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Libraries and Tools for accessing the COMBINE archive
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README.md

README.md

COMBINE Archive

In this project I keep a prototype library and a couple of applications that make working with the archive easier. This project contains of three parts: LibCombine, a library reading the format, CombineCLI a command line application and FormsCombineArchive that represents the information in a UI. At this point mostly the library is in use.

The UI

The CombineArchive execuable is a windows application for creating / reading / modifying COMBINE archives. It associates with all files of type *.omex during installation.

Frontend of CombineArchive

Once the archive is opened, the files are displayed on the left side. When selected, their contents is displayed on the right. A double click on the file opens it. A right click displays a context menu from where the file or its contents can be copied to the clipboard. If an SBML file is selected, and SBW is available on the machine, the file can be sent to any SBW capable application, such as COPASI, JDesigner, RoadRunner to name but a few.

Download

You can download the latest Windows binary from:

http://sourceforge.net/projects/sbw/files/modules/CombineArchive/

Command Line version

With CombineCLI, a basic command line interface is included. At this point in time it is rather basic, and only lists the contents, or displays meta information associated with a document. For example:

CombineCLI -o <path to omex file>

will list the contents of the archive.

CombineCLI -o <path to omex file> -v -l <location>

will display associated with the given location of the archive. Alternatively

CombineCLI -o <path to omex file> -v -f <format>

can be used to view the information with the first file of the given format.

Library

The main class of the library is CombineArchive, you can construct new classes, and add local documents to it before saving it, or load existing ones, and browse through the contents. If you want to get hold of the manifest document, call the .ToXML() method.

How to use

Simply reference LibCombine.dll in your project, ensure that the file ICSharpCode.SharpZipLib.dll is also available, and you are ready to call the library.

OmexDescription

Apart from that the library features an OmexDescription description class, that can be used by those that don't have a proper RDF library handy, with it you could create the description for an element like so:

		var desc =
            new OmexDescription
            {
                About = "./test.xml",
                Description = "Some Description about the file",
                Creators =
                    new List<VCard> 
                    { 
                        new VCard 
                        { 
                            FamilyName = "Bergmann", 
                            GivenName = "Frank", 
                            Email = "fbergman@caltech.edu", 
                            Organization = "California Institute of Technology" 
                        } 
                    },
                Created = DateTime.Parse("2013-04-04 16:00+1")
            };

To write that to an XML string, use the ToXML method. Conversely to parse from file or string, use the functions:

	var list = OmexDescription.ParseString(xmlString);

or:

	var list = OmexDescription.ParseFile(fileName);

Creating a New Archive

The following is an example on how I would create a new omex file, by bundling a local SBML file and accompabying paper together with a reference to the BioModel. First I define a BaseDirectory that serves as a root for my archive later on, and then I add a number of files:

         var newArchive = new CombineArchive
         {
             BaseDir = @"C:\Users\fbergmann\Documents\SBML Models\",
             Descriptions = new List<OmexDescription> { 
                 new OmexDescription
            {
                About = "./BorisEJB.xml",
                Description = "original JDesigner model for Kholodenko2000 - MAPK feedback",
                Creators =
                    new List<VCard> 
                    { 
                        new VCard 
                        { 
                            FamilyName = "Bergmann", 
                            GivenName = "Frank", 
                            Email = "fbergman@caltech.edu", 
                            Organization = "California Institute of Technology" 
                        } 
                    },
                Created = DateTime.Parse("2013-04-04 16:00+1")
            }
             },
             Entries = new List<Entry> { 
                 new Entry { Location = "./BorisEJB.xml", Format = Entry.KnownFormats["sbml"] }, 
                 new Entry { Location = "./paper/Kholodenko2000.pdf", Format = Entry.KnownFormats["pdf"] }, 
                 new Entry { Location = "http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010", Format = Entry.KnownFormats["sbml"] }, 
             }
         };

         newArchive.SaveTo(@"C:\Users\fbergmann\Desktop\Boris.omex");

Finding out what is in a COMBINE Archive

Suppose I would get a COMBINE archive, how would I find out about its contents? First you load the file:

var omex = CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\Boris.omex");

And then you would interrogate it by asking for its Entries property. Usually it will be the case that your application will only handle some of the COMBINE standards. In that case you want to use the methods:

// get the number of SBML files in the archive
omex.GetNumFilesWithFormat("sbml") 

// get the local filenames to them 
omex.GetFilesWithFormat("sbml")

// get the actual entries
omex.GetEntriesWithFormat("sbml")

Since there can be any number of files in the archive, I use the convention, that the first OmexDescription in the metadata file represents the MainFile the name of which you can get through the according property.

Using the Entry objects directly has the advantage, that you can open the files, in whatever application is associated with it, or read the contents either in form of byte[] or strings. Just as example, to open the PDF file encoded in the file above one could use these lines:

         var omex = CombineArchive.FromFile(@"C:\Users\fbergmann\Desktop\Boris.omex");

         if (omex.HasEntriesWithFormat("pdf"))
             omex.GetEntriesWithFormat("PDF").First().OpenLocation();

Here GetEntriesWithFormat returns a list of all PDFs, First() gives us the first entry, and OpenLocation opens the file.

The Format

Frequently we are faced with project spanning more than just one file. Be it experimental data, that should be stored together with a publication describing the experiment, or a computational model together with diagrams and metadata describing it in detail. SED-ML, one of the COMBINE Standards, started to develop a basic archive format that allowed storing a Simulation Experiment Description along with all computational models referenced. The COMBINE archive aims to broaden the scope. It still is a ZIP Archive, but also features a manifest called manifest.xml that describes the contents of the archive.

<?xml version="1.0" encoding="utf-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
  <content location="." format="http://identifiers.org/combine.specifications/omex-manifest"/>
  <content location="./model/model.xml" format="http://identifiers.org/combine.specifications/sbml"/>
  <content location="./simulation.xml" format="http://identifiers.org/combine.specifications/sedml"/>
  <content location="./article.pdf" format="application/pdf"/>
  <content location="./metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata"/>
</omexManifest>

Third party libraries used

This project uses the following third party libraries:

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Copyright (c) 2013-2014, Frank T. Bergmann
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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