Abstract: A high throughput system and method for analyzing the effects of a plurality of agents on planaria is disclosed. Multiple test zones are provided, where each test zone contains at least a portion of one planarian. The planaria in each test zone are then exposed to at least one agent, the test zones are sealed, and at various times, the test zones are moved automatically between a storage location and at least one assay station. At each assay station, the test zones are exposed to a set of conditions, and an image or video of the planaria in the test zones are captured. Automated image or video analysis is used to are evaluate and determine whether the agent has an effect.

Abstract: A screening method for a drought-resistant germplasm of Ophiopogon japonicus related to the field of Ophiopogon japonicus planting is provided. The method uses Ophiopogon japonicus of the main production areas, which requires a large amount of water and rainfall during the growth period, the drought-resistant germplasm that is suitable for growing well is conducted with drought stress under the drought condition. The growth indicators and the physiological indicators of different Ophiopogon japonicus germplasm under drought stress conditions are comprehensively evaluated and ranked to evaluate the drought-resistant ability of the different germplasm. The screening method is scientific and effective, and can comprehensively evaluate the drought resistance ability of Ophiopogon japonicus under the drought stress conditions, laying a technical foundation for the screening and promotion of in the Ophiopogon japonicus with drought resistance ability.

Abstract: To analyze spatial organization of chromatin a computing device may compile genomic element contacts or reads into variable size bins using a binary search tree. The bins may be selected to each represent a different cutsite increment or functional element within a genome, such as a gene, TAD, chromatin state segment, loop domain, chromatin domain, etc. Two sets of bins are selected to generate a squared genome matrix of bin pairs, where each set represent an axis of the matrix. Then a normalization method is applied to the interaction frequencies for the bin pairs having variable size and/or shape to generate normalized interaction frequencies for each bin pair. The normalized interaction frequencies may be used to identify bin pairs having enriched and depleted contacts for a variety of analyses, including the detection of target genes of genomic variants, as well as genome wide analysis of contacts.

Abstract: A field programmable gate array (FPGA) may: identify a continuous match of atoms between the search sequence and the reference sequence; divide the search sequence into a left portion of the search sequence that includes atoms before the continuous match of atoms in the search sequence, a center portion of the search sequence that includes the continuous match of atoms in the search sequence, and a right portion of the search sequence that includes atoms after the continuous match of atoms in the search sequence; match the left portion of the search sequence with the reference sequence; and match the right portion of the search sequence with the reference sequence.

Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.