NIBSys
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Funding details: Related items
Projects: INDIE - Biotechnological production of sustainable indole
Institutions: Axxence Aromatic GmbH
Project leader at Axxence Aromatic
Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato
Institutions: National Institute of Biology
https://orcid.org/0000-0003-4776-7164
Projects: WURSynBio, INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, INDIE - Biotechnological production of sustainable indole, _p_stRT, Public project, Playground, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Institutions: National Institute of Biology, NewHorizon
https://orcid.org/0000-0001-7484-6031
Projects: INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
Projects: WURSynBio, INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, FAIRDOM user meeting, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato
Institutions: National Institute of Biology
https://orcid.org/0000-0001-5906-8569
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP, BioCreative VII, MESI-STRAT Review, SDBV/HITS
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock, University of Innsbruck
https://orcid.org/0000-0003-3540-0402
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project ...
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological ...
Projects: INDIE - Biotechnological production of sustainable indole
Institutions: Wageningen University & Research
PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Projects: INDIE - Biotechnological production of sustainable indole
Institutions: UNIBI: Bielefeld University
Projects: _p_stRT
Institutions: Indiana University Bloomington
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
This is a project for testing
Programme: NIBSys
Public web page: Not specified
WARNING: THIS IS A TEST PROJECT CREATED FOR TESTING THE UPLOAD TO FAIRDOMHUB USING seekr AND SEEK API
pISA-tree: Standard project directory tree
A set of batch files is used to create standard directory tree for research projects. Batch files are provided to make standardized nested directories in accordance with the ISA Abstract Model levels (Investigation/Study/Assay).
https://github.com/NIB-SI/pISA-tree
Linked resources:
- R support for pISA-tree DOI ...
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Our world is changing fast! Key global trends are rapid urbanisation, growing and ageing populations, and increased prosperity. This results in depletion of natural and petrochemical resources and climate change, which affects the quality of the environment and people's lives. Therefore, developing a bio-based economy is key to sustain our planet in the long term. Raw materials will have to be recruited from renewable sources.
Industrial biotechnology is potentially a very powerful technology in ...
Programme: NIBSys
Public web page: https://indie.cebitec.uni-bielefeld.de/
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
In this project, the involved partners are trying to develop the knowledge base that will enable the breeding of new potato varieties, tolerant to multiple environmental stressors.
Programme: NIBSys
Public web page: https://adapt.univie.ac.at/
Start date: 1st Jul 2020
End date: 30th Jun 2024
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
This investigation is published under the CC BY 4.0 license.
Programme: NIBSys
Public web page: Not specified
Despite the intensive use of agrochemicals, plant pathogens are responsible for huge yield losses worldwide. Understanding the interaction between plant and pathogens is crucial to ensure long lasting and environmentally friendly system of plant protection. Therefore research of the most important human food crops in combination with their pathogens is one of the highest priorities for sustainable agriculture.
The aim of the proposed research project is to bring new perspective into understanding ...
