The document summarizes the BioLib project, which aims to create C/C++ libraries for common biological functionality that can be accessed from multiple bioinformatics programming languages to avoid duplication of efforts. It has created bindings for several existing libraries, including Affyio, Staden IO, GSL, Rlib, and others. The project uses Git for version control, CMake for building, and SWIG for generating language bindings in an effort to maximize code reuse across languages.

1. BioLib Development Report (BOSC
2009)
C and C++ libraries for BioPerl, BioJAVA,
BioPython, BioRuby. . .
Pjotr Prins (pjotr.prins at wur.nl)
Wageningen University, Dept. of Nematology; Groningen Bioinformatics Center
BioLib Development Report (BOSC 2009) – p.

2. The stated problem
Many high-level languages used in Biology
(Perl, R, Java. . . )
Duplication of effort in all Bio* efforts -
BioPerl, BioConductor, BioJAVA. . .
in particular for data IO/parsing/interpretation
(Alan’s keynote)
BioLib Development Report (BOSC 2009) – p.

3. What if?
What if you need some functionality (e.g. linear
regression) in Perl, you can
Roll your own in Perl (performance?)
Bind against existing clib using Perl-XS (ugh)
Bind using SWIG (better, but one-off like
Perl::GSL)
Bind using SWIG with Biolib (all languages)
In fact, it may already be there (GSL or Rlib)
BioLib Development Report (BOSC 2009) – p.

4. DRY-DRO
Do not repeat yourself (DRY)
Do not repeat ourselves (DRO)
Bio*: BioPerl, BioPython, BioRuby, BioJAVA,
BioConductor, BioHaskell, BioCPP, . . .
Limited pool of programmers in bioinformatics
Usually 2 or 3 competing implementations
Use existing implementations
BioLib Development Report (BOSC 2009) – p.

5. Why bother?
Open Source Software is about eyes
BioLib Development Report (BOSC 2009) – p.

6. Eyes!
Eyes like these!
BioLib Development Report (BOSC 2009) – p.

7. Eyes (3)
Eyes like these!. . .
BioLib Development Report (BOSC 2009) – p.

8. Eyes (5)
Well, realistically. . .
BioLib Development Report (BOSC 2009) – p.

9. BioLib project
Objectives:
Utilize existing C/C++ libraries
Create mappings to all Bio* languages
Focus on correctness and
performance
A central place (plumbing)
An OBF affiliated project
BioLib Development Report (BOSC 2009) – p.

10. Power Trio
Plumbing power trio:
Git - modular version control
Cmake - make file generator
SWIG - simplified wrapper and interface
generator
BioLib Development Report (BOSC 2009) – p. 1

11. Power trio (1)
GIT
Version control on steroids
What source control should be
Easy branching of development
Submodules
BioLib Development Report (BOSC 2009) – p. 1

12. Power trio (2)
CMake
Generator for make files
Very modular approach
Resolves complex dependencies
Looks like a simple
programming language
Easy on the eyes and mind
BioLib Development Report (BOSC 2009) – p. 1

13. Power trio (3)
SWIG
Code generator for mappings done right:
Rules for generating code
Macros (DRY)
Pattern matching
Flexible
Supports many languages
BioLib Development Report (BOSC 2009) – p. 1

14. Achievements (year one)
Affyio: Affymetrix arrays (357 methods; 10K lines)
Staden: Sequencer trace files (95; 16K)
GSL: GNU Science Library (2702; 200K)
Rlib: R routines (> 176; 43K)
R/qtl: Quantitative genetics (> 100; 10K)*
Libsequence: Sequence analysis (> 1000; 21K)*
Bio++: Sequence analysis (> 1000; 52K)*
Code base 350K lines USD 10 million R&D
BioLib Development Report (BOSC 2009) – p. 1

15. Source tree
|-- clibs
| |-- affyio-1.8
| |-- biolib_R
| |-- biolib_microarray
| |-- libsequence-1.6.6
|-- mappings
| ‘-- swig
| |-- perl
| | |-- affyio
| | |-- staden_io_lib
| | ‘-- test
| |-- python
| |-- ruby
104 directories, 668 files
BioLib Development Report (BOSC 2009) – p. 1

