SEQwiki:About
The SEQanswers wiki is a Semantic MediWiki (SMW) site that is edited and updated by the members of the SEQanswers community. The wiki provides an extensive catalogue of manually categorized analysis tools, technologies and information about service providers. Within two years, the SEQanswers community has created pages for over 400 unique software tools and associated them with around 350 literature references and 500 web links (9th Aug 2011)
Contact us
There are several ways to get in touch. Probably the best is to start a new topic in the Wiki Discussion Forum on the SEQanswers forum.
You can tweet @ the SEQanswers twitter account.
The most direct way is to email the wiki admin.
Citing SEQwiki
References
To add a reference for SEQwiki:About, enter the PubMed ID in the field below and click 'Add'.
Future directions?
You can help us!
SEQwiki is an on-going project. The number of records in the wiki will continue to increase as new software tools are announced and published. The wiki has served as a successful platform providing searching capabilities on software tools for users. We plan to further enhance the features of the wiki. In particular, we would like to improve the following areas:
- Community review system
- before SEQanswers, user feedback was almost exclusively directed to software authors. Only a few disparate, well established or well-funded groups provided publicly archived mailing lists for community discussion. Software reviews by bloggers were similarly posted independently and relatively rarely. SEQanswers has fostered lively review of both pre-publication and post-publication tools. Usually, long before peer review publication, tools have been announced in SEQanswers and tested extensively within the community. Post-publication improvement and benchmarking among developers is encouraged by discussions in the SEQanswers forum. SEQwiki currently provides a quality metric by presenting the total view count of a tool’s page and the citation count of its associated publications. In future, functionality to provide detailed ratings and reviews could be added to the wiki.
- Community-wide benchmarking
- Systematic benchmarking is a very important task that is rarely achieved. A few community-wide HTS benchmarking projects are currently underway, including the Critical Assessment of Genome Interpretation (CAGI), the Assemblathon (8), Genome Assembly Gold-Standard Evaluations (CAGE) and dbGASP. By using the wiki, we aim to distribute and ‘crowd source’ this type of data directly from the community. Data sets for benchmarking software tools could be hosted, and performance results could be collected by the community. Software developers would be motivated to provide information on their tools, and users would be motivated to feed back the results of their important individual and hitherto largely unpublishable experimentation.
- Integration with the semantic web
- there are several efforts to organize databases and software in the life sciences using ontologies, for example, the Software Ontology and the EDAM Ontology. The keywords describing software tools in SEQwiki could be organized using these controlled vocabularies. These data would be distributed over the semantic web using standards such as Resource Description Framework (RDF), which is integrated into Semantic MediaWiki. This approach allows reuse of data either directly on external web pages or by external tools that wish to query SEQwiki. Similarly, data could be queried from the semantic web and presented within SEQwiki.
