Tools and collaborative environments for bioinformatics research

• Published in: Briefings in bioinformatics Vol. 12; no. 6; pp. 549 - 561
• Main Authors: Romano, Paolo, Giugno, Rosalba, Pulvirenti, Alfredo
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.11.2011; Oxford Publishing Limited (England)
• Subjects: Bioinformatics; Collaboration; Computational Biology - methods; Cooperative Behavior; Identification; Internet; Social Networking; Social networks; Software; Special Issue Papers; collaborative development; open source; social networks; collaborative research; collaborative learning
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbr055

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies.