Technological Development and Advances for Constructing and Analyzing Plant Pangenomes

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.

A course-based undergraduate research experience for bioinformatics education in undergraduate students

With rapid development of sequencing technology and the continuous accumulation of biological big data, people who are capable of using bioinformatic skills to analyze omics data and work out biological problems are urgently needed in the workforce, which highlights the importance of developing bioinformatics skills early in the undergraduate curriculum. Meanwhile, course-based undergraduate research experience (CURE) courses have been proved to be an effective teaching format that have many advantages over traditional labs and lectures. Here we introduced an implementation of CURE course of bioinformatics data analysis and visualization for undergraduate students in major of bioinformatics and evaluated the learning outcomes. We were able to address 10 out of 15 core competencies identified by Network for Integrating Bioinformatics into Life Sciences Education. Besides, results evaluated by Laboratory Course Assessment Survey demonstrated the goals of collaboration, discovery and relevance, and iteration were accomplished in our course. Meanwhile, a significant increase in scores of final examinations and a long-term improvement on students' research ability on bioinformatics data analysis and visualization were also observed. In summary, this CURE course is useful for undergraduate students learning related knowledge and participate in authentic research in the field of bioinformatics.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations

This article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

Nebula: reconstruction and visualization of scattering data in reciprocal space

Two-dimensional solid-state X-ray detectors can now operate at considerable data throughput rates that allow full three-dimensional sampling of scattering data from extended volumes of reciprocal space within second to minute time-scales. For such experiments, simultaneous analysis and visualization allows for remeasurements and a more dynamic measurement strategy. A new software, Nebula, is presented. It efficiently reconstructs X-ray scattering data, generates three-dimensional reciprocal space data sets that can be visualized interactively, and aims to enable real-time processing in high-throughput measurements by employing parallel computing on commodity hardware.