LibSBML - open source software development

EBI is an Outstation of the European Molecular Biology Laboratory.

Sarah Keating

LibSBML

Overview 1. Brief overview of SBML

2. Evolution of libSBML

3. Does libSBML benefit SBML ?

4. Interlude

5. Users

6. Development

7. Issues




4. Interlude

5. Users

6. Development

7. Issues




4. Interlude

5. Users

6. Development

7. Issues

What are the outcomes of modelling/simulation ?

Models

many forms

What are the outcomes of modelling/simulation ?

How do we communicate a model ?

Publish a paper

Species s with initial concentration 2 nM reacts with species c with initial concentration 5 nM with a rate of p*s*c. Here are the equations:

dspdtdc

cspdtds

⋅⋅−=

⋅⋅= PROBLEMS

What is the value of p ?

Is this a typo ?


Publish code


Code for various models


Potential software




Hard, if not impossible, to reproduce a model

UNLESS

Interoperable data format


A machine-readable format for representing computational models in systems biology – a tool neutral exchange format

Brief (very brief) overview of SBML

More information on SBML: http://www.cds.caltech.edu/~mhucka/tmp/mhucka-ccb-2012.pdf

http://www.cds.caltech.edu/~mhucka/tmp/mhucka-ccb-2012.pdf

Independent of modelling formalism


<?xml version="1.0" encoding="UTF-8"?> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"> <model id="dimerization“ timeUnits="second" > <listOfCompartments> <compartment id="Cell" size="1e-15" spatialDimensions="3”/> </listOfCompartments> <listOfSpecies> <species id="P" compartment="Cell" initialAmount="301”/> <species id="P2" compartment="Cell" initialAmount="0" /> </listOfSpecies> <listOfInitialAssignments> <initialAssignment symbol="y"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <cn> 3.2 </cn> </math> </initialAssignment> </listOfInitialAssignments> </model> </sbml>

Expressed in XML

Independent of modelling formalism


<?xml version="1.0" encoding="UTF-8"?> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"> <model id="dimerization“ timeUnits="second" > <listOfCompartments> <compartment id="Cell" size="1e-15" spatialDimensions="3”/> </listOfCompartments> <listOfSpecies> <species id="P" compartment="Cell" initialAmount="301”/> <species id="P2" compartment="Cell" initialAmount="0" /> </listOfSpecies> <listOfInitialAssignments> <initialAssignment symbol="y"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <cn> 3.2 </cn> </math> </initialAssignment> </listOfInitialAssignments> </model> </sbml>

Expressed in XML




4. Interlude

5. Users

6. Development

7. Issues

Evolution of libSBML

2000 2001 2002 SBML Project begins

20


2000 2001 2002 20

SBML L1V1

SBML Project begins


2001 2002 2003

SBML L1V1


2001 2002 2003

SBML L1V1


2002 2003

V1

2004


2002 2003

V1

2004

libSBML-1.0.0

What is libSBML ?

• API library for working with SBML

What is libSBML ?

What is libSBML ?

libSBML-1 allowed you to • read

What is libSBML ?


• create

What is libSBML ?


• create

• manipulate

What is libSBML ?


• create

• manipulate

• write

What is libSBML ?


• create

• manipulate

• write

• validate

• Standard ANSI C libSBML-1

LGPL licence

What is libSBML ?


2002 2003

V1

2004

libSBML-1.0.0


2002 2003

V1

2004

libSBML-1.0.0

SBML L2V1


2002 2003

V1

2004

libSBML-1.0.0

SBML L2V1

libSBML-2.0.0

What is libSBML ?


• create

• manipulate

• write

• validate

What is libSBML ?


• create

• manipulate

• write

• validate

• convert between levels/versions

L1V1 L2V1

• Standard ANSI C++ libSBML-2

LGPL licence

What is libSBML ?

• Standard ANSI C++ libSBML-2

LGPL licence

What is libSBML ?

