Andrej Blejec

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

https://bio.tools/pisa-tree

Linked resources:

• R support for pISA-tree DOI ...

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, ...

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 ...

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 ...

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

Investigation files _I_Test

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

Investigation files _I_Test

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

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

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

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

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

Investigation files _I_Test

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

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

Investigation files _I_Test

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

Investigation files _I_Test

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

Investigation files _I_Test

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

Here is a collection of examples of possibilities for API communication in R

General sandbox

Empty assay

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:

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

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:

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:

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:

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:

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:

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:

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:

Files connected to investigation: _I_Test

Files connected to 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:

Files connected to investigation: _I_Test

Files connected to 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:

Files connected to investigation: _I_Test

Files connected to 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:

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/

_p_Demo/_I_Test/_S_Show/_A_Work-R/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_Demo/_I_Test/

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged

_p_stRT/_I_STRT/_S_04_stPanTr/_A_02_cdhit_3cvs-GFFmerged