Bilal Shaikh
Icahn School of Medicine at Mount Sinai
13 Papers
34 Citations
Bilal Shaikh is an academic researcher from Icahn School of Medicine at Mount Sinai. The author has contributed to research in topics: Computer science & Web application. The author has an hindex of 3, co-authored 11 publications. Previous affiliations of Bilal Shaikh include Rutgers University.
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Papers
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh,Lucian P. Smith,D. Vasilescu,Gnaneswara Marupilla,Michael Wilson,Eran Agmon,Henry Agnew,Steven S. Andrews,Azraf Anwar,Moritz Emanuel Beber,Frank Bergmann,David Brooks,Lutz Brusch,Laurence Calzone,Kiri Choi,Joshua Cooper,John Detloff,Brian Drawert,Michel Dumontier,G. Bard Ermentrout,James R. Faeder,Andrew Philip Freiburger,F. Frohlich,Akira Funahashi,Alan Garny,John H. Gennari,Padraig Gleeson,Anne Goelzer,Zachary B. Haiman,Joseph M. Hellerstein,Stefan Hoops,Jon Ison,Diego Jahn,Henry V. Jakubowski,Ryan M. Jordan,Mat'uvs Kalavs,M. Konig,Wolfram Liebermeister,Synchon Mandal,Robert A. McDougal,J. Kyle Medley,Pedro Mendes,Robert T. Muller,Chris J. Myers,Aurélien Naldi,Tung V N Nguyen,David P. Nickerson,Brett G. Olivier,Drashti Patoliya,Loic Paulev'e,Linda R. Petzold,Ankita Priya,Anand Rampadarath,Johann M. Rohwer,Ali S. Saglam,Dilawar Singh,Ankur Sinha,Jacky L. Snoep,Hugh Sorby,Ryan K. Spangler,Jörn Starruß,Payton J Thomas,D. D. van Niekerk,Daniel Weindl,Fengkai Zhang,Anna Zhukova,Arthur P. Goldberg,Michael L. Blinov,Herbert M. Sauro,Ion I. Moraru,Jonathan R. Karr +70 more
TL;DR: The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently.
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior.
TL;DR: 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.
BpForms and BcForms : a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
Paul F. Lang,Paul F. Lang,Yassmine Chebaro,Yassmine Chebaro,Xiaoyue Zheng,John A. P. Sekar,Bilal Shaikh,Darren A. Natale,Jonathan R. Karr +8 more
TL;DR: 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.
BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks
Paul F. Lang,Yassmine Chebaro,Xiaoyue Zheng,John A. P. Sekar,Bilal Shaikh,Darren A. Natale,Jonathan R. Karr +6 more
TL;DR: 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.
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
TL;DR: 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.
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