SEEK ID: https://fairdomhub.org/people/808
Locations:
Slovenia
, Not specified
ORCID:
https://orcid.org/0000-0001-7484-6031
Joined: 7th Nov 2016




Project roles
Project administrator
- HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato
- pISA-tree
- _p_stRT
- Public project
Asset gatekeeper
Asset housekeeper
pISA-tree (National Institute of Biology)
HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato (National Institute of Biology) ; INDIE - Biotechnological production of sustainable indole (National Institute of Biology) ; _p_stRT (National Institute of Biology) ; Public project (NewHorizon)
Related items
- Programmes (2)
- Projects (5)
- Institutions (2)
- Investigations (11+3)
- Studies (19+2)
- Assays (33+10)
- Data files (303+32)
- Presentations (1)
- Documents (93+127)
National Institute of Biology, Department of Biotechnology and Systems Biology projects
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, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
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
Organisms: Solanum tuberosum, Potato virus Y
Programme: Public
Public web page: Not specified
Organisms: Not specified
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/
Organisms: Corynebacterium glutamicum
pISA-tree: Standard project directory tree (ISA compliant)
Development of support for standardization of directory trees to suport ISA framework of research organization. We are developing a set of batch/make files to enable creation of trees for storage of assets (data/presentations/protocols/scripts) and description files that hold associated metadata for Investigation / Study / Assay levels.
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
Organisms: 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/
Organisms: Potato virus Y
Metadata
Investigation: _I_Test
Short Name: Test
Title: Test investigation
Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_Show
Assays: _A_Work-R, _I_Test-files, _S_Show-files
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_Show
Assays: _A_Work-R, _I_Test-files, _S_Show-files
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_Show
Assays: _A_Work-R, _I_Test-files, _S_Show-files
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_Show
Assays: _A_Work-R, _I_Test-files, _S_Show-files
Snapshots: No snapshots
Investigation: _I_Test Short Name: Test Title: Test investigation Description: Investigation - for demonstration purposes. Phenodata: ./phenodata_20191015.txt pISA Investigation creation date: 2019-10-15 pISA Investigation creator: Andrej Blejec Principal investigator: * Investigation Person Address: https://orcid.org/0000-0001-7484-6031 Investigation Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_Show
Assays: _A_Work-R, _I_Test-files, _S_Show-files
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_Test 2022-05-08 23:13:06
Assays: _A_Work-R, _S_Show-files
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_Sigma 2022-04-17 00:52:30
Assays: _A_Work-R, _S_Show-files
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_Sigma 2022-04-17 00:48:38
Assays: _A_Work-R, _S_Show-files
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Study: _S_Show Short Name: Show Title: Testing study Description: Test study for demonstration only. Raw Data: pISA Study creation date: 2019-10-15 pISA Study creator: Andrej Blejec Principal investigator: * Study Person Address: https://orcid.org/0000-0001-7484-6031 Study Person Address: https://orcid.org/0000-0003-3644-7827 License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_Sigma 2022-04-17 00:30:01
Assays: _A_Work-R, _S_Show-files
