Andrej Blejec

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About Andrej Blejec:

No description specified

SEEK ID: https://fairdomhub.org/people/808

Locations: Slovenia , Not specified

ORCID: https://orcid.org/0000-0001-7484-6031

Joined: 7th Nov 2016

Expertise: Mathematical and statistical modeling, Bioinformatics, Visualization, Statistics, R, Programming, Computational Statistics

Tools: R, Statistical tools, Statistics, Data Management, Computational Systems Biology, Data Integration

Their tags

API application/pdf data Data Management demo document experiment pISA pISA-tree R text/markdown text/plain

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Advanced Programmes list for this Person with search and filtering

Public

No description specified

Projects: Public project

Web page: Not specified

NIBSys

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, Playground

Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology

Advanced Projects list for this Person with search and filtering

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036

Programme: NIBSys

Public web page: http://susphire.info/susphireproject/

Start date: 1st Apr 2018

End date: 30th Sep 2021

Organisms: Planococcus citri, Nicotiana benthamiana, Penicillium chrysogenum

Playground

This is a project for testing

Programme: NIBSys

Public web page: Not specified

Organisms: Not specified

pISA-tree

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 ...

Programme: NIBSys

Public web page: http://ablejec.nib.si/doc

Organisms: Not specified

_p_stRT

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: Potato virus Y, Solanum tuberosum

Public project

No description specified

Programme: Public

Public web page: Not specified

Organisms: Not specified

INDIE - Biotechnological production of sustainable indole

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

HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato

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

Advanced Institutions list for this Person with search and filtering

National Institute of Biology

Country: Slovenia

City: Ljubljana

Web page: http://www.nib.si

NewHorizon

Country: Not specified

City: Not specified

Web page: Not specified

Advanced Investigations list for this Person with search and filtering

14 hidden items

Advanced Studies list for this Person with search and filtering

_S_04_stPanTr

_p_stRT

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

Created: 18th Mar 2020 at 20:44

FAIRDOMhub API usage in R

pISA-tree

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

Submitter: Andrej Blejec

Investigation: 1 hidden item

Assays: General, _A_99_Empty

Snapshots: No snapshots

Created: 11th Jun 2018 at 22:23

19 hidden items

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General

pISA-tree

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

Created: 11th Jun 2018 at 22:27, Last updated: 18th Aug 2021 at 23:39

_A_99_Empty

pISA-tree

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

DOI: 10.15490/fairdomhub.1.assay.1190.1

Created: 19th Nov 2019 at 10:37, Last updated: 20th Nov 2019 at 10:32

_A_02_cdhit_3cvs-GFFmerged

_p_stRT

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1263.2

Created: 18th Mar 2020 at 20:44, Last updated: 5th May 2022 at 23:36

_A_01_GC_content-count

_p_stRT

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

Created: 19th Mar 2020 at 10:02, Last updated: 5th May 2022 at 23:34

_A_04_BUSCO_3cvs-GFFmerged

_p_stRT

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

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:13, Last updated: 6th Apr 2020 at 23:46

_A_07_Desiree-mapping

_p_stRT

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

Snapshots: No snapshots

Created: 19th Mar 2020 at 10:38, Last updated: 12th Apr 2020 at 09:51

_A_09_annotation-GFFmerged

_p_stRT

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.1268.2

Created: 19th Mar 2020 at 10:41, Last updated: 9th Apr 2020 at 10:14

_A_03_components_3cvs-GFFmerged

_p_stRT

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

Created: 19th Mar 2020 at 10:55, Last updated: 6th Apr 2020 at 23:48

_A_05_MSA_3cvs-GFFmerged

_p_stRT

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

DOI: 10.15490/fairdomhub.1.assay.1270.2

Created: 19th Mar 2020 at 10:58, Last updated: 12th Apr 2020 at 09:42

_A_06_tr_rep-transrate

_p_stRT

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

Snapshots: No snapshots

Created: 19th Mar 2020 at 11:00, Last updated: 5th May 2022 at 23:38

_A_08_centrifuge_3cvs-GFFmerged

_p_stRT

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

Snapshots: No snapshots

Created: 22nd Mar 2020 at 23:09, Last updated: 6th Apr 2020 at 23:50

32 hidden items

Showing 20 out of a possible 249 Data files Advanced Data files list for this Person with search and filtering

dummy file

pISA-tree

No description specified