swertz molgenis bosc2009
DESCRIPTION
TRANSCRIPT
|[email protected] & BOSC 2009 | 1
MOLGENIS and the eXtensible Genotype And Phenotype database project (xgap)
Morris A. Swertz et al
DAM & BOSC sigsStockholm, June 27 2009
EBIBiobanking platform
EBI
DAM & BOSC 2009 |
Outline2
› MOLGENIS database generator- Free toolbox of automated best practices auot-
generate useful data apps (sql,java,R,soap) from simple models
- As open platform that harmonizes data syntax, programming interfaces, user interaction, pluggable
› Demo
› eXtensible Genotype And Phenotype (xgap)- To store various high-throughput genotype and
phenotypes harmonized- as platform for collaboration and analysis tools
› Current work
EBI
DAM & BOSC 2009 |
MOLGENIS, why and how 3
inbreed
100
10.000
1,000,000
100,000
10,000
10
10,000,00
QTL profiles
network
correlate
genomestrains
individuals
markers
expressions
preprocess
probesmicroarrays
100
hybridize
100,000
genotype genotypes
norm exprs.
map
biologistbiologist
biological challenges
EBI
DAM & BOSC 2009 |
MOLGENIS, why and how 4
inbreed
100
10.000
1,000,000
100,000
10,000
10
10,000,00
QTL profiles
network
correlate
genomestrains
individuals
markers
expressions
preprocess
probesmicroarrays
100
hybridize
100,000
genotype genotypes
norm exprs.
map
biologistbiologist
bioinformatician softw engineers
€
biological challenges suitable infrastructure
EBI
DAM & BOSC 2009 |
MOLGENIS, why and how5
biologistbiologist
bioinformatician softw engineers
arab 220903
100 200 300 400 500 600 700 800 900 1000m /z0
100
%
Koornneef0007 526 (11.117) AM (Top,4, Ar,10000.0,556.28,0.70,LS 10); Sm (Mn, 2x1.00); Sb (1,40.00 )1.40e3171.1702
1396
649.3804551
526.3066248172.1795
162
650.3882224
809.4496;80
inbreedinbreed
100
100.000
10,000,000
1000
10,000
10
1000genotypegenotypeindividualsindividuals
mass peaks
mass peaks
genotypesgenotypes QTL profiles
QTL profiles
strainsstrains
networknetwork
SNP arraysSNP arrays
correlatecorrelate
LC/MSLC/MS
genomegenome
mapmap
preprocesspreprocess aligned peaks
aligned peaks
Reinventing wheels,Wasting timeHard to integrate
Reinventing wheels,Wasting timeHard to integrate
€
biological challenges suitable infrastructure
EBI
DAM & BOSC 2009 |
Alternative strategy 6
http://www.molgenis.orgSwertz & Jansen (2007) Nature Reviews Genetics 8, 235-243
http://www.molgenis.org
EBI
DAM & BOSC 2009 |
MOLGENIS, why and how7
Platform and generatorsPlatform and generatorsLittle language<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Little language<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int" +
bioinformatician softw engineer
inbreed
100
10.000
1,000,000
100,000
10,000
10
10,000,00
QTL profiles
network
correlate
genomestrains
individuals
markers
expressions
preprocess
probesmicroarrays
100
hybridize
100,000
genotype genotypes
norm exprs.
