Engineering topics
Roberts, Jacob
Publications and source records attributed to Roberts, Jacob.
Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis
Not Available
SSGUI v1.0
SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file system directory that is organized by experiment and reference sequence. The output is an online dashboard containing various sequencing statistics for each sample and an integrated IGV plugin enabling rapid analysis of aligned NGS reads.
BaseBuddy v1
The software "BaseBuddy" (basebuddy.lbl.gov) is a user-friendly web app designed for codon optimization of heterologous genes. Codon optimization is a widely used technique to enhance the expression levels of non-native genes. Our app is built on the DNA Chisel Python library (Zulkower and Rosser, 2020), which offers highly customizable and transparent gene optimization. Unlike DNA Chisel, which is a command-line interface software with numerous optional functions, our web app simplifies the process for users. Additionally, while DNA Chisel relies on the outdated Kazusa codon usage database, our app introduces the option to utilize the most recent version of the CoCoPUTs database (Athey et al., 2017). By incorporating CoCoPUTs, we also expand the range of target organisms and maintain up-to-date sequencing data for more accurate codon optimization results.
Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase
Not Available
Foldy v1
We created a cloud-based application for running AlphaFold2 and related structural programs called Foldy. Foldy is built on Helm / Kubernetes, which enables a facile production deployment and a scalable backend. Once set up by an institution, Foldy requires no software expertise from its users. It can be used to predict the structure of large proteins (up to 3000 amino acids), to visualize Pfam and antiSMASH annotations, and to perform ligand docking with Autodock Vina.
Influence of electron evaporative cooling on ultracold plasma expansion
The expansion of ultracold neutral plasmas (UCP) is driven primarily by the thermal pressure of the electron component and is therefore sensitive to the electron temperature. For typical UCP spatial extents, evaporative cooling has a significant influence on the UCP expansion rate at lower densities (less than 10{sup 8}/cm{sup 3}). We studied the effect of electron evaporation in this density range. Owing to the low density, the effects of three-body recombination were negligible. We modeled the expansion by taking into account the change in electron temperature owing to evaporation as well as adiabatic expansion and found good agreement with our data. We also developed a simple model for initial evaporation over a range of ultracold plasma densities, sizes, and electron temperatures to determine over what parameter range electron evaporation is expected to have a significant effect. We also report on a signal calibration technique, which relates the signal at our detector to the total number of ions and electrons in the ultracold plasma.