The Development And Application Of The BioW Platform

In life science, new techniques and experimental methods produce explosive amounts of biological information. Accordingly, to analyze the experimental data, many algorithms and computer programs have been developed. Since these programs are developed by commercial companies or academic institutes independently, the lack of common standard makes the talks between them difficult. In one integrative analysis, when several of them are needed, the researchers are usually exhausted by the program switching and data transformation. Firstly, these software tools in corresponding field did not provide the standard data interface and algorithm interface. Secondly, all the tools and software mentioned above did not support collaborative analysis on the experimental data. Additionally, these tools and software are not operation system (OS) independent. Furthermore, the lack of a friendly interface, such as graphical user interface (GUI), will impede the efficiency of data analysis.In this paper, we developed an integrative workflow-based platform for the experimental data analysis, namely BioW (Bio-Workfow). BioW is built on the Java 2 Platform Enterprise Edition (J2EE), which provides (1) a general application development interface to integrate or bridge other programs and (2) a workflow mechanism to operate them and make them talk easily.The SDK provided by BioW defines a series of interface, such as Bio-data and Bio-node, with which the users can integrate any data sets, routines and viewers into the neural spike train data analysis without caring their input-output data formats, programming language and OS. The current existed algorithms (viewers) are classified into three categories: open source of algorithms programming with Java, open source of algorithms programming with other language (such as C, C++, etc.) and binary executable algorithms programs. The users can easily integrate all these kinds of algorithms into the platform through the interface Bio-node defined by SDK.The user management mechanism provided by BioW support collaborative mechanism, which enables multiple users share the same data and the same workflow without conflict. According to this mechanism, each user has a private user space where workflows and data are stored, and a public user space that be shared with other users belonging to the same group. With this sharing mechanism, the different users in the same group can not only share the same data, but also edit and execute the same workflow. Therefore many users can work together on the same experimental data analysis. This collaborative mechanism is necessary for the researchers to handle some complex neuroscience project.Moreover, as a Java-based software, BioW can be deployed in different OS without any modification, such as recompiling the whole project. Friendly GUI that provides the construction and management of workflows greatly facilitates the managing and processing the experimental data.