bioinformatics @ ipk gatersleben · bioinformatics @ ipk slide # 2 applied bioinformatics research...

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)


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


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


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


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


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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


Quantitative GeneticsProf. Dr. Jochen C. Reif

Biometric data analyses:

Genome-wide

prediction:

QTL and association mapping:


Bioinformatics and Information Technology

Research Data

Management:

Information Systems and Retrieval:

Sequence

Analysis:

Dr. Uwe Scholz


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


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


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


Bioinformatics

Publications2012 – 2017

© C

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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


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


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…


Bioinformatics @ IPK - Networking Activities

Open Data:Infrastructure:

Plant Phenotyping

Networks & Standards:

Plant Genetic Resources

and Biodiversity:

German Informatics

Society:

Crop Genome

Sequencing Consortia:

bioinformatics @ ipk gatersleben · bioinformatics @ ipk slide # 2 applied bioinformatics research...

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