Journal of Integrative Bioinformatics 2007 http://journal.imbio.de/ Community-based Linking of Biological Network Resources: Databases, Formats and Tools Michael Telgkamp, Dirk Kosch¨ utzki, Henning Schw ¨ obbermeyer and Falk Schreiber Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany {telgkamp,koschuet,schwoebb,schreibe}@ipk-gatersleben.de Summary The analysis of biological networks is increasingly important in the life sciences and in particular in systems biology. Computer-based analysis tools are exploited for the investi- gation of these networks. However, to find relevant data sources can be a time-consuming task, access to information changes, frequently it is not obvious to a user which tools can be used in combination with specific data sources, and network data is often not available in a format directly usable by analysis tools. To assist in collecting information about biological network data sources, and to help in investigating possible combinations of data sources and analysis software, we created BiNCo-wiki. BiNCo-wiki is a wiki system that stores information related to biological networks and allows all users to add or modify this information in an easy way. The collaborative character of a wiki system supports easy sharing of information and al- lows the community-based extension of the information already stored in BiNCo-wiki. We describe the general structure and functionality of the system and its initial content. BiNCo-wiki is accessible, free of charge, at http://pgrc.ipk-gatersleben.de/ BiNCO-wiki. 1 Introduction Biological networks are abstract representations of biological systems and their analysis is a growing field in modern biology. As the networks are often very large, software tools are used for their investigation. Examples are tools to find network motifs or to rank network elements according to centrality measures. However, there is a problem with the availability of network data in a format that is readable for analysis software. On one hand there are various databases that store and export information in different file formats. On the other hand there are various computer programs that are restricted to specific file formats and do not have the ability to read all of those formats. Researchers either have to use a large number of different analysis software or are bound to use the information stored in only some of the available data sources. Nevertheless, some software can be used to open specific file formats and save the data in different file formats. Therefore it would be very useful to have information about all different ways to exchange data between data sources (e. g. databases) and analysis tools. To overcome this problem and to assist users in finding possible combinations of data sources and analysis software, we created BiNCo-wiki (BIological Networks and COnverter wiki). BiNCo-wiki is a wiki system that stores information related to biological networks – databases, file formats, software, and literature – and allows users to add or modify this information. Journal of Integrative Bioinformatics, 4(3):71, 2007 1 Copyright 2007 The Author(s). Published by Journal of Integrative Bioinformatics. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).