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RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
RunBioSimulations is an extensible, standards-driven web application for executing models across a broad range of modeling frameworks, simulation algorithms, and model formats and visualizing and sharing their results.
Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L Blinov, Ion I Moraru, Jonathan R Karr
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RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
To facilitate biochemical research, we developed 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, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments.
Yosef D Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R Karr
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Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
BpForms and BcForms, are a toolkit for representing the primary structure of macromolecules as combinations of residues, caps, crosslinks, and nicks.
Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale, Jonathan R. Karr
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BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
Salts and energy balance: A special role for dietary salts in metabolic syndrome
Dietary salts sodium (Na+), potassium (K+), magnesium (Mg2+), and calcium (Ca2+) are important in metabolic diseases. Yet, we do not have sufficient understanding on the salts global molecular network in these diseases. In this systematic review we have pooled information to identify the general effect of salts on obesity, insulin resistance and hypertension
Christopher W. Brey, Safoura Akbari-Alavijeh, Jun Ling, Jordan Sheagley, Bilal Shaikh, Futwan Al-Mohanna, Yi Wang, Randy Gaugler, Sarwar Hashmi
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Salts and energy balance: A special role for dietary salts in metabolic syndrome