10.000
map
biologistbiologist
http://www.molgenis.orgSwertz & Jansen (2007) Nature Reviews Genetics 8, 235-243
EBI
DAM & BOSC 2009 | 8
Platform and generatorsPlatform and generatorsLittle language<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Little language<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
+
Upgrade to new researchbioinformatician softw engineer
biologist biologist
arab 220903
100 200 300 400 500 600 700 800 900 1000m /z0
100
%
Koornneef0007 526 (11.117) AM (Top,4, Ar,10000.0,556.28,0.70,LS 10); Sm (Mn, 2x1.00); Sb (1,40.00 )1.40e3171.1702
1396
649.3804551
526.3066248172.1795
162
650.3882224
809.4496;80
inbreedinbreed
100
100.000
10,000,000
1000
10,000
10
1000genotypegenotypeindividualsindividuals
mass peaks
mass peaks
genotypesgenotypes QTL profiles
QTL profiles
strainsstrains
networknetwork
SNP arraysSNP arrays
correlatecorrelate
LC/MSLC/MS
genomegenome
mapmap
preprocesspreprocess aligned peaks
aligned peaks
New Biology
New Biology
http://www.molgenis.orgSwertz & Jansen (2007) Nature Reviews Genetics 8, 235-243
EBI
DAM & BOSC 2009 |
Upgrade to new software tools9
Platform and software generators
Platform and software generatorsLittle language
<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Little language<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
Blueprint model<!-- entity organization --><entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"
+
bioinformatician softw engineer
biologistbiologist
arab 220903
100 200 300 400 500 600 700 800 900 1000m /z0
100
%
Koornneef0007 526 (11.117) AM (Top,4, Ar,10000.0,556.28,0.70,LS 10); Sm (Mn, 2x1.00); Sb (1,40.00 )1.40e3171.1702
1396
649.3804551
526.3066248172.1795
162
650.3882224
809.4496;80
inbreed
100
100.000
10,000,000
1000
10,000
10
1000
genotypeindividuals
mass peaks
genotypes QTL profiles
strains
network
SNP arrays
correlate
LC/MS
genome
map
preprocess aligned peaks
http://www.molgenis.orgSwertz & Jansen (2007) Nature Reviews Genetics 8, 235-243
EBI
DAM & BOSC 2009 | [email protected] / 11
Step 1: model*
Assay
ID : autoidName : varchar
ID : autoidValue : object
Data
Column
1
Assay 1Row 1
ID : autoidName : varchar
Experiment
Experiment 1Experiment1
ID : autoidName : varchar
Trait
ID : autoidName : varchar
Subject
Experiment1
individualsindividuals
expressionsexpressions
probesprobes
*Can also extract automatically from an existing database
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DAM & BOSC 2009 | [email protected] / 12Assay
ID : autoidName : varchar
ID : autoidValue : object
Data
Column
1
Assay 1Row 1
ID : autoidName : varchar
Experiment
Experiment 1Experiment1
ID : autoidName : varchar
Trait
ID : autoidName : varchar
Subject
Experiment1
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DAM & BOSC 2009 |
Step 2: generate13
Download and customize...
Model file XML
Generate
APIs in Java, R, Web services and HTTP
MyScriptPlugins
FormGen
MenuGenTreeGen
PluginGenMatrixGen
JTypeGenJDBCMapGen
JListGenJReadCsvGen
HSQLGen
JDatabaseGen
MySQLGen
RMatrixGen
WSGen
RListGen
datainfrastructure
user interactioninfrastructure
Communicationinfrastructure
|Date 24.06.2009
eXtensible Genotype And Phenotype database for QTL and GWAS experiments
15
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DAM & BOSC 2009 |
Locus Specific database
Clin. Trial metabase
NextGen sequencing
Proteo/Metabolomics
Animal Observations
Example projects16
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XGAP - DAM ChallengesChallenges:
› Share data between QTL collaborators
› Variety of species/methods
› Reuse the ad-hoc analysis protocols
Aim:› Simple common data
model and format
› Common interaction layers (R, SOAP)
› Platform for reusable protocols/tools
› Reuse between individual projects
17
inbreedinbreed
100
10.000
1,000,000
100,000
10,000
10
10,000,00
QTL profiles
QTL profiles
networknetwork
correlatecorrelate
genomegenomestrainsstrains
individualsindividuals
markersmarkers
expressionsexpressions preprocesspreprocess
probesprobesmicroarraysmicroarrays
100
hybridizehybridize
100,000
genotypegenotype genotypesgenotypes
norm exprs.norm exprs.
10.000
mapmap
Main work flow
Data dependency
Biomaterial/result
Lab/analysis process
Scale of information
Associated data files
processprocess
materialmaterial
10,000
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researcher
First objective
researcher
annotations
Raw and processed data
database
my GaP
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Genotype data
1. Data model 19
BxD1 BxD2 BxD3 BxD4 BxD5 BxD6 BxD7rs13475697 1 1 0 1 0 1 0rs13475698 1 0 0 0 0 0 1rs13475699 0 0 0 1 0 1 1rs13475700 1 1 1 1 0 1 0rs13475701 1 0 1 0 0 1 1rs2228909 1 1 0 1 0 0 0rs2228910 0 0 1 1 0 0 0rs3022775 0 0 0 1 1 0 1rs3024102 1 0 1 0 0 0 0rs3024103 1 0 0 1 0 0 0rs3024104 0 1 0 0 0 0 0rs3024105 0 0 1 0 0 0 1rs30462182 1 0 0 0 0 0 0rs30522279 0 1 0 0 1 0 0
MARKERS
Subjects: STRAINS
DATA ELEMENTS
Traits:
TRAIT SUBJECTTRAIT SUBJECT
Looking at standards and existing data setsSimple enough for everybody to create
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1. Data model
What about QTL data?
