FAIRDOMHub

26 items tagged with 'bash'.

Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map, NMTrypI - New Medicines for Trypanosomatidic Infections, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation

Institutions: Kinetics on the move Workshop at HITS, Heidelberg Institute for Theoretical Studies, University of Eastern Finland (UEF)

https://orcid.org/0000-0002-2801-8902

Expertise: Computer-aided drug design, computational structural biology, Data Management, molecular modeling

Tools: bash, Databases, Machine Learning, Molecular docking and simulation, Python

Gudrun Gygli

Polyglot European Scientist. I thrive working in interdisciplinary environments combining the study of enzyme reactions and mechanisms with bioinformatics, molecular modelling, automated data analysis and data stewardship.

Alex Bossers

Projects: Not specified

Institutions: Not specified

https://orcid.org/0000-0002-6586-717X

Expertise: Bioinformatics, Molecular Biology, Next Generation Sequencing, metagenomics, Proteomics, Programming

Tools: bash, Perl, R, Genomics, Proteomics, Biochemistry and protein analysis

Research scientist in multi-Omics, molecular (cell)biology and bioinformatics.

Thomas Hentrich

Projects: ICYSB 2015 - International Practical Course in Systems Biology

Institutions: University of Tübingen

Expertise: Bioinformatics, Software Engineering, Epigenomics, Biomolecular Computing, NGS analysis

Tools: Java, Matlab, bash, linux

Trained as a Computer Scientist at the University of Jena, Germany, my interests drifted more and more towards "computing life" during my PhD at Simon Fraser University and the University of British Columbia, Canada. On one hand, that term captures that I got fascinated by the idea to understand life as a form of computation and to describe, reprogram, and reassemble parts of cells as described in many brilliant experiments from a spectrum of disciplines ranging from DNA computing to Synthetic ...

Antoine Buetti-Dinh

Projects: SysMetEx, Kinetics on the move - Workshop 2016

Institutions: Università della Svizzera Italiana

Expertise: ODE modelling of biological interaction network, Bioinformatics

Tools: Python, c++, Java, bash, standard bioinformatic tools

http://tinyurl.com/jgget87

_A_05_BUSCO

_p_stRT

Assay: _A_05_BUSCO Short Name: 05_BUSCO Assay Class: DRY Assay Type: BUSCO Title: BUSCO post filtering and reassignment Description: BUSCO post filtering and reassignment 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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar, /transfer/transfer.zip

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1173.1

Created: 7th Nov 2019 at 17:11, Last updated: 16th Nov 2019 at 11:08

_A_04_TransRate

_p_stRT

Assay: _A_04_TransRate Short Name: 04_TransRate Assay Class: DRY Assay Type: TransRate Title: TransRate post filtering and reassignment Description: TransRate post filtering and reassignment 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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output.tar, /scripts/run_TransRate_commands.sh

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1172.1

Created: 7th Nov 2019 at 17:09, Last updated: 16th Nov 2019 at 11:22

_A_03.2_components

_p_stRT

Assay: _A_03.2_components Short Name: 03.2_components Assay Class: DRY Assay Type: components Title: Components: tr2aacds headers, cdhit-2d Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters pISA Assay creation date: 2019-10-22 pISA Assay creator: Ziva Ramsak Phenodata: None Featuredata: Data:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Created: 7th Nov 2019 at 17:06, Last updated: 15th Nov 2019 at 20:07

_A_03.1_filtering

_p_stRT

Assay: _A_03.1_filtering Short Name: 03.1_filtering Assay Class: DRY Assay Type: filtering Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs 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

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate/intermediate.tar, /output/Desiree_tr.cds.tsv.gz, /output/PW363_tr.cds.tsv.gz, /output/Rywal_tr.cds.tsv.gz, /output/other/output_full.tar.gz, /output/other/output_summary.tar.gz, /reports/03.1_Rywal_combo_withFiltering.html, /reports/03.2_PW363_combo_withFiltering.html, /reports/03.3_Desiree_combo_withFiltering.html, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

Created: 7th Nov 2019 at 17:04, Last updated: 18th Mar 2020 at 18:37

_A_02.8_DIAMOND

_p_stRT

Assay: _A_02.8_DIAMOND Short Name: 02.8_DIAMOND Assay Class: DRY Assay Type: DIAMOND Title: DIAMOND on raw tr2aacds output Description: DIAMOND on raw tr2aacds output, both .cds and .tr; including lost and found 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: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