Snapshots: No snapshots
Investigation files _I_Test
Snapshots: No snapshots
Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_STRT
Assays: _A_01_GC_content-count, _A_02_cdhit_3cvs-GFFmerged, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Snapshots: No snapshots
Here is a collection of examples of possibilities for API communication in R
Snapshots: No snapshots
General sandbox
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: FAIRDOMhub API usage in R
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Test API connection to FAIRDOMHub, Test API connection to FAIRDOMHub, dummy file
Snapshots: No snapshots
Empty assay
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: FAIRDOMhub API usage in R
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: Snapshot 1
Short Name: cdhit_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/Solanum_tuberosum_ITAG_DM_v1_description..., /input/Solanum_tuberosum_PGSC_DM_v4.04_converte..., /input/StPGSC4.04n_seq_4_PGSC-p-rep_ITAG-pep_gf..., /input/path_to_files.txt, /intermediate/singletons.DM.seqID.txt, /intermediate/singletons.seqID.txt, /intermediate/singletons.tetra.seqID.txt, /intermediate/stCuSTr_cds_repAlt_cdhitEST-conda..., /intermediate/stPanTr_aa_singletons_DM_on_tetra..., /intermediate/stPanTr_aa_singletons_tetra_on_DM..., /output/5cv_weak-components.txt, /output/5cv_weak-components_withAnnotation.tsv, /output/VennDiagrams/stPanTr+stCuSTr_geneCount_..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/VennDiagrams/stPanTr_geneCount_weak-com..., /output/annot.alias.aa.tsv, /output/annot.alias.cds.tsv, /output/cdhit-est_rep-alt_aS.75_c.90_pairs.tsv, /output/cdhit-est_representativesMatched_aS.75_..., /output/cdhit-est_singletons_aS.75_c.90.tsv, /output/stPanTr-clusters.tsv, /output/trueSingle.DM.ID, /output/trueSingle.polyploid.ID, /reports/SupplementaryFigure4.pdf, /reports/SupplementaryTableS7, /reports/cvID_group-Rplot.pdf, /reports/cv_group-Rplot.pdf, /scripts/01.1_commands-CDHIT-EST.txt, /scripts/01.2_commands-CDHIT-2D.txt, /scripts/02_cd-hit-est_cdhit-2d.html, /scripts/03_stPanTr_components_all.html, /scripts/04_summary_stPanTr_v4.html and 4 hidden items
Snapshots: Snapshot 1, Snapshot 2
Short Name: 01_GC_content-count Assay Class: DRY Assay Type: count Title: GC content and sequence length Description: A, C, T, G content and sequence length pISA Assay creation date: 2020-03-09 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data: ../input/path_to_files.txt
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/Solanum_tuberosum-ITAG_DM_v1_cds.fasta, /input/Solanum_tuberosum_PGSC_merged.fasta, /input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gf..., /output/Solanum_tuberosum-ITAG_DM_v1_cds_GC.txt, /output/Solanum_tuberosum_PGSC_merged.CDS_GC.txt, /output/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_g..., /scripts/GC_content.py, /scripts/tab_to_fasta.py and 12 hidden items
Snapshots: No snapshots
Short Name: 04_BUSCO_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /output/BUSCO_stPanTr_embryophyta_odb9.tsv, /output/BUSCO_stPanTr_solanaceae_odb10.tsv, /output/short_summary_BUSCO_Solanum_tuberosum-I..., /output/short_summary_BUSCO_Solanum_tuberosum-I..., /output/short_summary_BUSCO_Solanum_tuberosum-P..., /output/short_summary_BUSCO_Solanum_tuberosum-P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_Solanum_tuberosum_P..., /output/short_summary_BUSCO_StPGSC4.04n_seq_4_P..., /output/short_summary_BUSCO_StPGSC4.04n_seq_4_P..., /output/short_summary_BUSCO_stPanTr.aa.fasta_em..., /output/short_summary_BUSCO_stPanTr.aa.fasta_so..., /output/short_summary_BUSCO_stPanTr_alt.aa.fast..., /output/short_summary_BUSCO_stPanTr_alt.aa.fast..., /output/short_summary_BUSCO_stPanTr_rep.aa.fast..., /output/short_summary_BUSCO_stPanTr_rep.aa.fast..., /scripts/01_run_BUSCO_commands.sh, /scripts/02_BUSCO_plots.html
