Protemics bioinformatics tools

我们一直致力于几个蛋白质组学生物信息学工具：一个开发开源蛋白质组学表达数据挖掘工具集的项目（Open 2Dprot），用于来自各种来源的n维蛋白质数据（2D PAGE凝胶，2D LC-MS，蛋白质阵列等）;一种用于目视比较2D凝胶蛋白质样品的改进方法（闪烁程序）和进行推定的斑点鉴定，并增强表征纳米颗粒;我们最近开始研究二维DIGE图像（CmpDIGE程序）的细微特性，这可能有助于我们表征这些变化，然后建模和识别相对较小尺寸的翻译后蛋白质修饰。我们通过额外的数据和数据探索功能增强了ProtPlot工具。 Open 2Dprot-开放的2D蛋白质组学表达n维数据分析项目 Open 2Dprot是一个完全开源的社区蛋白质组学项目和网站，用于开发分析各种蛋白质分离方法的蛋白质表达数据的工具。数据通过分析管道进行分析，包括：样品数据的加入，样品中的斑点检测（使用图像分割、峰值聚类或其他方法），在需要时在样品之间配准，在需要时相对于参考样品进行点配对，将配对的点数据组装成存储在关系数据库中的复合点数据库，以及使用Java和R语言分析子集的数据挖掘工具。所有数据文件现在都完全与XML兼容。我们已经完成了Open 2Dprot管道数据分析器和管道进程调度器的初步设计，并使用动态方法实现了代码的主要部分。数据来源将包括：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，因此管道设计为可以根据数据源类型动态分配管道中的特定步骤。我们正在与国际团体合作开发蛋白质组学生物信息学数据库模式标准，用于这些类型的样品分离的实验信息和蛋白质表达（MIAPE/GelML XML标准）。我们的目标是努力开发与这些发展中的蛋白质组学数据库标准兼容的工具，以便数据和分析软件可以交换。作为一个开源工具集，它将能够整合定量和定性蛋白质表达分析的新学术（和其他）进展-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交互。已经在http://open2dprot.sourceforge.net/上建立了一个网站，提供更详细的信息。当管道软件的一部分变得可用时，它们可以在网站上获得（参见子项目）。这些程序是用Java编写的，可以在大多数计算机上运行。 互联网上生物样本的闪烁互动比对 Flicker，http：//open2dprot.sourceforge.net/Flicker，是一个独立的软件程序，用于促进互联网上生物样本的交互式比较。它是前一个子项目，闪烁小程序程序Lemkin PF等的主要更新。等人（1999）Mol Biotechnology 12（2）：159-172。Lemkin PF，et.（2005）（12Mb PDF）“Comparing 2-D Electrophoretic Gels Across Internet Databases”。在The Proteomics Handbook，JM步行者（艾德版），Humana Press Inc，Totowa，NJ，第279-305页中。世界各地的科学家经常研究类似的数据，因此需要定期分享结果和比较数据。Flicker是一种闪烁比较方法的Java计算机实现，用于比较在不同实验室创建的两个相似样品的2D凝胶图像数据，以帮助puppet识别用户2D凝胶中的蛋白质点。

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.