John Gennari - Dissemin

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All papers authored by John Gennari

This paper was not found in any repository, but could be made available legally by the author.

2023 Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari

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, Lucian P. Smith, Joseph L. Hellerstein

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, Herbert M. Sauro

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VSCode-Antimony: a source editor for building, analyzing, and translating antimony models

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Woosub Shin

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, John H. Gennari

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, Joseph L. Hellerstein

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, Herbert M. Sauro

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An automated model annotation system (AMAS) for SBML models

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2022 Bilal Shaikh

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, Lucian P. Smith

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, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson

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, Steven S. Andrews

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, Azraf Anwar, Moritz E. Beber

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, Frank T. Bergmann

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, Laurence Calzone

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and 60 other authors

BioSimulators: a central registry of simulation engines and services for recommending specific tools

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Yuda Munarko, Dewan M. Sarwar, Anand Rampadarath, Koray Atalag, John H. Gennari

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, Maxwell L. Neal, David P. Nickerson

NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories

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2021 Michael L. Blinov, John H. Gennari

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, Jonathan R. Karr

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, Ion I. Moraru, David P. Nickerson

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, Herbert M. Sauro

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Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

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John H. Gennari

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, Matthias König

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, Goksel Misirli, Maxwell L. Neal

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, David P. Nickerson

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, Dagmar Waltemath

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OMEX metadata specification (version 1.2)

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Ciaran Welsh

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, David P. Nickerson, Anand Rampadarath, Maxwell L. Neal, Herbert M. Sauro, John H. Gennari

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libOmexMeta: enabling semantic annotation of models to support FAIR principles

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2020 Maxwell L. Neal

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, John H. Gennari

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, Dagmar Waltemath

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, David P. Nickerson

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, Matthias König

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Open modeling and exchange (OMEX) metadata specification version 1.0

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2019 Dewan M. Sarwar, Bernard de Bono, Reza Kalbasi, John H. Gennari

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, Brian E. Carlson, Maxwell L. Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter, David P. Nickerson

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Model annotation and discovery with the Physiome Model Repository

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Lucy Lu Wang

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, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary E. Shimoyama, John H. Gennari

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Predicting instances of pathway ontology classes for pathway integration

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Göksel Mısırlı

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, Renee Taylor, Angel Goñi-Moreno, James Alastair McLaughlin, Chris Myers, John H. Gennari

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, Phillip Lord, Anil Wipat

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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information

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2018 Maxwell L. Neal

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, Christopher T. Thompson, Karam G. Kim

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, Ryan C. James, Daniel L. Cook, Brian E. Carlson

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, John H. Gennari

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SemGen: a tool for semantics-based annotation and composition of biosimulation models

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This paper is made freely available by the publisher.

2017 Alan M. Kalet, Jason N. Doctor, John H. Gennari

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, Mark H. Phillips

Developing Bayesian networks from a dependency-layered ontology: A proof-of-concept in radiation oncology

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

L. L. Wang, J. H. Gennari

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Similarity metrics for determining overlap among biological pathways

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

D. L. Cook, J. H. Gennari

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, M. L. Neal

Extending the ontology of physics for biology with thermodynamics

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2016 Nicholas Roehner, Jacob Beal, Kevin Clancy, Bryan Bartley, Goksel Misirli, Raik Grünberg, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Michael Zhang, Zhen Zhang, Zach Zundel, Douglas Densmore and 4 other authors

Sharing Structure and Function in Biological Design with SBOL 2.0

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

Maxwell L. Neal

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, John H. Gennari

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, Daniel L. Cook

Qualitative causal analyses of biosimulation models

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

L. L. Wang, J. H. Gennari

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, N. F. Abernethy

An analysis of differences in biological pathway resources

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Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Nicholas Roehner and 8 other authors

Synthetic Biology Open Language (SBOL) Version 2.1.0

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