C Java Python


2002 2003

V1

2004

libSBML-1.0.0

SBML L2V1

libSBML-2.0.0


2002 2003

V1

2004

libSBML-1.0.0

SBML L2V1

libSBML-2.0.0

SBML L1V2


2002 2003 2004

libSBML-1.0.0

SBML L2V1

libSBML-2.0.0

SBML L2V1

20


2002 2003 2004

libSBML-1.0.0

SBML L2V1

libSBML-2.0.0

SBML L2V1

20

libSBML-2.2.0


2003 2004

bSBML-1.0.0

SBML L2V1

libSBML-2.0.0

SBML L2V1

2005

libSBML-2.2.0 20


2004

ML-2.0.0

L L2V1

2005

libSBML-2.2.0 2006 20


2004

ML-2.0.0

L L2V1

2005

libSBML-2.2.0 2006 20

libSBML-3.0.0-a

libSBML-3

What is libSBML ?

libSBML-3

What is libSBML ?

Significantly changed the API

libSBML-3

What is libSBML ?


... Not good for users


2004

ML-2.0.0

L L2V1

2005

libSBML-2.2.0 2006 20

libSBML-3.0.0-a


04

2.0.0

2V1

2005

libSBML-2.2.0 2006 2007

libSBML-3.0.0-a

SBML L2V2


5 2006 2007

libSBML-3.0.0-a

SBML L2V2

2008


5 2006 2007

libSBML-3.0.0-a

SBML L2V2

2008

libSBML-3.0.0


5 2006 2007

libSBML-3.0.0-a

SBML L2V2

2008

libSBML-3.0.0

SBML L2V3


006 2007

BML-3.0.0-a

SBML L2V2

2008

libSBML-3.0.0

SBML L2V3

2009


006 2007

BML-3.0.0-a

SBML L2V2

2008

libSBML-3.0.0

SBML L2V3

2009

SBML L2V4


007 2008

libSBML-3.0.0

SBML L2V3

2009

SBML L2V4

2010


007 2008

libSBML-3.0.0

SBML L2V3

2009

SBML L2V4

2010

libSBML-4.0.0-b1

libSBML-4

What is libSBML ?


libSBML-4

What is libSBML ?


This time we involved the user


007 2008

libSBML-3.0.0

SBML L2V3

2009

SBML L2V4

2010

libSBML-4.0.0-b1


2008

.0.0

V3

2009

SBML L2V4

2010

libSBML-4.0.0-b1 20


2008

.0.0

V3

2009

SBML L2V4

2010

libSBML-4.0.0-b1 20

libSBML3.4.0


2008

.0.0

V3

2009

SBML L2V4

2010

libSBML-4.0.0-b1 20

libSBML3.4.0

libSBML4.0.0


2009

V4

2010

-4.0.0-b1 2011

libSBML3.4.0

libSBML4.0.0

20


2009

V4

2010

-4.0.0-b1 2011

libSBML3.4.0

libSBML4.0.0

20

SBML L3V1


2009

V4

2010

-4.0.0-b1 2011

libSBML3.4.0

libSBML4.0.0

20

SBML L3V1

libSBML-4.2.0


2009

V4

2010

-4.0.0-b1 2011

libSBML3.4.0

libSBML4.0.0

20

SBML L3V1

libSBML-4.2.0 libSBML-5.0.0

libSBML-5

What is libSBML ?

libSBML-5

What is libSBML ?

Seamlessly replaced libSBML-4

libSBML-5

What is libSBML ?

Seamlessly replaced libSBML-4

but added modular support for SBML L3 packages


2009

V4

2010

-4.0.0-b1 2011

libSBML3.4.0

libSBML4.0.0

20

SBML L3V1

libSBML-4.2.0 libSBML-5.0.0


2010 2011

libSBML4.0.0

2012

SBML L3V1

libSBML-4.2.0 libSBML-5.0.0 20

libSBML-5.6.0

• Standard ANSI C++ libSBML-5.6

LGPL licence

What is libSBML ?

C Java Python C# MATLAB Octave Perl R Ruby




4. Interlude

5. Users

6. Development

7. Issues

Does libSBML benefit SBML ?