rs13475697rs13475698rs13475699rs13475700rs13475701rs2228909 rs22289101415670_at 0,981848 0,293227 0,034092 0,360978 0,298958 0,466545 0,3703691415671_at 0,464346 0,817348 0,990231 0,204923 0,353808 0,668164 0,4493541415672_at 0,243834 0,900083 0,69971 0,217804 0,471408 0,701617 0,0266091415673_at 0,712543 0,001536 0,209082 0,196611 0,191452 0,91619 0,5356591415674_a_at 0,159777 0,101577 0,678902 0,233476 0,251812 0,349968 0,5671711415675_at 0,777691 0,371057 0,670919 0,410665 0,742277 0,142381 0,5409451415676_a_at 0,320175 0,358505 0,207274 0,952688 0,615915 0,07167 0,2258231415677_at 0,840063 0,281845 0,773908 0,396397 0,482995 0,56668 0,199461415678_at 0,880974 0,471662 0,906012 0,711181 0,622078 0,575441 0,8688161415679_at 0,164846 0,957785 0,794479 0,207902 0,091649 0,727786 0,7960581415680_at 0,56679 0,823206 0,321578 0,513087 0,593739 0,272818 0,6208171415681_at 0,215698 0,384919 0,691254 0,550108 0,603988 0,110792 0,3801261415682_at 0,45273 0,36089 0,733234 0,911573 0,549316 0,086473 0,6396251415683_at 0,526019 0,740045 0,955297 0,797566 0,149079 0,370645 0,57789
PROBES
Traits: MARKERS
Traits:
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DATA (matrix)
1. Model
TRAIT
SUBJECT
DATA ELEMENT
TRAIT SUBJECTTRAIT SUBJECT
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DATA ELEMENT
1. Model
TRAIT
SUBJECT
DATA ELEMENT columns
rows
dimension ELEMENT
Annotations:• Individual,• Strain,• Sample,• …
Annotations:• Individual,• Strain,• Sample,• …
Annotations• Phenotype• Probe• Marker• Mass Peak• …
Annotations• Phenotype• Probe• Marker• Mass Peak• …
Data:• Phenotype
Values• Raw• QTLs• other
Data:• Phenotype
Values• Raw• QTLs• other
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DATA ELEMENT
Extensions for new experiments
TRAIT
SUBJECT
columns
rows
dimension ELEMENT
PROBE-Name-Gene-Chromosme-Locus
PROBE-Name-Gene-Chromosme-Locus
MARKER-Name-Allele-Chromosme-Locus
MARKER-Name-Allele-Chromosme-Locus
MASSPEAK-Name-MZ-RetentionTime
MASSPEAK-Name-MZ-RetentionTime
Panel-Name-Type: CSS, RIL..-Parent Panels
Panel-Name-Type: CSS, RIL..-Parent Panels
INDIVIDUAL-Name-Strain-Mother-Father-Sex
INDIVIDUAL-Name-Strain-Mother-Father-Sex
SAMPLE-Name-Individual-Tissue
SAMPLE-Name-Individual-Tissue And so on
…
And so on…
And so on…And so on…
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Protocol graph from FuGE
› XGAP extends on standard FuGE (Jones ea, NatBiot 2007)
FuGE: Jones et al Nature Biotech 25, 1127-1133
DATA DATA
Genotype data QTL data
QTL Mapping
AffyArray
SNPArray
DATA
Expression data
MappingProtocol
Illumina
RSoftware
IlluminaProtocol
Affy M430Protocol
BeadStudio
DATA
application
Protocol
Software
Equipment
BioconductorNorm.