Programme: NIBSys
Public web page: http://projects.nib.si/hyp/
Country: Not specified
City: Not specified
Web page: Not specified
Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_SPv10T0andT1, _S_P1_SPv10T2andT3, _S_P1_SPv1TransientExp, _S_P1_SxPAltAcTransferases, _S_P1_SxPv10vsSxP12, _S_P1_SxPv12T2, _S_P4_CoExpNetViz, _S_P4_DiNAR, _S_P4_GAtreat, _S_P4_SxP10-newG-DE, _S_P4_SxP10-oldG-DE, _S_P4_SxP1012-finalG, _S_P4_SxP12-newG-DE
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_01_SxP_Data_Only-CoExp, _A_01_SxPv12_fastq-QC, _A_01_mapping-CLC, _A_01_toNewGenome-CLC-mapping, _A_02_FastQC-bioinfo, _A_02_Nb_datasets-CoExp, _A_02_SxPv12_mapping-CLC, _A_02_limmavoomDE-R, _A_02a_limmavoom-multim-R, _A_02a_limmavoomDEbylines-R, _A_02b_limmavoom-uniquem-R, _A_03_MapMan-visualisation, _A_03_NewGenome-MapMan, _A_03_SxPv12_limmavoom_DE-R, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_GSEA-Stat, _A_04_MapManBINenrich-GSEA, _A_04_Mercator-bioinfo, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _A_05_DEstat-R, _A_05_Phenotype_analysis-Stat, _A_05_VOCcomp-Bioinfo, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _A_07_transgenes-CLC, _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_LeavesSxPv10vsv12-GCMS, _A_P4_v10v12-phenotyping, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _A_RootsSxPv10vsv12-GCMS, _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _A_SPv10EaDActAnalysis-GCMS, _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _A_SxPAlternativeAcetyltransferases-GCMS, _A_SxPv10vsv12-phenotyping, _A_SxPv12ScreeningT2-GCMS, _A_TransientSPv11andSPv12-GCMS, _I_T21_SXPsysbio-files, _S_P1_SPv10T0andT1-files, _S_P1_SPv10T2andT3-files, _S_P1_SPv1TransientExp-files, _S_P1_SxPAltAcTransferases-files, _S_P1_SxPv10vsSxP12-files, _S_P1_SxPv12T2-files, _S_P4_CoExpNetViz-files, _S_P4_DiNAR-files, _S_P4_GAtreat-files, _S_P4_SxP10-newG-DE-files, _S_P4_SxP10-oldG-DE-files, _S_P4_SxP1012-finalG-files, _S_P4_SxP12-newG-DE-files
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Short Name: 02_FieldTrials Title: Field trials Description: Field trials - spraying CPB larvae on potato field with the insecticidal dsRNA validated for effectiveness in the laboratory trials Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_2019, _S_02_2020
Assays: _A_01_jun19-wet, _A_01_jun20-wet, _I_02_FieldTrials-files, _S_01_2019-files, _S_02_2020-files
Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_TargetSelect, _S_02_dsRNAorder, _S_03_dsRNAprod, _S_04_Stages, _S_05_jun2016, _S_06_oct2016, _S_07_dec2016, _S_08_jan2017, _S_09_jun2017, _S_10_apr2018, _S_11_may2018
Assays: _A_00_Ecoli-dry, _A_00_jun2017_dsRNA_stabil-wet, _A_01_AgroRNA-wet, _A_01_LitData-dry, _A_01_dec2016-phenotyping, _A_01_jan2017-phenotyping, _A_01_jun2016-phenotyping, _A_01_jun2017-phenotyping, _A_01_jun2017-phenotyping, _A_01_may2018-phenotyping, _A_01_oct2016-phenotyping, _A_01_pIsol-wet, _A_02_UlrichTop100-BLAST, _A_02_dec2016-RNAisol, _A_02_jun2016-RNAisol, _A_02_jun2017-RNAisol, _A_02_plasmid-SangerSeq, _A_02_qPCR_ampl_test-wet, _A_03_RNaseItreat-wet, _A_03_dec2016-qPCR, _A_03_jun2016-qPCR, _A_03_jun2017-qPCR, _A_03_patentDB-BLAST, _A_03_stages-RNAisol, _A_04_ortho-BLAST, _A_04_prod-qPCR, _A_04_stages-qPCR, _A_05_CPB_gene-annot, _A_06_splitter_BLAST-dry, _A_07_MergeEvi-dry, _A_08_SelTargetsA-dry, _I_01_LabTrials-files, _S_01_TargetSelect-files, _S_02_dsRNAorder-files, _S_03_dsRNAprod-files, _S_04_Stages-files, _S_05_jun2016-files, _S_06_oct2016-files, _S_07_dec2016-files, _S_08_jan2017-files, _S_09_jun2017-files, _S_10_apr2018-files, _S_11_may2018-files
Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED ...
Submitter: Maja Zagorscak
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
All the files available are published under the CC BY 4.0 license.
