myExperiment: a repository and social network for the sharing of bioinformatics workflows

Abstract

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org.

Making journal articles ‘live’: turning academic writing into scientific dialog

“…The action of the experiment could then for example be applied to other data of more recent time, another research place, or finer resolution than the original data, which could be obtained, synthesized, and concluded by the readers. As an example, using one such existing virtual research environment, in myExperiment (http:// www.myexperiment.org) users can share ''digital research objects'' such as ''workflows'' and ''files'' to facilitate various studies by multiple different researchers (Goble et al 2010). Benel and Lejeune (2009) provides another example with experiments showing how live data addition and analysis using tag information of texts could benefit from Web 2.0.…”

Ecoinformatics: supporting ecology as a data-intensive science

“…activities that support reproducible research) [69][70][71]. myExperiment was developed as a site where scientific workflows may be stored and shared [72]. However, many standard data center services, such as replication, verification, and migration and conversion to new technologies are more challenging for algorithms and workflows.…”

Scientific workflows for process mining: building blocks, scenarios, and implementation

“…Some of the SWFM systems (e.g., Kepler and Galaxy) also provide repositories of models. The website http://www.myExperiment.org lists over 3500 workflows shared by its members [19]. The diversity of the different approaches illustrates that the field is evolving in many different ways.…”