As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. JBrowse 2 retains the core features of the open-source JavaScript genome browser JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. The software readily allows users to share sessions, open multiple genomes or views, and navigate quickly between these views. It can be embedded in a web page, used as a standalone desktop application, or run from Jupyter notebooks or R sessions. Using a plugin framework, developers can create new data adapters, track types, and visualizations. These improvements are enabled by a ground-up redesign of the JBrowse architecture using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

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The Mojave Desert has been long considered a suitable terrestrial analogue to Mars in many geological and astrobiological aspects. The Silver Lake region in the Mojave Desert hosts several different rock types (talc, marble, quartz, white carbonate, and red-coated carbonate) colonized by hypoliths within a few kilometers. This provides an opportunity to investigate the effect of rock type on hypolithic colonization in a given environment. Transmission measurements from 300 to 800 nm showed that the transmission of blue and UVA varied between rock types. The wavelength at which the transmission fell to 1% of the transmission at 600 nm was 475 nm for white carbonate and quartz, 425 nm for red-coated carbonate and talc, and 380 nm for marble. The comparative analysis of the cyanobacterial component of hypoliths under different rocks, as revealed by sequencing 16S rRNA gene clone libraries, showed no significant variation with rock type; hypoliths were dominated by phylotypes of the genus Chroococcidiopsis, although less abundant phylotypes of the genus Loriellopsis, Leptolyngbya and Scytonema occurred. The comparison of the CLSM-λscan analysis of the spectral emission of the photosynthetic pigments of Chroococcidiopsis in different rocks with the spectrum of isolate Chroococcidiopsis sp. 029, revealed a 10 nm-red shift in the emission fingerprinting for quartz and carbonate and a 5 nm-red shift for talc samples. This result reflects the versatility of Chroococcidiopsis in inhabiting dry niches with different light availability for photosynthesis