Created: 7th Nov 2019 at 17:02, Last updated: 16th Nov 2019 at 11:28

_A_02.7_VecScreen

_p_stRT

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

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate.tar.gz, /output/Desiree_vecscreen.tsv, /output/PW363_vecscreen.tsv, /output/Rywal_vecscreen.tsv, /scripts/01_get_input.sh, /scripts/02_VecScreenPlus_blastn.sh, /scripts/ENCH_sumablastplus.pl

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

Created: 7th Nov 2019 at 16:58, Last updated: 16th Nov 2019 at 11:37

_A_02.6_TransRate

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 11:45

_A_02.4_STAR

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

Created: 7th Nov 2019 at 16:48, Last updated: 2nd Jun 2020 at 13:42

_A_02.5_STARlong_matchAnnot

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

Created: 7th Nov 2019 at 16:50, Last updated: 16th Nov 2019 at 11:55

_A_02.3_InterProScan

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

Created: 7th Nov 2019 at 16:46, Last updated: 16th Nov 2019 at 12:35

_A_02.2_assembly-contribution-count

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_Desiree.tar.gz, /intermediate_PW363.tar.gz, /intermediate_Rywal.tar.gz, /output/output.tar, /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryTableS6, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

Created: 7th Nov 2019 at 16:04, Last updated: 26th Feb 2020 at 13:00

_A_02.1_BUSCO

_p_stRT

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

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

Created: 7th Nov 2019 at 15:57, Last updated: 16th Nov 2019 at 12:40

_A_01_evigene

_p_stRT

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

Organisms: Solanum tuberosum, Potato virus Y

Models: No Models

SOPs: No SOPs

Data files: /input/path_to_files.txt, /intermediate_tr2aacds_Desiree.tar.gz, /intermediate_tr2aacds_PW363.tar.gz.aa, /intermediate_tr2aacds_PW363.tar.gz.ab, /intermediate_tr2aacds_Rywal.tar.gz, /output/output.tar, /scripts/01_run_commands.sh, /scripts/my_tr2aacds.sh, /scripts/run_tr2aacds.sh

Snapshots: Snapshot 1

Created: 7th Nov 2019 at 15:54, Last updated: 16th Nov 2019 at 13:21

Analysis Version 1.5

Simulation Foundries

This is the analysis part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

Submitter: Gudrun Gygli

Biological problem addressed: various analyses of molecular dynamics simulations

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

Models: No Models

SOPs: ANALYSIS_1.5

Data files: No Data files

Snapshots: No snapshots

Created: 24th Oct 2019 at 09:31, Last updated: 7th Nov 2019 at 12:28

Simulation Version 1.5

Simulation Foundries

This is the simulation part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

Submitter: Gudrun Gygli

Assay type: Molecular Dynamics

Technology type: All-Atom

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: SIMULATIONS_V1.5

Data files: No Data files

Snapshots: No snapshots

Created: 24th Oct 2019 at 09:17, Last updated: 7th Nov 2019 at 12:28

Preparation

Simulation Foundries

Preparation needed to use Simulation Foundry, Version 1.5.

Please read the manual before working with this Simulation Foundry.

Pay careful attention to the installation instructions.

Note the known issues.

Submitter: Gudrun Gygli

Assay type: Instructions

Technology type: Technical Computer Installation

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: No SOPs

Data files: Installation Instructions

Snapshots: No snapshots

Created: 24th Oct 2019 at 07:57, Last updated: 7th Nov 2019 at 12:28

ANALYSIS_1.5

Simulation Foundries

Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!

Creator: Gudrun Gygli

Submitter: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Analysis Version 1.5

Download

Created: 24th Oct 2019 at 09:33, Last updated: 7th Nov 2019 at 12:28

SIMULATIONS_V1.5

Simulation Foundries

Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!

Creator: Gudrun Gygli

Submitter: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Simulation Version 1.5

Download

Created: 24th Oct 2019 at 09:21, Last updated: 7th Nov 2019 at 12:28

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

_p_stRT

(Show All)

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

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

DOI: 10.1101/845818

Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Created: 19th Nov 2019 at 11:48, Last updated: 8th Dec 2022 at 17:26