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

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:
dsp
dt
dc
csp
dt
ds
⋅⋅−=
⋅⋅= 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

Independent of modelling formalism
Brief (very brief) overview of SBML
<?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

Evolution of libSBML
2000 2001 2002
SBML
Project
begins
20

2000 2001 2002 20
SBML L1V1
SBML
Project
begins

2001 2002 2003
SBML L1V1

2002 2003
V1
2004

2002 2003
V1
2004
libSBML-1.0.0

• API library for working with SBML
What is libSBML ?

What is libSBML ?
libSBML-1 allowed you to
• read

What is libSBML ?
• read
• create

What is libSBML ?
• read
• create
• manipulate

What is libSBML ?
• read
• create
• manipulate
• write

What is libSBML ?
• read
• create
• manipulate
• write
• validate

• Standard ANSI C
libSBML-1
LGPL licence
What is libSBML ?

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 ?
• read
• create
• manipulate
• write
• validate

What is libSBML ?
• read
• create
• manipulate
• write
• validate
• convert between
levels/versions
L1V1 L2V1

• Standard ANSI C++
libSBML-2
LGPL licence
What is libSBML ?

libSBML-2
LGPL licence
What is libSBML ?
C Java Python

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 ?
Significantly changed the API

libSBML-3
What is libSBML ?
... Not good for users

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

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
libSBML
3.4.0

2008
.0.0
V3
2009
SBML L2V4
2010
libSBML-4.0.0-b1
20
libSBML
3.4.0
libSBML
4.0.0

2009
V4
2010
-4.0.0-b1
2011
libSBML
3.4.0
libSBML
4.0.0
20

2009
V4
2010
-4.0.0-b1
2011
libSBML
3.4.0
libSBML
4.0.0
20
SBML L3V1

2009
V4
2010
-4.0.0-b1
2011
libSBML
3.4.0
libSBML
4.0.0
20
SBML L3V1
libSBML-4.2.0

2009
V4
2010
-4.0.0-b1
2011
libSBML
3.4.0
libSBML
4.0.0
20
SBML L3V1
libSBML-4.2.0 libSBML-5.0.0

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

2010 2011
libSBML
4.0.0
2012
SBML L3V1
libSBML-4.2.0 libSBML-5.0.0
20
libSBML-5.6.0

libSBML-5.6
LGPL licence
What is libSBML ?
C Java Python
C# MATLAB Octave
Perl R Ruby

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
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
libSBML-1.0.0
Does libSBML benefit SBML ?

Benefits of libSBML
• closely mimic SBML structure

Benefits of libSBML
Model UML diagram
from SBML specification

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
• 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>lenov@ebi.ac.uk</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
• interfaces to different languages

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
• 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
• develop in line with specification

Two branches for release
Benefits of libSBML

Benefits of libSBML
Stable branch
- code from accepted SBML
- installers for the above

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

Benefits of libSBML
Experimental branch
- binaries
- built with ALL experimental code

Benefits of libSBML
• XML parsers
• develop in line with specification
• backwards compatibility

Interlude
keating-libsbml-taster
SPIN_OSS – shared folder - keating

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

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 RubyR

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

Issues we face
as Open Source Developers

Issues we face
How well do we know our users ?

Issues we face
What are THEIR requirements ?

Issues we face
How do our design decisions impact them ?

Who are our users ?
Should we do this ?

Issues we face
Which OS/versions/compilers etc. to support ?

Issues we face
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.

Issues we face
Dependence on other third party developers
How do we keep up ?

Issues we face
Managing community contributions
Who has access ?
What if they break stuff ?

Issues we face
Attribution

Issues we face
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

• 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

LibSBML - open source software development

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