Jemboss的设计：一个用于EMBOSS的图形用户界面。

The design of Jemboss: a graphical user interface to EMBOSS.

作者信息

Carver Tim, Bleasby Alan

机构信息

MRC UK HGMP Resource Centre, Hinxton, Cambridge CB10 1SB, UK.

出版信息

Bioinformatics. 2003 Sep 22;19(14):1837-43. doi: 10.1093/bioinformatics/btg251.

DOI:10.1093/bioinformatics/btg251

PMID:14512356

Abstract

DESIGN

Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings.

RESULTS

This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users.

AVAILABILITY

The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/

摘要

设计

Jemboss是欧洲分子生物学开放软件套件（EMBOSS）的图形用户界面（GUI）。它作为EMBOSS项目的一部分，由英国医学研究理事会人类基因组图谱资源中心（MRC UK HGMP-RC）开发。本文解释了Jemboss客户端-服务器设计的技术方面。客户端-服务器模型允许Jemboss用户在远程服务器上拥有账户。Jemboss客户端用Java编写，并通过Java Web Start使用HTML协议自动下载到用户的工作站。然后客户端使用SOAP（简单对象访问协议）与远程服务器通信。一个Tomcat服务器在远程机器上监听，并将SOAP请求传递给同样用Java编写的Jemboss服务器。这个Java服务器解释客户端请求，并通过用C语言编写的Java本地接口（JNI）代码来执行这些请求。另一个具有设置用户ID权限的C程序jembossctl由JNI代码调用，以在服务器上用户的账户下执行客户端请求。这些命令包括执行EMBOSS应用程序、文件管理和项目管理任务。Jemboss允许使用JSSE对客户端和服务器之间的通信进行加密。GUI解析EMBOSS Ajax命令定义语言以生成表单并实现最大输入灵活性。Jemboss直接与EMBOSS库交互，以允许动态生成应用程序默认设置。