Short Name: DiNAR Title: DiNAR analyses of SxP DE data Description: DiNAR visualisation of SxPv1.0 and SxPv1.2 expressoin data in either PIS or CKN networks. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _S_P4_DiNAR-files
Short Name: Gibberelin_treatment Title: GA3 treatment of SxPs Description: SxP lines were treated with 3 different GA3 concentrations (1, 10 and 100 micromolar) and control solution. WT Nb plants were used for control. From v1.0 T3, low producing line 5_2_5 and high producing line 5_1_7 were used and from v1.2 T2 lines 4_1 and 4_3. Treatment was done for 5 consecutive weeks, once per week with spraying the leaves. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Short Name: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_toNewGenome-CLC-mapping, _A_02_limmavoomDE-R, _A_02a_limmavoomDEbylines-R, _A_03_NewGenome-MapMan, _A_04_GSEA-Stat, _A_05_Phenotype_analysis-Stat, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _S_P4_SxP10-newG-DE-files
Short Name: P4_SxP10-oldG-DE Title: SxPv1.0 RNA-seq analysis using old Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the published (old) genome of Nicotiana benthamiana. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: No
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_02_FastQC-bioinfo, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_Mercator-bioinfo, _A_05_DEstat-R, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_07_transgenes-CLC, _S_P4_SxP10-oldG-DE-files
Short Name: P4_SxP1012-finalG Title: Reanalysis of SxP Illumina reads with Nb genome V3.5 Description: * Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Short Name: P4_SxP12-newG-DE Title: Gene expression analysis of Sxp 1.2 Description: exp4 in phenodata Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxPv12_fastq-QC, _A_02_SxPv12_mapping-CLC, _A_03_SxPv12_limmavoom_DE-R, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _S_P4_SxP12-newG-DE-files
Short Name: P1_SPv10T2andT3 Title: Characterization of SPv1.0 plants of the T2 and T3 generations Description: Plants of the SxP v1 second and third generation were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS) and transcriptome (via RNA-seq). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2018-11-09 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _S_P1_SPv10T2andT3-files
Short Name: P1_SPv1TransientExp Title: Transient expression in Nicotiana benthamiana leaves of constructs for SPv1 Description: The constructs for stable transformation of SPv1.X versions were tested transiently via agroinfiltration of Nicotiana benthamiana leaves. Pheromone content was analysed via GC-MS Raw Data: pISA Study creation date: 2019-12-08 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10EaDActAnalysis-GCMS, _A_TransientSPv11andSPv12-GCMS, _S_P1_SPv1TransientExp-files
Short Name: P1_SxPAltAcTransferases Title: Study of alternative acetyltransferases for future SxP versions Description: Study of transient expression of different acetyltransferase genes responsible of the catalysis of the conversion of Z11-16OH into Z11-16OAc, assayed in Nicotiana benthamiana WT plants. Raw Data: pISA Study creation date: 2021-11-25 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SxPAlternativeAcetyltransferases-GCMS, _S_P1_SxPAltAcTransferases-files
Short Name: P1_SxPv10vsSxP12 Title: Comparison between SxPv1.0 and SxPv1.2 Description: Volatilome characterization of SxPv1.0 T3 plants, SxPv1.2 T1 plants and WT plants. Raw Data: pISA Study creation date: 2020-11-01 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_LeavesSxPv10vsv12-GCMS, _A_RootsSxPv10vsv12-GCMS, _A_SxPv10vsv12-phenotyping, _S_P1_SxPv10vsSxP12-files
Short Name: SxPv12T2Analysis Title: Analysis of second generation of SxPv1.2 plants Description: Characterization of SxPv1.2 T2 plants. Raw Data: pISA Study creation date: 2021-12-09 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes Institutions involved: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Spain; Institute of Agrochemistry and Food Technology (IATA), Spain; The ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Short Name: CoExpNetViz Title: CoExpNetViz Description: Coexpression analyses with CoExpNetViz tool. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxP_Data_Only-CoExp, _A_02_Nb_datasets-CoExp, _S_P4_CoExpNetViz-files
Investigation files _I_T21_SXPsysbio