Snapshots: No snapshots
Short Name: 07_Desiree-mapping Assay Class: DRY Assay Type: mapping Title: Desiree mapping Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/PGSC_DM_v3.4_transcript-update_represent..., /intermediate/Desiree/chrLength.txt, /intermediate/Desiree/chrName.txt, /intermediate/Desiree/chrNameLength.txt, /intermediate/Desiree/chrStart.txt, /intermediate/Desiree/genomeParameters.txt, /intermediate/PGSC/chrLength.txt, /intermediate/PGSC/chrName.txt, /intermediate/PGSC/chrNameLength.txt, /intermediate/PGSC/chrStart.txt, /intermediate/PGSC/genomeParameters.txt, /intermediate/gff-merged/chrLength.txt, /intermediate/gff-merged/chrName.txt, /intermediate/gff-merged/chrNameLength.txt, /intermediate/gff-merged/chrStart.txt, /intermediate/gff-merged/genomeParameters.txt, /intermediate/indexDesiree.log, /intermediate/indexGFFmerged.log, /intermediate/indexPGSC.log, /output/Desiree_SRR10416847/Log.final.out, /output/Desiree_SRR10416847/Log.out, /output/Desiree_SRR10416847/Log.progress.out, /output/Desiree_SRR10416847/SJ.out.tab, /output/Desiree_SRR10416848/Log.final.out, /output/Desiree_SRR10416848/Log.out, /output/Desiree_SRR10416848/Log.progress.out, /output/Desiree_SRR10416848/SJ.out.tab, /output/Desiree_SRR10416849/Log.final.out, /output/Desiree_SRR10416849/Log.out, /output/Desiree_SRR10416849/Log.progress.out, /output/Desiree_SRR10416849/SJ.out.tab, /output/Desiree_drought123/Desiree_Aligned.sort..., /output/Desiree_drought123/Log.final.out, /output/Desiree_drought123/Log.out, /output/Desiree_drought123/Log.progress.out, /output/Desiree_drought123/SJ.out.tab, /output/PGSC_SRR10416847/Log.final.out, /output/PGSC_SRR10416847/Log.out, /output/PGSC_SRR10416847/Log.progress.out, /output/PGSC_SRR10416847/SJ.out.tab, /output/PGSC_SRR10416848/Log.final.out, /output/PGSC_SRR10416848/Log.out, /output/PGSC_SRR10416848/Log.progress.out, /output/PGSC_SRR10416848/SJ.out.tab, /output/PGSC_SRR10416849/Log.final.out, /output/PGSC_SRR10416849/Log.out, /output/PGSC_SRR10416849/Log.progress.out, /output/PGSC_SRR10416849/SJ.out.tab, /output/PGSC_drought123/DM_Aligned.sortedByCoor..., /output/PGSC_drought123/Log.final.out, /output/PGSC_drought123/Log.out, /output/PGSC_drought123/Log.progress.out, /output/PGSC_drought123/SJ.out.tab, /output/gff-merged_SRR10416847/Log.final.out, /output/gff-merged_SRR10416847/Log.out, /output/gff-merged_SRR10416847/Log.progress.out, /output/gff-merged_SRR10416847/SJ.out.tab, /output/gff-merged_SRR10416848/Log.final.out, /output/gff-merged_SRR10416848/Log.out, /output/gff-merged_SRR10416848/Log.progress.out, /output/gff-merged_SRR10416848/SJ.out.tab, /output/gff-merged_SRR10416849/Log.final.out, /output/gff-merged_SRR10416849/Log.out, /output/gff-merged_SRR10416849/Log.progress.out, /output/gff-merged_SRR10416849/SJ.out.tab, /output/gff-merged_drought123/Log.final.out, /output/gff-merged_drought123/Log.out, /output/gff-merged_drought123/Log.progress.out, /output/gff-merged_drought123/SJ.out.tab, /reports/SupplementaryTableS8, /scripts/00_wget.txt, /scripts/01_index_ref.txt, /scripts/02_map.txt, /scripts/03_clean-dir.txt
Snapshots: No snapshots
