EcoCyc.org, the most comprehensive curated genome database for the model microorganism E. coli K-12, has implemented a new categorization schema that indicates the degree to which a gene has been characterized: well-characterized (54%), partially (26%) and uncharacterized (16%). This searchable category adds to the wealth of information and bioinformatics tools in EcoCyc aiding research decisions to further the study of gene function in E. coli.

The post Revisiting the y-ome of Escherichia coli appeared first on SRI.

Abstract We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts […]

The post Visual Analysis of Multi-Omics Data appeared first on SRI.

The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.

The post The Comparative Genome Dashboard appeared first on SRI.

In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest.

The post The Genome Explorer Genome Browser appeared first on SRI.

The unification algorithm has long been a target for program synthesis research, but a fully automatic derivation remains a research goal.

The post Automating the Derivation of Unification Algorithms. A Case Study in Deductive Program Synthesis appeared first on SRI.

We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.

The post An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval appeared first on SRI.

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools.

The post CyanoCyc Cyanobacterial Web Portal appeared first on SRI.