The FAIRDOMHub

25 items tagged with 'bash'.

Gudrun Gygli

Projects: Simulation Foundries, CML for thermophysical properties of mixtures

Institutions: University of Stuttgart

https://orcid.org/0000-0001-9119-1778

Roles: Postdoc

Expertise: enzyme kinetics, enzymes, Enzymatic reactions, biochemical enzyme characterization, Biochemistry, molecular simulation, molecular modeling, Programming, Bioinformatics, computational biology

Tools: Gromacs, Python, Molecular Dynamics, bash

Well rounded biologist/biotechnologist/biochemist/enzymologist/bioinformatician/computational biologist.

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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1173.1

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

Created: 7th Nov 2019 at 18:11, Last updated: 16th Nov 2019 at 12:08

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1172.1

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

Created: 7th Nov 2019 at 18:09, Last updated: 16th Nov 2019 at 12:22

_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:

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

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

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1170.1

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

Created: 7th Nov 2019 at 18:04, Last updated: 18th Mar 2020 at 19:37

_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

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1169.1

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

Created: 7th Nov 2019 at 18:02, Last updated: 16th Nov 2019 at 12:28

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1168.1

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

Created: 7th Nov 2019 at 17:58, Last updated: 16th Nov 2019 at 12:37

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1167.1

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

Created: 7th Nov 2019 at 17:54, Last updated: 16th Nov 2019 at 12:45

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1165.1

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, /scripts/STAR_commands.txt

Created: 7th Nov 2019 at 17:48, Last updated: 16th Nov 2019 at 13:03

_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
...

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1166.1

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...

Created: 7th Nov 2019 at 17:50, Last updated: 16th Nov 2019 at 12:55

_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

Contributor: Maja Zagorscak

Biological problem addressed: Annotation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1164.1

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

Created: 7th Nov 2019 at 17:46, Last updated: 16th Nov 2019 at 13:35

_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

Contributor: Maja Zagorscak

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1163.1

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

Created: 7th Nov 2019 at 17:04, Last updated: 26th Feb 2020 at 14:00

_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

Contributor: Maja Zagorscak

Biological problem addressed: Validation

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1162.1

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

Created: 7th Nov 2019 at 16:57, Last updated: 16th Nov 2019 at 13:40

_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

Contributor: Maja Zagorscak

Biological problem addressed: Integration

Snapshots: Snapshot 1

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

Created: 7th Nov 2019 at 16:54, Last updated: 16th Nov 2019 at 14:21

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.

Contributor: Gudrun Gygli

Biological problem addressed: various analyses of molecular dynamics simulations

Snapshots: No snapshots

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

Created: 24th Oct 2019 at 11:31, Last updated: 7th Nov 2019 at 13:28

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.

Contributor: Gudrun Gygli

Assay type: Molecular Dynamics

Technology type: All-Atom

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: SIMULATIONS_V1.5

Data files: No Data files

Created: 24th Oct 2019 at 11:17, Last updated: 7th Nov 2019 at 13:28

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.

Contributor: Gudrun Gygli

Assay type: Instructions

Technology type: Technical Computer Installation

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Simulation Foundry for Methanol-Water Mixtures

Organisms: No organisms

SOPs: No SOPs

Data files: Installation Instructions

Created: 24th Oct 2019 at 09:57, Last updated: 7th Nov 2019 at 13:28

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

Contributor: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Analysis Version 1.5

Download

Created: 24th Oct 2019 at 11:33, Last updated: 7th Nov 2019 at 13:28

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

Contributor: Gudrun Gygli

Investigations: 1 hidden item

Studies: Simulation Foundry for Methanol-Water Mixtures

Assays: Simulation Version 1.5

Download

Created: 24th Oct 2019 at 11:21, Last updated: 7th Nov 2019 at 13:28

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 12:48, Last updated: 19th Nov 2019 at 12:57