D1274 Nucleic Acids Research, 2012, Vol. 40, Database issue Table 2. Major types of pages in EcoliWiki Page type Gene-centric pages Strains Plasmids Databases Bioinformatics tools Methods Education & Teaching Tools Literature Cis Elements Mobile Genetic Elements Transcription Units Promoters General Information (biology, complexes, genome sequencing projects, phantom genes, genes not mapped to a genome sequence) User pages Infrastructure (templates, notices, etc.) Total (including Talk pages, genes, etc.) Number of pages 37 362 419 347 205 68 66 22 23 906 23 61 4164 31 51 763 10 695 154 887 division of pages into sections of tables and notes makes EcoliWiki more complex than some biological wikis, and it has been criticized for that complexity (7). However, this structure provides us with the ability to retrieve data from the wiki without the need for natural language processing to extract speciﬁc types of information from free text. This allows us to integrate EcoliWiki content with internal and external tools in ways that would otherwise be much more difﬁcult (Supplementary Data: Technical and Table S1). Within the wiki itself, data from tables on other pages is used in the Quickview table. The Quickview table not only looks up nomenclature from the Gene and Gene Product(s) pages, but also uses coordinates and sequences to provide data to linked tools for displaying the sequence or viewing alternative reading frames using EMBOSS (33), designing PCR primers with GBrowse (25) and Primer3 (34), and engineering silent restriction sites (35). On the Gene Product(s) page, a graphical display of the locations of domains and mutations is generated from in- formation in two different tables on the Gene and Gene Product(s) pages. As noted above, EcoliWiki Gene pages incorporate thumbnail images of local genome context using our in- stallation of GBrowse (25). Our instance of GBrowse provides genome browsing for all the E. coli and phage genomes in EcoliWiki, and for several plasmids and mobile elements. We have added several custom tracks to the E. coli MG1655 GBrowse, including transcription units from RegulonDB (1), rRNA operons, cryptic prophage, repetitive elements and others. We have been adding tracks for data from ChIP-chip studies available from public repositories or from authors (36–41). These tracks link to EcoliWiki reference pages for more detailed descriptions of the experiments and data processing. EcoliWiki has implemented a modiﬁed version of Textpresso (42), a full-text literature search engine. Our Textpresso periodically updates its corpus from reference information added to EcoliWiki. In 2011, EcoliWiki deployed a tool that allows users to search ﬁtness data and correlations from a large-scale phenotyping study pub- lished by Nichols et al. (43). This tool uses EcoliWiki to match gene names and synonyms to genes used in the study. Structured data allows EcoliWiki to provide web services for the integrated PortEco search of different E. coli resources. EcoliWiki web services can also be used to identify pages that have been edited in a speciﬁed date range. DISCUSSION EcoliWiki and other wiki-based resources show that wiki software can be adapted for many of the purposes of an online model organism database. EcoliWiki adds other freely available tools such as GBrowse and Jmol, and our own open-source development to extend the capabilities of the basic Mediawiki platform. Both web analytics (Figure 3) and anecdotal feedback from users suggest that EcoliWiki is successful in the sense that it is widely used by our target community, and is viewed as a useful resource. As a community annotation system, however, our goals also include encouraging users to contribute to the content. Any user can view content on the EcoliWiki website; however, users must register in order to create or edit content on the site. Although the requirement for an account presents an unfortunate disin- centive for community participation, requiring account creation is a relatively quick and simple method to avoid spam and vandalism. We use a ‘vampire model’ for user registration, where any registered user can create new users. Non-staff users have contributed 1513 edits to 485 pages since its rollout in 2007 as of 10 August 2011. While this is encouraging, the majority of the manually curated content in EcoliWiki is still generated by members of the EcoliWiki project. Only a small fraction of the user base has contributed content. EcoliWiki is viewed by sev- eral thousand users who are identiﬁed as repeat visitors (e.g. 6668 visited at least 5 times between 11 August 2010 and 10 August 2011), but there are only 710 non-staff registered users. Of these, only 170 have edited EcoliWiki, and many of these have only edited it once (Figure 3). Increased user participation is needed to realize one of the basic ideas of the wiki model: that quality is improved by multiple users reviewing and reﬁning the same content. To further encourage community participation, we display contributor usernames for each page on the sidebar in addition to the standard display of editors in the page history. We also promote editing the wiki in workshops and through email contact with authors of recent papers. Nevertheless, in the absence of other incentives, the low editing participation is consistent with what is seen in other resources built on voluntary collaboration, includ- ing Wikipedia (http://stats.wikimedia.org/EN/Sitemap. htm). Wikipedia overcomes this by having such a large user base that even a small fraction of users are sufﬁcient to create and improve millions of pages of content.