助的实验者（Marder，Lisman，Turrigiano，纳尔逊）发表了许多 计算和建模论文，阐明和/或推动了他们的许多实验 调查结果。目前，我们有一个强大的计算期刊俱乐部，每周一与 大约20名教师，博士后和研究生出席，其中许多人在NINDS资助的工作 labs.例如，Marder现在有4名博士后和3名研究生，他们专门从事或 部分计算工作，其中一人现在正在建立Birren的神经元模型Lisman长期以来一直 计算项目和保罗米勒，一个理论家和新雇员，已经在合作工作 和Lisman Fiser Katz Turrigiano一起 我们相信我们建立和分析计算模型的能力正变得越来越重要 产生与实验工作相关的新假设。我们现在所处的时代， 生物学的研究方法正被解释系统行为的努力所补充， 底层组件。无论我们称之为“系统生物学”还是其他名称，情况仍然是这样， 如果人们想了解多个非线性过程的相互作用， 建立模型并确定系统的哪些属性取决于哪些组件 交互.例如，Birren/Marder计算合作是为了响应数据而出现的。 在Birren实验室产生的，“乞求”一个模型来帮助理解这些数据， 从他们那里做进一步的预测。因此，我们设想，越来越多的实验 同事们会发现，在校园里拥有计算专业知识和核心设施是很有用的， 将可以运行大大小小的模拟。计算核心的加入将使 我们坚信，计算和建模工作对所有人都将变得越来越重要， 我们的实验室，这些设施是容易获得和支持。 最初，我们的计算工作是用实验室计算机和/或小的单个集群完成的。 处理器.这有两个缺点：相对较少的处理器数量可用于任何给定的 调查员，以及花费太多时间维护太多小集群。因此， 在史蒂文·卡雷尔博士的建议和帮助下，我们的生物学 计算专家和LTS，大学的技术部门，以巩固各种小的 神经科学、生物化学和物理学中发现的集群，合并成一个大集群。我们正在 通过使用我们所有现有的机器，然后添加新的硬件来实现这一点;我们希望这样做 这一进程将于2007年底完成。这个新的计算集群将需要监督， 此外，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的一部分，我们觉得， 这一集群将为我们正在进行的由国家核动力学和核安全研究所资助的研究提供重要的资产，我们希望 将这个新的集中设施添加到这个核心赠款中。这对于维护 集群维护和运行的一致性。