bioinformatics@ ipk · pdf fileaba fatty acid catabolism peroxisome mrna related processes...

Biodiversity Informatics - Systems Analysis and Modelling

Bioinformatics @ IPK Gatersleben

Slide # 2Biodiversity Informatics - Systems Analysis and Modelling

Applied Bioinformatics Research @ IPK

Systems Analysis and Modelling (coordination: N.N.)

Biodiverstity Informatics(coordination: Uwe Scholz)

28 research groups in total at IPK (as of October, 2017)

Prof. Dr. Thomas Altmann (temporary)


Network Analysis and ModellingGroup Leader: Prof. Dr. Thomas Altmann (temporary)

model test of model revised model

metabolic networkZ. mays

increasedauxin more

time

venation regulatory network

signaling network in photorespiration

mutants

metabolite mediated ROS

PR

pathogen

immunityresponse

cryopreservation, rootformation, iron toxicity,spike development, C4metabolism, biomass,drought, ...

... ...External stimulusResponseExternal stimulusResponseExternal stimulusResponseExternal stimulusResponseExternal stimulusResponse

Chloroplast oganizationProtein localizationChloroplast oganizationProtein localizationChloroplast oganizationProtein localizationChloroplast oganizationProtein localizationChloroplast oganizationProtein localization Catabolic processesCatabolic processesCatabolic processesCatabolic processesCatabolic processes Response

EthyleneResponseEthyleneResponseEthyleneResponseEthyleneResponseEthylene

ABAFatty acid catabolismPeroxisome





mRNA related processesDevelopmentProtein modification





Cell cycleReplicationRibosome biogenesis





Cell wall related processesCytoskeletonCell wall related processesCytoskeletonCell wall related processesCytoskeletonCell wall related processesCytoskeletonCell wall related processesCytoskeleton

Cell wall related processesAmino acid metabolismPhotosynthesis





Endomembrane systemProtein localizationin secretory pathway





ATP metabolic processesATP metabolic processesATP metabolic processesATP metabolic processesATP metabolic processes PhosphorylationTransportPhosphorylationTransportPhosphorylationTransportPhosphorylationTransportPhosphorylationTransport

Cluster 1 (375 genes) Cluster 2 (696 genes) Cluster 3 (979 genes) Cluster 4 (155 genes) Cluster 5 (448 genes) Cluster 6 (471 genes)

Cluster 7 (543 genes) Cluster 8 (1023 genes) Cluster 9 (1046 genes) Cluster 10 (258 genes) Cluster 11 (208 genes) Cluster 12 (598 genes)

−1

0

1

−1

0

1

0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2

0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2 0 4 9 12 re2Days after drought

Rel

ative

exp

ress

ion

[z−s

core

]


Image Analysis Group Leader: Dr. Evgeny Gladilin

Analysis-Report

IAP (Integrated Analysis Platform)• Systems biology cloud storage, analysis and visualization system• Web-based GUI, command line client• Integration of data sets (LemnaTec, greenhouse climate data, …)• Statistic analysis (R-based diagrams, PDF reports)

IAP - Web-based GUI

VolumeIAP formular

areatopareaside average ..Biomass Digital 2IAP ×=

Area Ratio (dry/normal)

Image

Pipline

Research Areas• Advanced image analysis algorithms for

automated phenotyping• Software system development (IAP) • Cooperation with the biological research groups

VolumeIAP


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


Bioinformatics and Information TechnologyGroup Leader: Dr. Uwe Scholz

Research DataManagement:

Information Systems and Retrieval:

Sequence Analysis:


Genebank DocumentationGroup Leader: Dr. Helmut Knüpffer

Information systems for Plant Genetic Resources

Participation in international networks for PGR and biodiversity informatics

PGR-related data analysis

http://www.ecpgr.cgiar.org/ http://www.tdwg.org/ http://www.gbif.org/ http://www.europeana.eu


