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Biodiversity Informatics - Systems Analysis and Modelling
Bioinformatics @ IPK Gatersleben
Slide # 2Bioinformatics @ IPK
Applied Bioinformatics Research @ IPK
Systems Analysis and Modelling
(coordination: N.N.)
Biodiverstity Informatics
(coordination: Uwe Scholz)30 research groups in total at IPK (as of August, 2018)
Slide # 3Bioinformatics @ IPK
Network Analysis and ModellingDr. Jedrzej Szymanski
Experimentally observed
lipidomes (MS/MS data)
Systems biology of lipid metabolism (Arabidopsis, Rapeseed)
Allelic variation and metabolic fluxes (Rapeseed, Tomato)
Inferring levels of regulation from multi-omic data
Context-specific
metabolic models
Nutrients,
light, CO2 ...
Adjustment
of reaction ratesMETABOLIC
MODELLING
Differential
flux distribution
xBREEDING
Differential
phenotype
(e.g. heterosis)
Allelic variation
of reaction rates
DE
SIG
N
RE
FIN
EM
EN
T
Proteomics
RNASeq
Analysing C3/C4 Metabolism
Metabolomics
Transcriptional
Post-transcriptional
Enzymatic activity
Rule-based reconstruction
of minimal biosynthetic
networks
(Arabidopsis, Tomato)
Mapping levels of regulation in
metabolic pathways
LEVELS OF REGULATION
Reproducible C4 Evolution
Is the C4 cycle an emergent property?
What are evolutionary drivers for the choice of decarb. enzyme?
Which evolutionary traces in the metabolic network lead to the
development of the C4 cycle?
Metabolic Modelling
C3 Model
Cytosolic Metabolites
C3 Model
Bundle SheathMesophyll
Light, CO2, NO3, Pi,
SO4, O2, H2O
Light, NO3, Pi,
SO4, O2, H2O
AAs, sugarsC4 Model
Flux Balance Analysis
Slide # 4Bioinformatics @ IPK
Image Analysis Dr. Evgeny Gladilin
Detection of plants and plant organs
Data fusion from different imaging techniques
(RBG, fluorescence, infrared, 3D-Scanning)
and time points
Computation of relevant biological parameters
(color, shape, surface, volume, curve, …)
Development of new measurement and analysis methods
(e.g., 3D data collection and data processing
Slide # 5Bioinformatics @ IPK
Bioinformatics @ Dept. of Physiology & Cell Biology
Dr. Anja Hartmann
• Modelling, analysis, simulation and visualization of biological
processes using systems biology standards
• Integration and exploration of multi-omics data within the functional
context of biological networks
Multi-omics data Visualization + Exploration
MetaCrop
Tools + Methods
VANTED
Slide # 6Bioinformatics @ IPK
Genebank DocumentationMarkus Oppermann
Information systems for Plant Genetic Resources
PGR-related data analysisParticipation in
international networks
www.ecpgr.cgiar.org www.tdwg.org
www.gbif.org
EURISCO
Research activitiesGBIS
Slide # 7Bioinformatics @ IPK
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Domestication GenomicsDr. Martin Mascher
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ancient samples
landraces
wild barley
PC1 (3.4 %)
PC
2 (
2.1
%)
EGY
SYR
SYR
SYRISR
JOR
LBN
ISR
Slide # 8Bioinformatics @ IPK
Quantitative GeneticsProf. Dr. Jochen C. Reif
Biometric data analyses:
Genome-wide
prediction:
QTL and association mapping:
Slide # 9Bioinformatics @ IPK
Bioinformatics and Information Technology
Research Data
Management:
Information Systems and Retrieval:
Sequence
Analysis:
Dr. Uwe Scholz
Slide # 10Bioinformatics @ IPK
Computational Resources (as of August, 2018)Hardware
• Compute power:
11 SMP machines with total:
o 900 physical cores
o 9 Terabyte main memory
• Storage capacity:
• Network attached storage capacity: 700 Terabyte
• Storage and archive capacity: 1.1 Petabyte
• Network: 2 x 500 MBits internet connection, internal 10 GBits backbone
Software
• Oracle Database
• Oracle WebLogic Application Server
• Various web-based information systems
• Infrastructure for IPK internal use
• Laboratory information management system
• Data publication infrastructure
• The Integrated Analysis Platform for high throughput plant image analysis
Slide # 11Bioinformatics @ IPK
The Use of IPK Resources - EURISCO
• 372 institutes
• 43 countries
• 1,974,291 accessions
• 1,652,895 C&E records
• 13 publications
+ reports
http://e
urisco.e
cpg
r.org
Slide # 12Bioinformatics @ IPK
http://edal-pgp.ipk-gatersleben.de/
• Stored data volume: 2.2 TB
• Number of files: 1,222,975
• Downloaded data volume: 161.2 TB
• Unique users: 29,068
Slide # 13Bioinformatics @ IPK
Bioinformatics
Publications2012 – 2017
© C
atr
inK
ayd
am
ov
# IPK Pubs with IF: 921
Sum IFs: 4,480.8
# Pubs with BI: 195 (21%)
Sum IFs with BI: 1,135.1 (25%)
BI = BA+BIT+DG+DI+DOK+NAM+PBI+SYS
BR
GBMOG
UAG
PZB
Slide # 14Bioinformatics @ IPK
Bioinformatics @ IPK - Training ActivitiesRecommendation of online trainings:
• Primer in Linux - http://linuxsurvival.com/
• Primer in R - http://tryr.codeschool.com/
• Primer in regular expressions - http://regexone.com/
Annual BioEXCEL courses:
• Excel-1: Basic excel functions in logic, string manipulation, calculation, and advanced
logic for the analysis of -omics data
• Excel-2: Pivot tables for the analysis of -omics data
(Bi)-annual R courses:
• R-1: Basic R functions
• R-2: Statistics with R
• R-3: Quantitative genetics with R
Training courses in the framework of collaborative projects as example:
User Training
Summer School: BBB – Basic Bioinformatics training for Biologists
Experts Training Workshops
Slide # 15Bioinformatics @ IPK
Data Management @ IPK
Coordinated by a Data Management Task Force
• Goals: in-house data management infrastructures, training for
experimental groups, support for data publication, support FAIR data
principles by research data mangement plans
• Composition: experimentalists/bioinformaticians from all departments and
scientific data management, LIMS and bioinformatics coordination
LIMS, Databases & File Storage
Experimental Descriptions
Raw Data
Processed Data
Interpreted Data
Access Solutions
Information Retrieval
Programmatic Access
Permanent Unique Identifiers
Data Publication
Support the pipeline from experiment to publication
Assessment of Data Types
Pheno-CE
Pheno-F
RNA-seq
Genome-seq
metabolomics…
Slide # 16Bioinformatics @ IPK
Bioinformatics @ IPK - Networking Activities
Open Data:Infrastructure:
Plant Phenotyping
Networks & Standards:
Plant Genetic Resources
and Biodiversity:
German Informatics
Society:
Crop Genome
Sequencing Consortia:
Slide # 17Bioinformatics @ IPK