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Williams, Jason

Publications and source records attributed to Williams, Jason.

BOSC 2025, the 26th Bioinformatics Open Source Conference

The 26th annual Bioinformatics Open Source Conference (BOSC 2025, open-bio.org/events/bosc-2025) brought its community-driven focus on open-source bioinformatics and open science to the 2025 conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2025). Since its launch in 2000, BOSC has been the premier annual meeting covering open-source bioinformatics and open science. Framed by two keynote addresses and a thought-provoking panel discussion, the two-day conference included sessions dedicated to open data, analytic tools and pipelines, workflow platforms, knowledge representation, and the application of AI/ML. The first keynote talk was delivered by Christine Orengo: “Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED.” A joint session with the Bio-Ontologies and Knowledge Representation (BOKR) track the second day of BOSC started with a keynote talk by Chris Mungall entitled “Open Knowledge Bases in the Age of Generative AI”. A closing panel on Data Sustainability, moderated by Mónica Muñoz Torres, featured panelists Scott Edmunds, Varsha Khodiyar, Tony Burdett, Nicky Mulder, and Chris Mungall. This year, the CollaborationFest collaborative work event that typically precedes or follows ISMB was incorporated as part of the main conference and organized by BOSC with help from the Function and 3D-SIG tracks.

bioinformatics↗

Optical atomic clock aboard an Earth-orbiting space station (OACESS): enhancing searches for physics beyond the standard model in space

We present a concept for a high-precision optical atomic clock (OAC) operating on an Earth-orbiting space station. This pathfinder science mission will compare the space-based OAC with one or more ultra-stable terrestrial OACs to search for space-time-dependent signatures of dark scalar fields that manifest as anomalies in the relative frequencies of station-based and ground-based clocks. This opens the possibility of probing models of new physics that are inaccessible to purely ground-based OAC experiments where a dark scalar field may potentially be strongly screened near Earth's surface. This unique enhancement of sensitivity to potential dark matter candidates harnesses the potential of space-based OACs.

79 ASTRONOMY AND ASTROPHYSICS↗

Synchrotron CT imaging of lattice structures with engineered defects

Understanding mechanical failure, crack propagation, and compressive behavior at the micrometer scale is essential for tailoring material properties for structural performance in cellular materials. Typically, modeling of traditional polymer foam materials is clouded by the lack of control in material morphology and its inherent stochastic structure. Additive manufacturing with sub-micrometer resolution provides a direct path for experimenters to specifically tailor structures needed by modelers to explicitly probe mechanical performance. Using laboratory-based 3D X-ray computed tomographic imaging (CT), the examination of deformation and damage provides a critical path to understand how these soft materials behave. Additionally, synchrotron CT yields realistic information at higher strain rates to directly validate the robustness of our finite element modeling. For this study, nanolithographic printing was employed to generate a series of engineered lattices with increasing levels of defects through the random removal of ligaments. These structures were mechanically tested and imaged with laboratory-based microCT. Additionally, synchrotron experiments were conducted in which the structures were imaged in 3D at 14 Hz during compression at a 0.4 s –1 strain rate. These 3D images show the changes in the structure as the ligaments bend, buckle and fracture in real time. This technique provides a robust framework for developing our methodologies and future exploration of engineered structures.

36 MATERIALS SCIENCE↗

Team Training and Retention of Skills Acquired Above Real Time Training on a Flight Simulator

Above Real-Time Training (ARTT) is the training acquired on a real time simulator when it is modified to present events at a faster pace than normal. The experiments related to training of pilots performed by NASA engineers (Kolf in 1973, Hoey in 1976) and others (Guckenberger, Crane and their associates in the nineties) have shown that in comparison with the real time training (RTT), ARTT provides the following benefits: increased rate of skill acquisition, reduced simulator and aircraft training time, and more effective training for emergency procedures. Two sets of experiments have been performed; they are reported in professional conferences and the respective papers are included in this report. The retention of effects of ARTT has been studied in the first set of experiments and the use of ARTT as top-off training has been examined in the second set of experiments. In ARTT, the pace of events was 1.5 times the pace in RTT. In both sets of experiments, university students were trained to perform an aerial gunnery task. The training unit was equipped with a joystick and a throttle. The student acted as a nose gunner in a hypothetical two place attack aircraft. The flight simulation software was installed on a Universal Distributed Interactive Simulator platform supplied by ECC International of Orlando, Florida. In the first set of experiments, two training programs RTT or ART7 were used. Students were then tested in real time on more demanding scenarios: either immediately after training or two days later. The effects of ARTT did not decrease over a two day retention interval and ARTT was more time efficient than real time training. Therefore, equal test performance could be achieved with less clock-time spent in the simulator. In the second set of experiments three training programs RTT or ARTT or RARTT, were used. In RTT, students received 36 minutes of real time training. In ARTT, students received 36 minutes of above real time training. In RARTT, students received 18 minutes of real time training and 18 minutes of above real time training as top-off training. Students were then tested in real time on more demanding scenarios. The use of ARTT as top-off training after RTT offered better training than RTT alone or ARTT alone. It is, however, suggested that a similar experiment be conducted on a relatively more complex task with a larger sample of participants. Within the proposed duration of the research effort, the setting up of experiments and trial runs on using ARTT for team training were also scheduled but they could not be accomplished due to extra ordinary challenges faced in developing the required software configuration. Team training is, however, scheduled in a future study sponsored by NASA at Tuskegee University.

Ali, Syed Friasat↗

Flow Analysis Software Toolkit

Flow Analysis Software Toolkit (FAST) computer program provides software environment facilitating visualization of data. Collection of separate programs (modules) running simultaneously and helps user to examine results of numerical and experimental simulations. Intended for graphical depiction of computed flows, also assists in analysis of other types of data. Combines capabilities of such programs as PLOT3D, RIP, SURF, and GAS into one software environment with modules sharing data. All modules have consistent, highly interactive graphical user interface. Modular construction makes it flexible and extensible. Environment custom-configured, and new modules developed and added as needed. Written in ANSI compliant FORTRAN 77 and C language.

Watson, Velvin↗