The analysis of 3D genomic data is expected to revolutionize our understanding of genome organization and regulatory mechanisms. Yet, the complex spatial organization of this information can be difficult to interpret with 2D viewers. Virtual Reality (VR) technologies offer an opportunity to rethink our methods to visualize and navigate 3D objects. In this paper, we introduce the Virtual Reality 3D Genome Viewer (3DGV), an open platform to experiment and develop VR solutions to explore 3D genome structures.Availability: http://3dgv.cs.mcgill.ca/
Clustering is a central task in many data analysis applications. However, there is no universally accepted metric to decide the occurrence of clusters. Ultimately, we have to resort to a consensus between experts. The problem is amplified with high-dimensional datasets where classical distances become uninformative and the ability of humans to fully apprehend the distribution of the data is challenged. In this paper, we design a mobile human-computing game as a tool to query human perception for the multidimensional data clustering problem. We propose two clustering algorithms that partially or entirely rely on aggregated human answers and report the results of two experiments conducted on synthetic and real-world datasets. We show that our methods perform on par or better than the most popular automated clustering algorithms. Our results suggest that hybrid systems leveraging annotations of partial datasets collected through crowdsourcing platforms can be an efficient strategy to capture the collective wisdom for solving abstract computational problems.
Video game is a versatile and powerful media to communicate and engage the public in life science research and education, where it is increasingly used as a teaching support tool in higher education. At the same time, video games are also becoming common vehicles for citizen science initiatives in molecular and cell biology that allows participants to contribute to real scientific data analysis. Since 2010, our citizen science game Phylo (http://phylo.cs.mcgill.ca) enlists internet users in comparative genomic data analysis. Although it was not its initial purpose, Phylo also quickly became a popular resource for biology instructors. Here, we introduce a new release of Phylo and its web platform for advanced users OpenPhylo, which have been redesigned to facilitate educational uses. Phylo now features a story mode that progressively introduces basic comparative genomic concepts to the participants and allow them to contribute to improve the alignment of real DNA and RNA sequences. We also implement new roles and functionalities in OpenPhylo that enable instructors to easily create, invite, and monitor progresses of students on assignments using Phylo. Our data shows that our approach promotes student engagement and contributes to support the teaching of basic comparative genomics principles.
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