MAGMA: analysis of two-channel microarrays made easy

The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch

An Open Framework for Integrating Widely Distributed Hypermedia Resources

The success of the WWW has served as an illustration of how hypermedia functionality can enhance access to large amounts of distributed information. However, the WWW and many other distributed hypermedia systems offer very simple forms of hypermedia functionality which are not easily applied to existing applications and data formats, and cannot easily incorporate alternative functions which would aid hypermedia navigation to and from existing documents that have not been developed with hypermedia access in mind. This paper describes the extension to a distributed environment of the open hypermedia functionality of the Microcosm system, which is designed to support the provision of hypermedia access to a wide range of source material and application, and to offer straightforward extension of the system to incorporate new forms of information access

Unifying Distributed Processing and Open Hypertext through a Heterogeneous Communication Model

A successful distributed open hypermedia system can be characterised by a scaleable architecture which is inherently distributed. While the architects of distributed hypermedia systems have addressed the issues of providing and retrieving distributed resources, they have often neglected to design systems with the inherent capability to exploit the distributed processing of this information. The research presented in this paper describes the construction and use of an open hypermedia system concerned equally with both of these facets

Design of a shared whiteboard component for multimedia conferencing

This paper reports on the development of a framework for multimedia applications in the domain of tele-education. The paper focuses on the protocol design of a specific component of the framework, namely a shared whiteboard application. The relationship of this component with other components of the framework is also discussed. A salient feature of the framework is that it uses an advanced ATM-based network service. The design of the shared whiteboard component is considered representative for the design as a whole, and is used to illustrate how a flexible protocol architecture utilizing innovative network functions and satisfying demanding user requirements can be developed

Proceedings of the ECSCW'95 Workshop on the Role of Version Control in CSCW Applications

The workshop entitled "The Role of Version Control in Computer Supported Cooperative Work Applications" was held on September 10, 1995 in Stockholm, Sweden in conjunction with the ECSCW'95 conference. Version control, the ability to manage relationships between successive instances of artifacts, organize those instances into meaningful structures, and support navigation and other operations on those structures, is an important problem in CSCW applications. It has long been recognized as a critical issue for inherently cooperative tasks such as software engineering, technical documentation, and authoring. The primary challenge for versioning in these areas is to support opportunistic, open-ended design processes requiring the preservation of historical perspectives in the design process, the reuse of previous designs, and the exploitation of alternative designs. The primary goal of this workshop was to bring together a diverse group of individuals interested in examining the role of versioning in Computer Supported Cooperative Work. Participation was encouraged from members of the research community currently investigating the versioning process in CSCW as well as application designers and developers who are familiar with the real-world requirements for versioning in CSCW. Both groups were represented at the workshop resulting in an exchange of ideas and information that helped to familiarize developers with the most recent research results in the area, and to provide researchers with an updated view of the needs and challenges faced by application developers. In preparing for this workshop, the organizers were able to build upon the results of their previous one entitled "The Workshop on Versioning in Hypertext" held in conjunction with the ECHT'94 conference. The following section of this report contains a summary in which the workshop organizers report the major results of the workshop. The summary is followed by a section that contains the position papers that were accepted to the workshop. The position papers provide more detailed information describing recent research efforts of the workshop participants as well as current challenges that are being encountered in the development of CSCW applications. A list of workshop participants is provided at the end of the report. The organizers would like to thank all of the participants for their contributions which were, of course, vital to the success of the workshop. We would also like to thank the ECSCW'95 conference organizers for providing a forum in which this workshop was possible