Short Name: 09_annotation-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Pan-transcriptome fasta files annotation Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/annot_stCuSTr-D_aa_all.zip, /output/annot_stCuSTr-D_aa_representatives.zip, /output/annot_stCuSTr-D_cds_all.zip, /output/annot_stCuSTr-D_cds_representatives.zip, /output/annot_stCuSTr-D_tr_all.zip, /output/annot_stCuSTr-D_tr_representatives.zip, /output/annot_stCuSTr-P_aa_all.zip, /output/annot_stCuSTr-P_aa_representatives.zip, /output/annot_stCuSTr-P_cds_all.zip, /output/annot_stCuSTr-P_cds_representatives.zip, /output/annot_stCuSTr-P_tr_all.zip, /output/annot_stCuSTr-P_tr_representatives.zip, /output/annot_stCuSTr-R_aa_all.zip, /output/annot_stCuSTr-R_aa_representatives.zip, /output/annot_stCuSTr-R_cds_all.zip, /output/annot_stCuSTr-R_cds_representatives.zip, /output/annot_stCuSTr-R_tr_all.zip, /output/annot_stCuSTr-R_tr_representatives.zip, /output/annot_stPanTr.aa.zip, /output/annot_stPanTr.cds.zip, /output/annot_stPanTr_rep.aa.zip, /output/annot_stPanTr_rep.cds.zip, /scripts/annotate.sh
Snapshots: Snapshot 1, Snapshot 2
Short Name: 03_components_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/Solanum_tuberosum_PGSC_DM_v4.04_CDS-to-..., /output/alt.aa.IDs, /output/alt.cds.IDs, /output/rep.aa.IDs, /output/rep.cds.IDs, /scripts/commands-components_1_3cvs-gffmerged.txt
Snapshots: No snapshots
Short Name: 05_MSA_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: MSA 3cv and GFF-merged Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/folderWithIds/test.IDs1, /input/folderWithIds/test.IDs2, /input/my.test.aa.fasta, /input/path_to_files.txt, /reports/SupplementaryFile2.html, /scripts/MSA-commands.txt, /scripts/MSA.py, /scripts/print.sh
Snapshots: Snapshot 1, Snapshot 2
Short Name: 06_tr_rep-transrate Assay Class: DRY Assay Type: transrate Title: Cultivar representative transcriptome transrate Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/PGSC_DM_v3.4_transcript-update_represent..., /input/path_to_files.txt, /output/PGSC_DM_v3.4_transcript-update_represen..., /output/PGSC_DM_v3.4_transcript-update_represen..., /output/PGSC_DM_v3.4_transcript-update_represen..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-D_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-P_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /output/stCuSTr-R_tr_representatives_transrate_..., /scripts/run_TransRate_commands.sh
Snapshots: No snapshots
Short Name: 08_centrifuge_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Centrigufe pan-transcriptome sequence classification Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:
Submitter: Andrej Blejec
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: _S_04_stPanTr
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /input/taxdmp.tgz, /input/trueSingle.DM.ID, /input/trueSingle.polyploid.ID, /intermediate/trueSingle.DM.cds.fasta, /intermediate/trueSingle.polyploid.cds.fasta, /intermediate/trueSingle.polyploid.tr.fasta, /output/Desiree_centrifuge.txt, /output/Desiree_kreport.txt, /output/Desiree_report.txt, /output/PW363_centrifuge.txt, /output/PW363_kreport.txt, /output/PW363_report.txt, /output/Rywal_centrifuge.txt, /output/Rywal_kreport.txt, /output/Rywal_report.txt, /output/Tetraploid_transcriptomes-report.html, /output/Uploaded_sample_set-report.html, /output/pavian_class_summary_No.csv, /output/pavian_class_summary_perc.csv, /output/sankey-Desiree.html, /output/sankey-PW363.html, /output/sankey-Rywal.html, /output/sankey-trueSingle.DM.cds.html, /output/sankey-trueSingle.polyploid.cds.html, /output/sankey-trueSingle.polyploid.tr.html, /output/trueSingle.DM.cds_centrifuge.txt, /output/trueSingle.DM.cds_kreport.txt, /output/trueSingle.DM.cds_report.txt, /output/trueSingle.polyploid.cds_centrifuge.txt, /output/trueSingle.polyploid.cds_kreport.txt, /output/trueSingle.polyploid.cds_report.txt, /output/trueSingle.polyploid.tr_centrifuge.txt, /output/trueSingle.polyploid.tr_kreport.txt, /output/trueSingle.polyploid.tr_report.txt, /reports/SupplementaryFile3.html, /scripts/01_prepareFasta.sh, /scripts/02_centrifuge_commands.txt
