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https://github.com/mschubert/biomodels_curation

Scripts used for curation of Blood Coagulation models for the BioModels database
https://github.com/mschubert/biomodels_curation

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Scripts used for curation of Blood Coagulation models for the BioModels database

Host: GitHub
URL: https://github.com/mschubert/biomodels_curation
Owner: mschubert
Created: 2011-11-24T13:55:23.000Z (about 13 years ago)
Default Branch: master
Last Pushed: 2013-04-11T11:57:22.000Z (almost 12 years ago)
Last Synced: 2023-03-13T18:12:49.537Z (almost 2 years ago)
Language: Python
Homepage:
Size: 563 KB
Stars: 0
Watchers: 2
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md

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README

        BioModels curation scripts

==========================

This is a collection of scripts that were used to curate Blood Coagulation

models. Those were taken from various scientific articles and encoded in

the [Systems Biology Markup Language][sbml] (SBML) and subsequently annotated

with identifiers from e.g. [UniProt][uniprot], so that the model entities

could be linked to physical ones. Additionally, one or more figures from the 

original article were reproduced in order to validate the model and its

simulation results.

Note that the models deposited in the [BioModels database][bmdb] will always 

be more complete and up-to-date than the ones provided here. If plan on using 

the models instead of the curation framework, please use them from the database

directly.

All models published in the BioModels database are released without copyright

under a [CC0][cc0] license. The Framework is (c) [EMBL][embl], 2011 but may

be used under the terms of the [GPL][gpl] version 2 or later.

Usage

-----

The sample models are provided either as Copasi or unannotated SBML files.

Using the Make framework, they are transformed into annotated SBML files and

those are plotted using specific plotting scripts. To run, type:

    ./configure

    make

Upon which all model files and figures are created. Note that you can run

`make` in only one subdirectory as well, `configure` needs to be called before,

however.

Requirements

------------

The following software is required to successfully run the curation framework

with the sample models provided:

 * [Python][python]

                - A high-level scripting language that can be used for rapid

                  development and comes a lot of functionality included. Extra

                  libraries required are [NumPy][numpy] (for numerical data 

                  structures), [matplotlib][matplotlib] (for plotting), 

                  [libSBML][libsbml] (for manipulation of SBML files), 

                  [SymPy][sympy] (for matching of kinetic laws to 

                  [SBO terms][sbo]) and [SUDS][suds] (for interacting with the 

                  SBO webservice via [SOAP][soap]).

 * [Coapsi][copasi]

                - An application for simulation and analysis of biochemical

                  networks and their dynamics. It is a stand-alone application 

                  that comes with a command-line (CopasiSE) and GUI (CopasiUI) 

                  version and supports the [SBML][sbml] standard. The program

                  needs to be compiled with Python bindings enabled.

 * [HTML Tidy][tidy]

                - An application to clean up HTML and XML formatting. This

                  tool is used to format the SBML files nicely after 

                  annotation.

Sample models

-------------

In the course of the curation project, about 30 models were curated for the

BioModels database. Some from the following five articles are provided as

sample files for the framework here:

 * K. C. Jones and K. G. Mann. A model for the tissue factor pathway to 

   thrombin. II. a mathematical simulation. Journal of Biological Chemistry, 

   269(37):23367, 1994.

 * M. F. Hockin, K. C. Jones, S. J. Everse, and K. G. Mann. A model for the

   stoichiometric regulation of blood coagulation. Journal of Biological 

   Chemistry, 277(21):18322-18333, 2002.

 * S. D. Bungay, P. A. Gentry, and R. D. Gentry. A mathematical model of lipid-

   mediated thrombin generation. Mathematical Medicine and Biology, 20(1):105-

   129, 2003.

 * T. Wajima, G. K. Isbister, and S. B. Duffull. A comprehensive model for the

   humoral coagulation network in humans. Clinical Pharmacology and 

   Therapeutics, 86(3):290–298, 2009.

 * C. J. Lee, S. Wu, C. Eun, and L. G. Pedersen. A revisit to the one form 

   kinetic model of prothrombinase. Biophysical chemistry, 149(1-2):28–33, 2010.

[sbml]: http://sbml.org/Basic_Introduction_to_SBML

[uniprot]: http://www.uniprot.org/

[embl]: http://www.embl.de/

[bmdb]: http://www.ebi.ac.uk/biomodels-main/

[gpl]: http://www.gnu.org/licenses/gpl.html

[cc0]: http://creativecommons.org/publicdomain/zero/1.0/

[python]: http://python.org/

[copasi]: http://www.copasi.org/tiki-view_articles.php

[tidy]: http://tidy.sourceforge.net/

[numpy]: http://numpy.scipy.org/

[matplotlib]: http://matplotlib.sourceforge.net/

[libsbml]: http://sbml.org/Software/libSBML

[sympy]: http://code.google.com/p/sympy/

[sbo]: http://www.ebi.ac.uk/sbo/main/

[suds]: https://fedorahosted.org/suds/

[soap]: http://de.wikipedia.org/wiki/SOAP