Engineering topics
Publications and source records attributed to Boverhof, Joshua.
CCSI Toolset 3.23 Release Highlights The user interface was updated to allow timeouts in Aspen Custom Modeler and AspenPlus. The installation was updated to use 64-bit versions of TurbineLite and SimSinter by default. The documentation was improved for clarity.
Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.
CCSI Toolset 3.22 Release Highlights The Sequential Design of Experiments user interface was updated to resolve an issue where the results would fail to plot in some cases (e.g., Non-Uniform Space Filling designs). The Machine Learning/Artificial Intelligence module was updated to support Keras 3 and to reflect changes made to dependencies’ syntax. A check was added to ensure PSUADE is installed and available at FOQUS startup. If PSUADE is not installed, a link to the FOQUS documentation is displayed and FOQUS is closed. The copyright year was updated to include 2024 in places where it had not previously been updated. Typographical errors were corrected to improve clarity in variable names and documentation. The FOQUS documentation was updated to reflect the fact that ALAMO can have two executables and indicates the correct executable to add to the Settings path. SimSinter was updated to version 3.1.0. This version removed gPROMS support and included security updates.