●●●●

●

●

●●

●●●

● ●

●

●

●●

●●

●●

●

●

●

●●

●

●

●

●

●●

●

●●●●●●

●●●●●●●

●●

●

●●●

●●●

●

●●

●

●

●●

●

●● ●

●●

●●

●

●

●

●

●●●●●

●

●

●●●

●

● ●

●●

●

●

●

●

●

●

●

●

●

●●●

●●

●●● ●

●●●●●●●

●

●●

●

●●

●●

●

●●●

●●●●●●

●

●

●

●●

●●●

●●

●

●

●●

●

●

●

●●●

●

●

●

●

●

●

●

● ●●

●

●

●

●●

●

●●●●

●

●

● ●●

●

●

●

●●

●●

●●

●

●

●

●●

●

●

●

●

●

●

●●

●

●

●

●

●●●

●●

●

●

●

●●

●

●

●

●

●

● ●

●

●

●

●

●

●

●●

●

Domestication GenomicsGroup Leader: Dr. Martin Mascher

−0.05 0.00 0.05 0.10

−0.2

−0.1

0.0

0.1

●

●

●

●

●

●●

●●

●

●●●

●● ●● ● ●●●

●

● ●

●

●

●

●

●●●●

●●●●

●●●●●●

●●

●●

●● ●●●

●●

●

●

●

●●

●

●

●

●●

●●●

●

●

●

●

●

●

●

●

●

●●

●

●●●●

●

●●

●

●

●

●●●

●●

●●●

●●

●

●

●

●● ●

●

●●

●

●

●●●

●● ●

●●

●●

●●

●

●

●

●●●

● ●●

●●●

●●● ●

●

●●●●

●

●●●

●●

●●●

●● ●

●

●●

●●

●

●

●

●

●

●

●

● ●

●

●●

●

●

●

●●

●

●

●

●

●

●

●

●●●

●

●

●

●●●

●● ●●●

●

●

●●●●●

●● ●

●

●

●

●

●

●

●●

●

●

●

●

●

●●

●

●●●

●

●

●

●

ancient sampleslandraceswild barley

PC1 (3.4 %)PC

2 (2

.1 %

)

EGY

SYR

SYRSYR

ISR

JOR

LBN

ISR


Quantitative GeneticsGroup Leader: Prof. Dr. Jochen C. Reif

Biometric data analyses:

Genome-wide prediction:

QTL and association mapping:


Computational Resources (as of October, 2017)Hardware• Compute power:

11 SMP machines with total:o 912 physical coreso 9 Terabyte main memory

• Storage capacity:• Network attached storage capacity: 646 Terabyte• Storage and archive capacity: 1.1 Petabyte

• Network: 2 x 200 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


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


Data Management @ IPK

Support the pipeline from experiment to publication

AnalysisSamples Measurement Quantification Publication

Establishment of a data management task force• Goal: Development of a data management plan • Composition: experimentalists/bioinformaticians from all departments and

scientific data management, LIMS and bioinformatics coordination

Development of integrated infrastructure for standardized dataAssessment of Data Types

Pheno-CEPheno-FRNA-seq

Genome-seqmetabolomics

…

Storage SolutionsExperimental Descriptions

Raw DataProcessed DataInterpreted Data

Access SolutionsSearch

Restricted AccessMaterial IDs

Data Publication


© Anja HartmannVisualized with VANTED

Bioinformatics Publications2012 – 2017 (Jul)

© C

atrin

Kayd

amov # IPK Pubs with IF: 891

Sum IFs: 4,314.2# Pubs with BI: 190 (21%)Sum IFs with BI: 1,097.6 (25%)BI = BA+BIT+DG+DI+DOK+NAM+PBI+SYS


Bioinformatics @ IPK - Networking ActivitiesData Publication:Infrastructure:

Plant PhenotypingNetworks & Standards:

Plant Genetic Resourcesand Biodiversity:

German InformaticsSociety:

Crop Genome Sequencing Consortia:

bioinformatics@ ipk · pdf fileaba fatty acid catabolism peroxisome mrna related processes...

Documents