Social support for collaboration and group awareness in life science research teams
Tóm tắt
Next-generation sequencing (NGS) technologies have revolutionarily reshaped the landscape of ’-omics’ research areas. They produce a plethora of information requiring specific knowledge in sample preparation, analysis and characterization. Additionally, expertise and competencies are required when using bioinformatics tools and methods for efficient analysis, interpretation, and visualization of data. These skills are rarely covered in a single laboratory. More often the samples are isolated and purified in a first laboratory, sequencing is performed by a private company or a specialized lab, while the produced data are analyzed by a third group of researchers. In this scenario, the support, the communication, and the information sharing among researchers represent the key points to build a common knowledge and to meet the project objectives. We present ElGalaxy, a system designed and developed to support collaboration and information sharing among researchers. Specifically, we integrated collaborative functionalities within an application usually adopted by Life Science researchers. ElGalaxy, therefore, is the result of the integration of Galaxy, i.e., a Workflow Management System, with Elgg, i.e., a Social Network Engine. ElGalaxy enables scientists, that work on the same experiment, to collaborate and share information, to discuss about methods, and to evaluate results of the individual steps, as well as of entire activities, performed during their experiments. ElGalaxy also allows a greater team awareness, especially when experiments are carried out with researchers which belong to different and distributed research centers.
Tài liệu tham khảo
Johansen R. GroupWare: Computer Support for Business Teams. New York: The Free Press; 1988.
Gutwin C, Penner R, Schneider K. Group awareness in distributed software development. In: Proceedings of the 2004 Conference on Computer Supported Cooperative Work. New York: ACM: 2004. p. 72–81.
Afgan E, Baker D, Batut B, Van Den Beek M, Bouvier D, Ech M, Chilton J, Clements D, Coraor N, Grüning B, Guerler A, Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D. The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018; 46(W1):537–44.
Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: A web-based genome analysis tool for experimentalists. Curr Protoc Mole Biol. 2010; 89(1):19.10.1–19.10.21.
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller WC, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005; 15(10):1451–5.
Goecks J, Nekrutenko A, Taylor J, Team TG. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11(8):86.
Elgg. Open Source Social Networking Engine. http://www.elgg.org/. Accessed 3 July 2019.
Malandrino D, Manno I, Negro A, Petta A, Scarano V, Serra L. Social team awareness. In: Proceedings of the 9th International Conference on Collaborative Computing: Networking, Applications and Worksharing (Collaboratecom), 2013. IEEE: 2013. p. 305–14.
Dai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z. AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics. 2013; 29(14):1837–9.
De Roure D, Goble C, Bhagat J, Cruickshank D, Goderis A, Michaelides D, Newman D. myExperiment: Defining the Social Virtual Research Environment. In: IEEE Fourth International Conference on eScience, 2008. IEEE: 2008. p. 182–9.
Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010; 38(Web-Server-Issue):677–82.
De Roure D, Goble C. Software Design for Empowering Scientists. Softw, IEEE. 2009; 26(1):88–95.
Grieco R, Malandrino D, Scarano V. A scalable cluster-based infrastructure for edge-computing services. World Wide Web. 2006; 9(3):317–41.
De Prisco R, Malandrino D, Pirozzi D, Zaccagnino G, Zaccagnino R. Understanding the structure of musical compositions: Is visualization an effective approach?Inf Vis. 2017; 16(2):139–52.
Malandrino D, Scarano V, Spinelli R. How Increased Awareness Can Impact Attitudes and Behaviors toward Online Privacy Protection. In: 2013 International Conference on Social Computing (SocialCom). IEEE: 2013. p. 57–62.
Malandrino D, Manno I, Palmieri G, Scarano V, Tateo L, Casola D, Ferrante I, Foresta F. A tailorable infrastructure to enhance mobile seamless learning. TLT. 2015; 8(1):18–30.