Snapshots: No snapshots
Files connected to investigation: _I_Test
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:30:01
Study: Investigation files
Organisms: No organisms
SOPs: No SOPs
Data files: _INVESTIGATION_METADATA.TXT, phenodata_20191015.txt, seekignore.txt
Snapshots: No snapshots
Files connected to study: _S_Show
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:30:01
Study: _S_Show
Assay: _A_Work-R Short Name: Work-R Assay Class: DRY Assay Type: R Title: Working in assay Description: Not really working, just testing :) pISA Assay creation date: 2019-10-15 pISA Assay creator: Andrej Blejec Analyst: Andrej Blejec Sharing permission: Public Phenodata: ../../phenodata_20191015.txt Featuredata: Data:
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:30:01
Study: _S_Show
Organisms: No organisms
SOPs: No SOPs
Data files: Upload-2022-04-16_19_33_49.txt, Upload-2022-04-16_19_42_28.txt, Upload-2022-04-16_19_45_01.txt, Upload-2022-04-16_23_52_56.txt, Upload-2022-04-17_00_09_44.txt, Upload-2022-04-17_00_11_49.txt, UploadSigma.txt, _Assay_METADATA.TXT, input/filename with blanks.txt, input/some-data.txt
Snapshots: No snapshots
Files connected to investigation: _I_Test
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:48:38
Study: Investigation files
Organisms: No organisms
SOPs: No SOPs
Data files: _INVESTIGATION_METADATA.TXT, phenodata_20191015.txt, seekignore.txt
Snapshots: No snapshots
Files connected to study: _S_Show
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:48:38
Study: _S_Show
Assay: _A_Work-R Short Name: Work-R Assay Class: DRY Assay Type: R Title: Working in assay Description: Not really working, just testing :) pISA Assay creation date: 2019-10-15 pISA Assay creator: Andrej Blejec Analyst: Andrej Blejec Sharing permission: Public Phenodata: ../../phenodata_20191015.txt Featuredata: Data:
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:48:38
Study: _S_Show
Organisms: No organisms
SOPs: No SOPs
Data files: Upload-2022-04-16_19_33_49.txt, Upload-2022-04-16_19_42_28.txt, Upload-2022-04-16_19_45_01.txt, Upload-2022-04-16_23_52_56.txt, Upload-2022-04-17_00_09_44.txt, Upload-2022-04-17_00_11_49.txt, UploadSigma.txt, _Assay_METADATA.TXT, input/filename with blanks.txt, input/some-data.txt
Snapshots: No snapshots
Files connected to investigation: _I_Test
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:52:30
Study: Investigation files
Organisms: No organisms
SOPs: No SOPs
Data files: _INVESTIGATION_METADATA.TXT, phenodata_20191015.txt, seekignore.txt
Snapshots: No snapshots
Files connected to study: _S_Show
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:52:30
Study: _S_Show
Assay: _A_Work-R Short Name: Work-R Assay Class: DRY Assay Type: R Title: Working in assay Description: Not really working, just testing :) pISA Assay creation date: 2019-10-15 pISA Assay creator: Andrej Blejec Analyst: Andrej Blejec Sharing permission: Public Phenodata: ../../phenodata_20191015.txt Featuredata: Data:
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_Sigma 2022-04-17 00:52:30
Study: _S_Show
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/_S_Show/_A_Work-R/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_Demo/_I_Test/
Creator: Andrej Blejec
Submitter: Andrej Blejec
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak
_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged
Creator: Andrej Blejec
Submitters: Andrej Blejec, Maja Zagorscak