0

50

100

150

200

250

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

(counted in middle of each year)

Number of tools supporting SBML


0

50

100

150

200

250

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012



libSBML-1.0.0


0

50

100

150

200

250

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012



libSBML-1.0.0



Benefits of libSBML

Benefits of libSBML

• closely mimic SBML structure

Benefits of libSBML

Model UML diagram from SBML specification

Benefits of libSBML

Benefits of libSBML SBase

id: SId name: string { use=”optional” } compartmentType: SId { use=”optional” } spatialDimensions: int { use=”optional” default=”3” } size: double { use=”optional” } units: UnitSId { use=”optional” } outside: SId { use=”optional” } constant: boolean { use=”optional” default=”true” }

Compartment

Benefits of libSBML

Benefits of libSBML

Benefits of libSBML


Benefits of libSBML


• API for working with annotations

Minimum Information

Requested In the

Annotation of biochemical Models

Benefits of libSBML

Benefits of libSBML

Standard scheme for machine-readable annotations

- Authorship, publication info

- Links to other data resources

Semantics of the mathematics

Guidelines for model quality Defined by SBML

Benefits of libSBML





Guidelines for model quality Within the annotation

Benefits of libSBML

ModelHistory class

Benefits of libSBML

CVTerm class

Benefits of libSBML

<rdf:RDF> <rdf:Description rdf:about="#_000001"> <dc:creator rdf:parseType="Resource"> <vCard:Family>Le Novère</vCard:Family> <vCard:Given>Nicolas</vCard:Given> <vCard:EMAIL>[email protected]</vCard:EMAIL> <vCard:Orgname>EMBL-EBI</vCard:Orgname> </dc:creator> <dcterms:created rdf:parseType="Resource"> <dcterms:W3CDTF>2005-02-02T14:56:11Z <bqmodel:is> <rdf:li rdf:resource="urn:miriam:biomodels.db:BIOMD0000000001"/> </bqmodel:is> <bqmodel:isDescribedBy> <rdf:li rdf:resource="urn:miriam:pubmed:8983160"/> </bqmodel:isDescribedBy>

Benefits of libSBML




Guidelines for model quality Defined by SBO


<listOfSpecies> <species id="P" compartment="Cell" initialAmount="301" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false" sboTerm="SBO:0000252"/> <species id="P2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false" sboTerm="SBO:0000420"/> </listOfSpecies>

Benefits of libSBML

Benefits of libSBML



Benefits of libSBML


• interfaces to different languages


• Standard ANSI C++ language bindings

C Java Python C# MATLAB Octave Perl R Ruby

Benefits of libSBML

Contributed by users

language bindings

Benefits of libSBML

PHP

Pascal ???

Benefits of libSBML




Benefits of libSBML


• XML parsers



Benefits of libSBML

Abstract XML Layer

XML Parser XMLInput Stream

XMLOutput Stream

XMLToken

XMLNode

XMLAttributes

Expat Attributes

Xerces Attributes

LibXML Attributes

Benefits of libSBML


• XML parsers



Benefits of libSBML


• XML parsers

• develop in line with specification



Benefits of libSBML

Two branches for release

Benefits of libSBML

Benefits of libSBML

Benefits of libSBML

Stable branch - code from accepted SBML - installers for the above

Benefits of libSBML

Benefits of libSBML

Experimental branch - src - code from core and any L3 packages with code under development

Benefits of libSBML

Benefits of libSBML

Experimental branch - binaries - built with ALL experimental code

Benefits of libSBML


• XML parsers




Benefits of libSBML


• XML parsers


• backwards compatibility






4. Interlude

5. Users

6. Development

7. Issues

Interlude

Interlude

keating-libsbml-taster

SPIN_OSS – shared folder - keating




4. Interlude

5. Users

6. Development

7. Issues

Who are our users ?

Who are our users ?

Who are our users ?

docs 4%

src code 24%

installers 72%

libSBML downloads

Who are our users ?