Affy M430platform
DATA DATA
DATA
FuGE:
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UML: XGAP extends FuGE
INVESTIGATION (Core)
SUBJECT VARIANTS (Extensions)
TRAIT VARIANTS (Extensions)
DATA (Core)
ID : autoidInvestigation : xrefName : stringactivityDate : DateTimeInputData : mrefOutputData : mrefProtocol : xref
ProtocolApplication*
Trait
Alleles : stringGene : xref
Marker
Species : OntologyTermChromosome : varchar(5)BPstart : decimalBPend : decimalcMPosition : decimalSequence : text
Locus
Gene : xref
ProbeSet
Control : bool
Gene
Protocol : xref
ProtocolElement
Y : intX : intGridX : intGridY : int
Spot
Species : OntologyTerm
Subject
Type : [Natural,RI,RCC,CSS,..]FounderStrains : mref
StrainStrain
0..1
RetentionTime : decimalmz : decimal
MassPeak
Mass : decimalFormula : stringStructure : string
MetaboliteProtocol
0..1
Data*
ID : autoidInvestigation : xrefName : string
ID : autoidDataSet : xrefColumn : xrefRow : xrefValue : object
DataElement
Column
DataSet
Protocol
Strain : xrefMother : xrefFather : xrefSex : [male,female,unknown,malefemale]
Individual
Individual
0..1
Father0..1 Mother
0..1
PairedSample
Individual2 : xrefLabel : OntologyTermLabel2 : OntologyTerm
Row
ID : autoidName : stringStart : DateTimeEnd : DateTimeProviders : mref
Investigation*
Investigation
Investigation
ID : autoidInvestigation : xrefType : Item.TypeName : string
DimensionElement*
Individual2
MisMatch : boolProbeSet : xrefGene : xref
Probe
Investigation
B
A
C
ID : autoidName : stringProtocolText : text
Protocol*
OutputData*
*
InputData
* *
-FounderStrains
0..*
*
Sample
Tissue : stringIndividual : xref
Unit : OntologyTerm
Phenotype
Gene : xrefSequence : textMass : decimal
Protein
Uniform core to ease sharing of data and tools
Various traits for new research
Various subjects for new research
?
?
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DAM & BOSC 2009 |
2. Mode, run MOLGENIS26
<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE molgenis PUBLIC "MOLGENIS 1.0" "http://molgenis.sourceforge.net/dtd/molgenis_v_1_0.dtd"><molgenis name="xgap" label="XGAP - eXtensible Genotype and Phenotype database">
<!-- INVESTIGATION --><module name="xgap.core">
<description>Core entities.</description><entity name="Investigation" extends="FugeInvestigation">
<unique fields="name" description="Name is unique" /></entity><entity name="ProtocolApplication"
extends="FugeProtocolApplication"><field name="Status" type="enum"
enum_options="[inprocess, final]" default="inprocess"description="The status of this protocolapplication (inprocess = still working on it, final = ready for further analysis)."/>
<field name="Investigation" type="xref"xref_entity="Investigation" xref_field="id"xref_label="name"description="Reference to the Investigation this protocolapplication belongs to."/>
<unique fields="name,Investigation"description="Name is unique within an Investigation" />
</entity><!-- DATA --><entity name="Data" extends="FugeData">
<description>Generic structure for describing data matrices such asgenotype result, gene expression measurement, QTLcalculation, etc.
</description><field name="Investigation" type="xref"
xref_entity="Investigation" xref_field="id"xref_label="name"description="Reference to the Investigation this data is measured as part of."/>
<!--field name="DataType" type="xref"xref_entity="DataType" xref_field="id"xref_label="name" description="Added to distinguish betweenqtl and raw data etc." /-->
<field name="RowType" type="enum"enum_options="[Marker,Probe,ProbeSet,Individual,Sample,PairedSample,MassPeak,Gene,Trait,Subject,Strain,Metabolite,Spot,Phenotype,NMRBin]"description="Type of the columns of this matrix. Each column refers to a Trait or Subject (DimensionElement). "/>
<field name="ColType" type="enum"enum_options="[Marker,Probe,ProbeSet,Individual,Sample,PairedSample,MassPeak,Gene,Trait,Subject,Strain,Metabolite,Spot,Phenotype,NMRBin]"description="Type of the rows of this matrix. Each row refers to a Trait or Subject (DimensionElement)"/>
<field name="ValueType" type="enum"enum_options="[Text,Decimal]"description="Type of the values of this matrix. E.g. text strings or decimal numbers." />
<field name="TotalRows" type="int" default="0"/><field name="TotalCols" type="int" default="0"/><unique fields="name,Investigation" />
</entity><entity name="DimensionElement"
extends="FugeDimensionElement"><description>
Describes the biological material or subject which isbeing 'measured' by an Data set.<br />For example an 'Sample' extends from Item, which makesit possible that a microarray-assay Data set such sample(as DataElement can reference any Item).<br />An DimensionElement is always linked to a single oneInvestigation.
