Aquarium: open-source laboratory software for design, execution and data management.

Automation has been shown to improve the replicability and scalability of biomedical and bioindustrial research. Although the work performed in many labs is repetitive and can be standardized, few academic labs can afford the time and money required to automate their workflows with robotics. We propose that human-in-the-loop automation can fill this critical gap. To this end, we present Aquarium, an open-source, web-based software application that integrates experimental design, inventory management, protocol execution and data capture. We provide a high-level view of how researchers can install Aquarium and use it in their own labs. We discuss the impacts of the Aquarium on working practices, use in biofoundries and opportunities it affords for collaboration and education in life science laboratory research and manufacture.

Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays.

BACKGROUND: Detection of SARS-CoV-2 infections is important for treatment, isolation of infected and exposed individuals, and contact tracing. RT-qPCR is the "gold-standard" method to sensitively detect SARS-CoV-2 RNA, but most laboratory-developed RT-qPCR assays involve complex steps. Here, we aimed to simplify RT-qPCR assays by streamlining reaction setup, eliminating RNA extraction, and proposing reduced-cost detection workflows that avoid the need for expensive qPCR instruments. METHOD: A low-cost RT-PCR based "kit" was developed for faster turnaround than the CDC developed protocol. We demonstrated three detection workflows: two that can be deployed in laboratories conducting assays of variable complexity, and one that could be simple enough for point-of-care. Analytical sensitivity was assessed using SARS-CoV-2 RNA spiked in simulated nasal matrix. Clinical performance was evaluated using contrived human nasal matrix (n = 41) and clinical nasal specimens collected from individuals with respiratory symptoms (n = 110). FINDING: The analytical sensitivity of the lyophilised RT-PCR was 10 copies/reaction using purified SARS-CoV-2 RNA, and 20 copies/reaction when using direct lysate in simulated nasal matrix. Evaluation of assay performance on contrived human matrix showed 96.7-100% specificity and 100% sensitivity at ≥20 RNA copies. A head-to-head comparison with the standard CDC protocol on clinical specimens showed 83.8-94.6% sensitivity and 96.8-100% specificity. We found 3.6% indeterminate samples (undetected human control), lower than 8.1% with the standard protocol. INTERPRETATION: This preliminary work should support laboratories or commercial entities to develop and expand access to Covid-19 testing. Software guidance development for this assay is ongoing to enable implementation in other settings. FUND: USA NIH R01AI140845 and Seattle Children's Research Institute.

Effects of various warm-up devices and rest period lengths on batting velocity and acceleration of intercollegiate baseball players.

It is common among competitive baseball players to swing bats while in the batter's box in an attempt to improve their batting performance. Players use bats of different weights during this time, and only a few studies have evaluated the optimal bat weight to increase performance. Previous studies have not investigated the optimal rest period after a warm-up with bats of varying weights. Therefore, we tested the peak bat velocity of 16 National Collegiate Athletic Association Division II intercollegiate baseball players at 1, 2, 4, and 8 minutes, after warming up with bats of 5 different weights. Measured variables were peak bat velocity at peak acceleration (PVPA), peak bat velocity of the swing (PV), peak bat acceleration (PA), and time to reach peak acceleration (TPA) using a chronograph, which measured the batting velocity in real time every 10 milliseconds throughout the swing. A repeated measure analysis of variance was run to assess group, time, and group by time interactions. If any main effects were found, a Tukey post hoc was employed to locate differences. There were significant (p ≤ 0.05) time effects for PVPA, PV, and PA but not for TPA. The PVPA, PV, and PA all increased over time, peaking from 4 to 8 minutes. There were no significant differences in any of the variables among the 5 bat weights used in the warm-up (p > 0.05). However, there were significant differences in PVPA, PV, and PA after 2, 4, and 8 minutes of rest compared with the preexperimental warm-up and 1-minute post-warm-up. From a practical standpoint, batters should warm up early and quickly in the batter's box to maximize the amount of recovery time before they swing at the plate. In addition, batters may want to take their time getting ready at the plate or take some pitches while at-bat in an attempt to maximize performance. Alternatively, the data imply that pitchers should throw their fastest pitch near the beginning of the at-bat to correspond with the potentially slower bat speeds of the batter.