Mac OS X 28%

Win 36%

Linux 36%

Figures here do not include installers that target a particular programming language (e.g. R, MATLAB)

Installer downloads

Who are our users ?

Mac OS X 28%

Win 36%

Linux-32-deb

7% Linux-32-rpm

3%

Linux-64-deb 14% Linux-64-rpm

12% Other 36%

Installer downloads


Who are our users ?

Win 36%

Linux 36%

MacOSX - snow leopard

9%

Mac OS X - lion 19%

Other 28%

Installer downloads


Who are our users ?

Installer downloads


Mac OS X 28%

Linux 36%

Win32 17%

Win64 19%

Other 36%

Who are our users ?

MATLAB

R

Python 2.5 Python 2.6

Python 2.7 Python 3.2

Targeted win installers

Who are our users ?

Targeted win installers

R

Python 2.5

Python 2.6

Python 2.7

Python 3.2

Who are our users ?

VCell – The Virtual Cell

iBioSim




4. Interlude

5. Users

6. Development

7. Issues

Development

Development

Test driven development

10200 unit tests

43500 assertions

4330 invalid SBML files – test validation code

Development

Simplified Wrapper and Interface Generator

language interfaces

Java Python C# Perl Ruby R

Development

Autogenerate test code for bindings

Nightly builds

Stable release cycle (ish)

Autogenerate documentation

Development

Open Build Service – create linux installers

Future ...

Include libSBML in the linux distributions

Code refactoring




4. Interlude

5. Users

6. Development

7. Issues

Issues we face as Open Source Developers


How well do we know our users ?



What are THEIR requirements ?



How do our design decisions impact them ?

Who are our users ?

Should we do this ?


Which OS/versions/compilers etc. to support ?


Linux Different versions using different defaults for other programs

http://stackoverflow.com/questions/10960805/apt-get-install-for-different-python-versions

ubuntu 10.04 with python2.6 by default

Ideally Maverick would support Python 2.6, 2.7, and 3.2 (beta), with Python 2.7 as the default.


Dependence on other third party developers

How do we keep up ?


Managing community contributions

Who has access ?

What if they break stuff ?



Attribution



Which OS/versions/compilers etc. to support ?

Dependence on other third party developers



Lucian Smith

Mike Hucka

Frank Bergmann

Linda Taddeo

Nicolas Rodriguez

Sarah Keating

SBML Team

Previous members:

Akira Funahashi; Andrew Finney; Ben Bornstein; Akiya Jouraku; Ben Kovitz; Herbert Sauro; Maria Schilstra; Jo Matthews; Hamid Bolouri;

John Doyle; Hiroaki Kitano

U. of Washington, USA

Caltech, USA

University of Heidelberg, DE

Caltech, USA

EMBL-EBI, UK

EMBL-EBI, UK

Community

• Gordon Ball • Alex Gutteridge

• Bill Denny • Stefan Hoops

• Christoph Flamm • Totte Karlsson

• Akira Funahashi • Moriyoshi Koizumi

• Ralph Gauges • Rainer Machné

• Martin Ginkel • Nicolas Rodriguez

Acknowledgements

Acknowledgements

๏ NIH National Institute of General Medical Sciences (USA) ๏ JST ERATO Kitano Symbiotic Systems Project (Japan) (to 2003) ๏ National Science Foundation (USA) ๏ International Joint Research Program of NEDO (Japan) ๏ JST ERATO-SORST Program (Japan) ๏ Japanese Ministry of Agriculture ๏ Japanese Ministry of Educ., Culture, Sports, Science and Tech. ๏ EMBL-EBI (UK) ๏ BBSRC e-Science Initiative (UK) ๏ DARPA IPTO Bio-SPICE Bio-Computation Program (USA) ๏ Air Force Office of Scientific Research (USA) ๏ STRI, University of Hertfordshire (UK) ๏ Beckman Institute, Caltech (USA) ๏ Molecular Sciences Institute (USA)

SBML Funding over the years

Education

LibSBML - open source software development