16. Adding a C lib
Unpack C/C++ library in
./src/clibs/modulename
Add CMake file - compiles into .so shared
library
Create Perl mapping in
./src/mapping/swig/perl/module
Add SWIG .i file
Add CMake file - compiles into .pm and .so
shared library
BioLib Development Report (BOSC 2009) – p. 1

17. CMake goodies
# Defining a C library build in Biolib:
SET (M_NAME staden_io_lib)
SET (M_VERSION 1.11.6)
FIND_PACKAGE(ZLIB REQUIRED)
BUILD_CLIB()
ADD_LIBRARY(${LIBNAME} SHARED
array.c
compress.c
compression.c
ctfCompress.c
(...)
INSTALL_CLIB()
BioLib Development Report (BOSC 2009) – p. 1

18. CMake for Perl
# Defining a C library mapping for Perl
SET (USE_ZLIB TRUE)
SET (USE_INCLUDEPATH io_lib)
FIND_PACKAGE(MapPerl)
POST_BUILD_PERL_BINDINGS()
TEST_PERL_BINDINGS()
INSTALL_PERL_BINDINGS()
BioLib Development Report (BOSC 2009) – p. 1

19. SWIG Map
%include <Read.h>
#define TT_ANY 0
#define TT_ZTR 7
typedef struct
{
int format;
char *trace_name;
int NPoints;
int NBases;
(...)
} Read;
Read *read_reading(char *fn, int format);
BioLib Development Report (BOSC 2009) – p. 1

20. Perl
use biolib::staden_io_lib;
$result = staden_io_lib::read_reading($fn,
$staden_io_lib::TT_ANY);
print("format=",staden_io_libc::Read_format_get($result));
print("NBases=",$result->{NBases});
print("base=",staden_io_libc::Read_base_get($result));
Outputs:
format=7
NBases=766
base=NCTTGGGAAAGCATAAACCATGTATTATCGAATTCGAGCT
CGGTCCCAACTTAATTGTACA...
BioLib Development Report (BOSC 2009) – p. 2

21. Python
import biolib.staden_io_lib as io_lib
result = io_lib.read_reading(procsrffn,
io_lib.TT_ANY)
print result.format
print result.NBases
print result.base
7
766
NCTTGGGAAAGCATAAACCATGTATTATCGAATTCGAGCT
CGGTCCCAACTTAATTGTACA...
BioLib Development Report (BOSC 2009) – p. 2

22. For the Perl coder
Adding functionality in language of choice
Easier deployment - ’install biolib-perl’
Shared correctness testing
Generated API documentation
BioLib Development Report (BOSC 2009) – p. 2

23. For the authors
Independent source trees
Increased exposure (Ruby, Perl. . . )
Added unit/integration testing environment
Deployment, multi-platform support (Linux,
OSX, Windows)
No autoconf pain (./configure and friends)
Implicit access to other libraries (GSL, Rlib)
Online generated API documentation
BioLib Development Report (BOSC 2009) – p. 2

24. Future work
Automated API documentation (with doctests)
More libraries (Emboss, NCBI, . . . )
New code (HPC)
More languages (JAVA, R, OCaml, . . . )
Bio* integration (CPAN, Ruby gems, Python
eggs)
Debian/Fedora/OSX/Windows packages
More platforms (Windows without Cygwin)
BioLib Development Report (BOSC 2009) – p. 2

25. Credits
Ben Bolstad (Affyio), James Bonfield (Staden), Karl Broman (R/qtl)
Jonathan Leto (GSL SWIG)
Xin Shuai (Google SoC libsequence)
Adam Smith (Google SoC Bio++)
Oswaldo Trelles, José Manuel Mateos-Duran and Andrés Rodríguez (UMA)
Chris Fields (BioPerl), Mark Jensen (BioPerl), Hilmar Lap (Nescent, OBF)
Jaap Bakker (WU), Geert Smant (WU), Ritsert Jansen (GBIC)
BioLib Development Report (BOSC 2009) – p. 2

26. BoF
BioLib: Birds of a Feather Session (BoF) at 16:50 hours
BioLib Development Report (BOSC 2009) – p. 2