Short Name: P1_SPv10T0andT1 Title: Characterization of SPv1.0 plants of the T0 and T1 generations Description: SP v1.0 plants were generated and studied (T0), as well as the first generation (T1). Plants were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2021-11-01 pISA Study creator: AlfredoQR Principal investigator: Diego Orzaez License: Creative ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _S_P1_SPv10T0andT1-files
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
Short Name: 01_ns-dsRNA_trans Title: CPB transcriptome response to non-specific dsRNA feeding Description: Global transcriptome response of CPB gut tissue to non-specific dsRNA (dsEGFP) feeding Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01_RNA-Seq_dsEGFP-NGS, _A_02_CLC-RNASeq, _S_01_ns-dsRNA_trans-files
Investigation files _I_03_Omics
Short Name: 02_2020 Title: Field trial in the year 2020 Description: Field trial in the year 2020 Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Short Name: 01_2019 Title: Field trial in the year 2019 Description: Field trial in the year 2019 Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Investigation files _I_02_FieldTrials
General sandbox
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: FAIRDOMhub API usage in R
Description of observed phenotypic variables in the MOA investigation.
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Imaging
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Leaf Chamber Fluorometer
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Gene Expression Profiling
Technology type: Custom Array
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: MicroRNA Profiling
Technology type: Next generation sequencing
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Bioinformatics
Technology type: Interactions
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Degradome-Seq
Technology type: Next generation sequencing
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Ziva Ramsak
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2013-12
Submitter: Ziva Ramsak
Assay type: Protein Quantification
Technology type: Orbitrap Velos
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Assay: _A_01_evigene Short Name: 01_evigene Assay Class: DRY Assay Type: evigene Title: EvidentialGene tr2aacds.pl VERSION 2016.07.11 Description: See http://eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Integration
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.1_BUSCO Short Name: 02.1_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO on assemblies and tr2aacds output Description: BUSCO on assemblies and tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.2_assembly-contribution-count Short Name: 02.2_assembly-contribution-count Assay Class: DRY Assay Type: count Title: assembly contribution count Description: assembly contribution count, input/output tr2aacds pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.6_TransRate Short Name: 02.6_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate stat on raw tr2aacds transcriptomes Description: TransRate stat on raw (initial) tr2aacds transcriptomes, basic and reference-based pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Nonde Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Assay: _A_02.7_VecScreen Short Name: 02.7_VecScreen Assay Class: DRY Assay Type: VecScreen Title: VecScreen on raw tr2aacds output Description: VecScreen (contamination screening) and blastn (contaminants annotation) on raw (initial) tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
Download
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
Abstract (Expand)
Authors: Lenny Ferrer, Melanie Mindt, Maria Suarez-Diez, Tatjana Jilg, Maja Zagorščak, Jin-Ho Lee, Kristina Gruden, Volker F. Wendisch, Katarina Cankar
Date Published: 11th May 2022
Publication Type: Journal
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll, Špela Baebler, Kristina Gruden
Date Published: 21st Nov 2021
Publication Type: Journal
Abstract
Authors: Tatjana Walter, Kareen H. Veldmann, Susanne Götker, Tobias Busche, Christian Rückert, Arman Beyraghdar Kashkooli, Jannik Paulus, Katarina Cankar, Volker F. Wendisch
Date Published: 1st Dec 2020
Publication Type: Journal
Abstract
Authors: Tatjana Walter, Nour Al Medani, Arthur Burgardt, Katarina Cankar, Lenny Ferrer, Anastasia Kerbs, Jin-Ho Lee, Melanie Mindt, Joe Max Risse, Volker F. Wendisch
Date Published: 1st Jun 2020
Publication Type: Journal
Abstract
Authors: A. Schmoldt, H. F. Benthe, G. Haberland
Date Published: 1st Sep 1975
Publication Type: Journal
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
