We propose to further develop a set of robust software components for constructing model-organism databases (MODs). Those software components will support 3 main types of operations: creation of new MODs, interactive editing and curation of MODs, and Web publishing of MODs. Those 3 types of operations will be supported for the following bioinformatics datatypes: genome maps, genes, operons, promoters, proteins, biochemical reactions, metabolic and signaling pathways, and small-molecule metabolites. These software components will be based on the Pathway Tools software that underlies the EcoCyc database, and other MODs. Pathway Tools is a mature, sophisticated, production-quality software environment that has been licensed by 60 groups who have constructed 20 existing MODs and plan to construct more than 20 additional MODs. We further propose to provide support services for the large and growing user community for the Pathway Tools, to maintain quality documentation for the software, and to create 2 thoroughly tested releases of the software per year. We will also interact with the community of developers of other MOD software components to ensure interoperability of our software components with components developed by other groups.
| Caspi, Ron; Billington, Richard; Fulcher, Carol A et al. (2018) The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res 46:D633-D639 |
| Karp, Peter D; Weaver, Daniel; Latendresse, Mario (2018) How accurate is automated gap filling of metabolic models? BMC Syst Biol 12:73 |
| Latendresse, Mario; Karp, Peter D (2018) Evaluation of reaction gap-filling accuracy by randomization. BMC Bioinformatics 19:53 |
| Karp, Peter D; Billington, Richard; Caspi, Ron et al. (2017) The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform : |
| Paley, Suzanne; Karp, Peter D (2017) Update notifications for the BioCyc collection of databases. Database (Oxford) 2017: |
| Paley, Suzanne; Parker, Karen; Spaulding, Aaron et al. (2017) The Omics Dashboard for interactive exploration of gene-expression data. Nucleic Acids Res 45:12113-12124 |
| Karp, Peter D; Latendresse, Mario; Paley, Suzanne M et al. (2016) Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform 17:877-90 |
| Paley, Suzanne; O'Maille, Paul E; Weaver, Daniel et al. (2016) Pathway collages: personalized multi-pathway diagrams. BMC Bioinformatics 17:529 |
| Paley, Suzanne; Krummenacker, Markus; Karp, Peter D (2016) Representation and inference of cellular architecture for metabolic reconstruction and modeling. Bioinformatics 32:1074-9 |
| Edison, Arthur S; Hall, Robert D; Junot, Christophe et al. (2016) The Time Is Right to Focus on Model Organism Metabolomes. Metabolites 6: |
Showing the most recent 10 out of 34 publications
