Protemics Bioinformatics Tools

我们一直在研究几种蛋白质组生物信息学工具：为来自不同来源(2D PAGE凝胶、2D LC-MS、蛋白质阵列等)的n维蛋白质数据开发一个开源的蛋白质组表达数据挖掘工具集(Open2Dprot)；改进的目测比较2D凝胶蛋白质样本的方法(Flicker程序)以及用于鉴定纳米颗粒的增强的斑点鉴定；我们最近开始研究2D DGE图像的精细属性(CmpDIGE计划)，它可能有助于我们表征这些变化，然后建模和识别相对较小的翻译后蛋白质修改。Open2Dprot-开放的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，用于开发工具来分析来自各种蛋白质分离方法的蛋白质表达数据。通过分析管道来分析数据，该分析管道包括：样本数据的加入、样本中的斑点检测(使用图像分割、峰值聚类或其他方法)、在需要时样本之间的配准、在需要时相对于参考样本的斑点配对、将配对的斑点数据汇编到存储在关系数据库中的复合斑点数据库中、以及使用Java和R语言分析两者的子集上的数据挖掘工具。所有数据文件现在都完全兼容XML。我们已经完成了Open2Dprot流水线数据分析器和流水线进程调度器的初步设计，并使用动态方法实现了大部分代码。数据来源将包括：2D-PAGE(聚丙烯酰胺凝胶电泳法)、2D LC-MS、蛋白质阵列等。由于不同的分离来源需要不同的分析方法，因此管道的设计使得管道中的特定步骤可以根据数据源类型动态分配。我们正在与国际组织合作，为这些类型的样品分离开发实验信息和蛋白质表达的蛋白质组学生物信息学数据库模式标准(MIAPE/GelML XML标准)。我们的目标是致力于开发与这些正在开发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。作为一套开源工具，它将能够纳入定量和定性蛋白质表达分析方面的新的学术(和其他)进展--包括与各种互联网蛋白质组数据库和系统生物学数据库的交互。Http://open2dprot.sourceforge.net/上已经建立了一个网站，详细介绍了这一点。当管道软件的部分变得可用时，它们就可以在网站上的网站上使用(见分项目)。这些程序是用JAVA编写的，可以在大多数计算机上运行。Flicker是一个独立的软件程序，用于促进互联网上的生物样本的交互比较。它是对上一个子项目Flicker小程序Lemkin PF，ET的重大更新。艾尔(1999)摩尔生物技术12(2)：159-172。新程序被描述为Lemkin PF，et。艾尔(2005)(12Mb PDF)“比较互联网数据库中的二维电泳胶”。在蛋白质组学手册中，JM Walker(Ed)，Humana Press Inc.，Toowa，NJ，第279-305页。世界各地的科学家经常研究类似的数据，因此定期出现分享结果和比较数据的需求。Flicker是一种Java计算机实现的闪烁比较方法，用于比较在不同实验室创建的两个类似样本的2D凝胶图像数据，以帮助假定识别用户2D凝胶中的蛋白质斑点。

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. 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.