Protemics bioinformatics tools

Protemics 生物信息学工具

• 批准号: 7292172
• 负责人: peter f lemkin
• 金额: --
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7292172
• 关键词: Protemics; bioinformatics; tools

We have been working on several proteomics bioinformatics tools: a project to develop an open-source proteomics expression data mining tool set (Open2Dprot) for n-dimensional protein data from various sources (2D PAGE gels, 2D LC-MS, protein arrays, etc); an improved method for visually comparing 2D gel protein samples (Flicker program) and making putative spot identifications with enhancements for characterizing nanoparticles; we recently started investigating subtle properties of 2D DIGE images (CmpDIGE program) that may help us characterize these changes, and then model and identify post-translational protein modifications of relatively small size. We enhanced the ProtPlot tool with additional data and data-exploration capabilities. Open2Dprot - the open 2D proteomics expression n-dimensional data analysis project Open2Dprot is a fully open-source community proteomics project and Web site for developing tools for analyzing protein expression data from a variety of protein separation methods. Data is analyzed through an analysis pipeline that includes: accession of sample data, spot detection in samples (using image segmentation, peak clustering or other methods), registration between samples where required, spot pairing with respect to a reference sample where required, assembly of paired spot data into a composite spot database stored in a relational database, and data mining tools on subsets using both Java and R language analyses. All data files are now fully XML compatible. We have completed the initial design of the Open2Dprot pipeline data analyzer and pipeline process scheduler and have implemented a major portion of the code using dynamic methods. Data sources will include: 2D-PAGE (polyacrylamide gel electrophoresis), 2D LC-MS, protein arrays, etc. Because different separation sources require different analysis methods, the pipeline is designed so that particular steps in the pipeline can be assigned dynamically depending on the data source type. We are working with international groups developing proteomics bioinformatics database schema standards for experiment information and protein expression for these types of sample separations (MIAPE/GelML XML standards). Our goal is to work towards developing tools compatible with these developing proteomics database standards so data and analysis software could be exchanged. As an open-source tool set, it will be able to incorporate new academic (and other) advances in quantitative and qualitative protein expression analysis - including interaction with various Internet proteomic databases and system biology databases. A Web site has been set up at http://open2dprot.sourceforge.net/ that goes into more detail. As parts of the pipeline software become usable, they are made available on the Web site (see Subprojects) on the web site. These programs are written in Java and run on most computers. Flicker interactive comparison of biological samples across the Internet Flicker, http://open2dprot.sourceforge.net/Flicker, is a stand-alone software program to facilitate the interactive comparison of biological samples across the Internet. It is a major update of the previous subproject, the Flicker applet program Lemkin PF, et. al. (1999) Mol Biotechnology 12(2): 159-172. The new program is described Lemkin PF, et. al. (2005)(12Mb PDF) "Comparing 2-D Electrophoretic Gels Across Internet Databases". In The Proteomics Handbook, JM Walker (Ed), Humana Press Inc, Totowa, NJ, pp 279-305. Scientists around the world often work on similar data so the need to share results and compare data arises periodically. Flicker is a Java computer-implementation of a flicker-comparison method for comparing 2D gel image data of two similar samples created in different laboratories to help putatively identify protein spots in user's 2D gels.

我们一直在开发多种蛋白质组学生物信息学工具：开发开源蛋白质组学表达数据挖掘工具集（OPEN2DPROT）的项目，用于来自各种来源的N维蛋白数据（2D Page Gels，2D LC-MS，2D LC-MS，蛋白质阵列等）；一种改进的方法，可在视觉上比较2D凝胶蛋白样品（闪烁程序），并通过以增强纳米颗粒为特征的假定点标识。我们最近开始研究2D DIGE图像（CMPDIGE程序）的微妙特性，这些特性可能有助于我们表征这些变化，然后建模并识别相对较小尺寸的翻译后蛋白质修饰。我们使用其他数据和数据探索功能增强了Protplot工具。 Open2DPROT-开放2D蛋白质组学表达n维数据分析项目 Open2Dprot是一个完全开源的社区蛋白质组学项目和网站，用于开发用于分析各种蛋白质分离方法的蛋白质表达数据的工具。通过分析管道进行分析数据，该管道包括：样本数据的访问，样品中的点检测（使用图像分割，峰值聚类或其他方法），在需要的情况下在样本之间进行注册，相对于参考样品的点配对，需要在需要的参考样品中，将配对的点数据组装到相关数据库中，将配对的点数据存储在相关数据库中，并分析了java和java andsect和java andsect和java。现在，所有数据文件均完全兼容。我们已经完成了Open2Dprot管道数据分析仪和管道过程调度程序的初始设计，并使用动态方法实现了代码的很大一部分。数据源将包括：2D-PAGE（聚丙烯酰胺凝胶电泳），2D LC-MS，蛋白质阵列等。由于不同的分离源需要不同的分析方法，因此设计了管道，因此可以根据数据源类型动态分配管道中的特定步骤。我们正在与开发蛋白质组学生物信息学数据库架构标准的国际团体合作，以实验信息和蛋白质表达这些样品分离（MIAPE/GELML XML标准）。我们的目标是致力于开发与这些开发的蛋白质组学数据库标准兼容的工具，以便可以交换数据和分析软件。作为开源工具集，它将能够在定量和定性蛋白质表达分析中纳入新的学术（和其他）进步，包括与各种互联网蛋白质组学数据库和系统生物学数据库的互动。已经在http://open2dprot.sourceforge.net/上设置了一个网站，该网站更详细地了。随着管道软件的一部分变得可用，它们将在网站上的网站上提供（请参见子标记）。这些程序用Java编写，并在大多数计算机上运行。 跨越互联网的生物样品的闪烁互动比较 Flicker，http：//open2dprot.sourceforge.net/flicker是一个独立的软件程序，可促进互联网上生物样品的交互式比较。这是先前的子标记，“闪烁applet程序Lemkin PF等”的重大更新。 al。 （1999）Mol Biotechnology 12（2）：159-172。新程序被描述为Lemkin PF等。 al。 （2005）（12MB PDF）“比较跨互联网数据库的2-D电泳凝胶”。在《蛋白质组学手册》中，JM Walker（ED），Humana Press Inc，Totowa，NJ，第279-305页。世界各地的科学家经常致力于类似的数据，因此需要分享结果并定期比较数据。 Flicker是一种闪烁量化方法的Java计算机实践，用于比较在不同实验室中创建的两个类似样品的2D凝胶图像数据，以帮助俯冲地识别用户2D凝胶中的蛋白质斑点。