</description><field name="Investigation" type="xref_single"
xref_entity="Investigation" xref_field=
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DAM & BOSC 2009 |27
Connect to R statistics
Connect to R statistics
Workflow ready web-services
Workflow ready web-services
UML documentation of your model
UML documentation of your model
Edit & trace your data
Edit & trace your data
Import/export to Excel
Import/export to Excel
plugin your own scripts (R/QTL)
plugin your own scripts (R/QTL)
Tech keywords: object oriented data models, multi-platform java, tomcat/glassfish web server, mysql/postgresql database, Eclipse/Netbeans IDE, Java API, WSDL/SOAP API, R-project API, MVC, freemarker templates and css for custom layout, open source.
m<-find.markers()544 markers downloaded.…library(qtl)#qtl analysis here
add.data(qtl, name = “QTLs”)2,448,000 data elements added.
s tra in .tx tspec ies .tx tp ro toco l.tx tp robe .tx tm arker.tx tinvestiga tion .tx tind iv idua l.tx tgene .tx tda ta .tx tconstan t.p ropertiesda ta
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DAM & BOSC 2009 |
Next step: add processing30
Sheets thanks to Joeri van der Velde and Danny Arends
Generalize for all MOLGENIS instances:
(1) Extend MOLGENIS model for tool integration<tool name=“rqtl”>
<input name=“data” entity=“data”/>…
</tool>
(2) Integrate workflow definition and execution
Extending on Taverna/Galaxy model & APIs…
Generalize for all MOLGENIS instances:
(1) Extend MOLGENIS model for tool integration<tool name=“rqtl”>
<input name=“data” entity=“data”/>…
</tool>
(2) Integrate workflow definition and execution
Extending on Taverna/Galaxy model & APIs…
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DAM & BOSC 2009 |
Next step: semantics
The Pheno-OM project› Integrating mouse and man
Generalize for all MOLGENIS instances:
Next: Add MOLGENIS components to integrate:
(1) Ontology browsing Extending on BioPortal/OLS frameworks?
(2) Semantic integration layer ???
Generalize for all MOLGENIS instances:
Next: Add MOLGENIS components to integrate:
(1) Ontology browsing Extending on BioPortal/OLS frameworks?
(2) Semantic integration layer ???
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DAM & BOSC 2009 |
› Exploit standard generated interfaces› Big distribute big data and tools› Meta analysis
Federation? Cloud computing?32
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DAM & BOSC 2009 |
Acknowledgements
Joeri van der VeldeJoris LopsTomasz AdamusiakDanny ArendsMartijn DijkstraMatthijs KattenbergTjeerd AbmaAte BoeremaHenrikki AlmusaRudi AlbertsDamian SmedleyKaty WolstencroftAndrew R. Jones Bruno M. TessonRichard A. ScheltemaGonzalo Vera RodriguezRene Oostergo
Helen E. Parkinson Ritsert C. JansenCisca WijmengaCarole GobleMarco RoosM. Scott MarshallPaul Schofield John M. HancockJuha MuiluKlaus SchughartEngbert O. de BrockHans Hillegethe LifeLines consortiumthe Trial Coordination Centerthe GEN2PHEN consortiumthe CASIMIR consortiumthe NBIC/BioAssist consortium
33
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DAM & BOSC 2009 |
› See us at the NBIC booth
› Add generator targets- We have funding for
several positions (PhD,SE)
› Read more:- MOLGENIS for data integration:
Smedley et al 2009, Brief. in Bioinformatics 9(6):532- Review of MOLGENIS type of systems (dated)
Swertz & Jansen 2007, Nature Rev. Genetics 8(3):235- First MOLGENIS, in those times in PHP
Swertz et al 2004, Bioinformatics 20(4)L2075
Questions34
http://www.molgenis.org
http://www.xgap.org