An overview of CellML 1.1, a biological model description language
…, PF Nielsen, DP Bullivant, DP Nickerson… - …, 2003 - journals.sagepub.com
CellML is an XML-based exchange format developed by the University of Auckland in
collaboration with Physiome Sciences, Inc. CellML 1.1 has a component-based architecture …
collaboration with Physiome Sciences, Inc. CellML 1.1 has a component-based architecture …
Vps-C complexes: gatekeepers of endolysosomal traffic
Genetic studies in yeast, plants, insects, and mammals have identified four universally
conserved proteins, together called Vps Class C, that are essential for late endosome and …
conserved proteins, together called Vps Class C, that are essential for late endosome and …
Multiscale computational modelling of the heart
A computational framework is presented for integrating the electrical, mechanical and
biochemical functions of the heart. Finite element techniques are used to solve the large-…
biochemical functions of the heart. Finite element techniques are used to solve the large-…
The physiome model repository 2
T Yu, CM Lloyd, DP Nickerson, MT Cooling… - …, 2011 - academic.oup.com
Motivation: The Physiome Model Repository 2 (PMR2) software was created as part of the
IUPS Physiome Project ( Hunter and Borg, 2003 ), and today it serves as the foundation for the …
IUPS Physiome Project ( Hunter and Borg, 2003 ), and today it serves as the foundation for the …
Did2 coordinates Vps4-mediated dissociation of ESCRT-III from endosomes
The sorting of transmembrane cargo proteins into the lumenal vesicles of multivesicular
bodies (MVBs) depends on the recruitment of endosomal sorting complexes required for …
bodies (MVBs) depends on the recruitment of endosomal sorting complexes required for …
[HTML][HTML] COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
…, M Hucka, C Laibe, AK Miller, DP Nickerson… - BMC …, 2014 - Springer
Background With the ever increasing use of computational models in the biosciences, the
need to share models and reproduce the results of published studies efficiently and easily is …
need to share models and reproduce the results of published studies efficiently and easily is …
Subunit organization and Rab interactions of Vps-C protein complexes that control endolysosomal membrane traffic
…, CL Brett, CG Angers, DP Nickerson… - Molecular biology of …, 2011 - Am Soc Cell Biol
Traffic through late endolysosomal compartments is regulated by sequential signaling of small
G proteins of the Rab5 and Rab7 families. The Saccharomyces cerevisiae Vps-C protein …
G proteins of the Rab5 and Rab7 families. The Saccharomyces cerevisiae Vps-C protein …
CellML and associated tools and techniques
We have, in the last few years, witnessed the development and availability of an ever increasing
number of computer models that describe complex biological structures and processes. …
number of computer models that describe complex biological structures and processes. …
Molecular mechanisms of late endosome morphology, identity and sorting
Recent studies using electron microscopy, protein crystallography, classic biochemistry and
novel live-cell imaging have provided numerous insights into the endocytic pathway, …
novel live-cell imaging have provided numerous insights into the endocytic pathway, …
[HTML][HTML] Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
The Computational Modeling in Biology Network (COMBINE) is a consortium of groups
involved in the development of open community standards and formats used in computational …
involved in the development of open community standards and formats used in computational …