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BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
TLDR
BpForms and BcForms are developed, a toolkit for representing the primary structure of macromolecules as combinations of residues, caps, crosslinks, and nicks that can help omics researchers perform quality control and exchange information about macromolescules, and help systems biologists assemble global models of cells that encompass processes such as post-translational modification. Expand
Structured spreadsheets with ObjTables enable data reuse and integration
A central challenge in science is to understand how behaviors emerge from complex networks. This often requires reusing and integrating heterogeneous information. Supplementary spreadsheets toExpand
BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks
TLDR
BpForms and BcForms are developed, a toolkit of ontologies, grammars, and software for abstracting the primary structure of polymers and complexes as combinations of residues, caps, crosslinks, and nicks. Expand
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
TLDR
Datanator, an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms. Expand
ObjTables: structured spreadsheets that promote data quality, reuse, and integration
A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. SupplementaryExpand
runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
TLDR
This work developed runBioSimulations, a single web application for executing a broad range of models that will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models. Expand
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
TLDR
RunBioSimulations is developed, a single web application for executing a broad range of models that will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models. Expand
SED-ML Validator: tool for debugging simulation experiments
TLDR
A tool for validating SED-ML files is developed and it is anticipated that the validator will be a valuable tool for developing more predictive simulations and that it will help increase the adoption and interoperability of S ED-ML. Expand
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
TLDR
Datanator, an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms. Expand
Structuring spreadsheets with ObjTables enables data quality control, reuse, and integration
A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. SupplementaryExpand