Zobrazeno 1 - 10
of 408
pro vyhledávání: '"Sauro Herbert M"'
Publikováno v:
Journal of Integrative Bioinformatics, Vol 21, Iss 1, Pp 524-31 (2024)
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web applicati
Externí odkaz:
https://doaj.org/article/d3755ccf88c14fee85023b9c54c5c842
Autor:
Sego, T. J., König, Matthias, Fonseca, Luis L., Fain, Baylor, Knapp, Adam C., Tiwari, Krishna, Hermjakob, Henning, Sauro, Herbert M., Glazier, James A., Laubenbacher, Reinhard C., Malik-Sheriff, Rahuman S.
Reproducibility is a foundational standard for validating scientific claims in computational research. Stochastic computational models are employed across diverse fields such as systems biology, financial modelling and environmental sciences. Existin
Externí odkaz:
http://arxiv.org/abs/2406.16820
Autor:
Sauro, Herbert M
In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models can be provided in standard SBML or Antimony format. The code takes into acc
Externí odkaz:
http://arxiv.org/abs/2406.11140
Autor:
Waltemath Dagmar, Golebiewski Martin, Blinov Michael L, Gleeson Padraig, Hermjakob Henning, Hucka Michael, Inau Esther Thea, Keating Sarah M, König Matthias, Krebs Olga, Malik-Sheriff Rahuman S, Nickerson David, Oberortner Ernst, Sauro Herbert M, Schreiber Falk, Smith Lucian, Stefan Melanie I, Wittig Ulrike, Myers Chris J
Publikováno v:
Journal of Integrative Bioinformatics, Vol 17, Iss 2-3, Pp 19-895 (2020)
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers t
Externí odkaz:
https://doaj.org/article/3095111417c745328ed4dceb6bee80ef
Autor:
Smith, Lucian, Sauro, Herbert M
Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax. It allows
Externí odkaz:
http://arxiv.org/abs/2405.15109
Autor:
Sauro, Herbert M
This paper explores some basic concepts of Biochemical Systems Theory (BST) and Metabolic Control Analysis (MCA), two frameworks developed to understand the behavior of biochemical networks. Initially introduced by Savageau, BST focuses on system sta
Externí odkaz:
http://arxiv.org/abs/2405.00810
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology
Externí odkaz:
http://arxiv.org/abs/2310.07880
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent properties such as
Externí odkaz:
http://arxiv.org/abs/2309.04039
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web applicati
Externí odkaz:
http://arxiv.org/abs/2309.03344
Autor:
Xu, Jin, Geng, Gary, Nguyen, Nhan D., Perena-Cortes, Carmen, Samuels, Claire, Sauro, Herbert M.
SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization and editing
Externí odkaz:
http://arxiv.org/abs/2302.09151