160,411 research outputs found
An online model composition tool for system biology models
Background: There are multiple representation formats for Systems Biology computational models, and the
Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and
distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers.
Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as
uploading, editing, composing, visualizing, simulating, querying, and browsing computational models.
Results: We present the design and implementation of the Model Composition Tool (Interface) within the PathCaseSB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the
complex process of merging systems biology models. We also present three tools that support the model
composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to
user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool
that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a
web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models.
Conclusions: Model composition tool (and the other three tools) can be used with little or no knowledge of the
SBML document structure. For this reason, students or anyone who wants to learn about systems biology will
benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And,
for more advanced purposes, users will able to access and employ models of the BioModels Database as well
SBML models and MathSBML
MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation
TumorML: Concept and requirements of an in silico cancer modelling markup language
This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the
biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in
the use of models as well as the development of improved software systems and the availability of better, cheaper
computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model
repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in
these repositories should be extensively tested and encoded in community-supported and standardised formats. In
addition, the models and their components should be cross-referenced with other resources in order to allow their
unambiguous identification.
Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a
freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative
models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by
BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled
vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various
formats. Reaction network diagrams generated from the models are also available in several formats. BioModels
Database also provides features such as online simulation and the extraction of components from large scale models
into smaller submodels. Finally, the system provides a range of web services that external software systems can use to
access up-to-date data from the database.
Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by
the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the
clustering of models based upon their annotations. Model deposition to the database today is advised by several
publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying
software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU
General Public License
Annotations for Rule-Based Models
The chapter reviews the syntax to store machine-readable annotations and
describes the mapping between rule-based modelling entities (e.g., agents and
rules) and these annotations. In particular, we review an annotation framework
and the associated guidelines for annotating rule-based models of molecular
interactions, encoded in the commonly used Kappa and BioNetGen languages, and
present prototypes that can be used to extract and query the annotations. An
ontology is used to annotate models and facilitate their description
Mathematical modelling in animal nutrition: a centenary review
A centenary review presents an opportunity to ponder over the processes of concept development and give thought to future directions. The current review aims to ascertain the ontogeny of current concepts, underline the connection between ideas and people and pay tribute to those pioneers who have contributed significantly to modelling in animal nutrition. Firstly, the paper draws a brief portrait of the use of mathematics in agriculture and animal nutrition prior to 1925. Thereafter, attention turns towards the historical development of growth modelling, feed evaluation systems and animal response models. Introduction of the factorial and compartmental approaches into animal nutrition is noted along with the particular branches of mathematics encountered in various models. Furthermore, certain concepts, especially bioenergetics or the heat doctrine, are challenged and alternatives are reviewed. The current state of knowledge of animal nutrition modelling results mostly from the discernment and unceasing efforts of our predecessors rather than serendipitous discoveries. The current review may stimulate those who wish for greater understanding and appreciation
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