Assays

What is an Assay?
978 Assays visible to you, out of a total of 1941

Simple overview of all samples used for training, internal validation by copasi en external validation. Overview of samples metadata, mean metabolite concentration and enzyme concentrations used in the model. Only metabolites present in the model are shown.

Empty assay

Submitter: Andrej Blejec

Biological problem addressed: Model Analysis Type

Investigation: 1 hidden item

Study: FAIRDOMhub API usage in R

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

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

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

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 ...

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

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

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

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

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

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

No description specified

Submitter: Dorothee Houry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Manuscript: structural determinants of substrat...

No description specified

Submitter: Dorothee Houry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Manuscript: structural determinants of substrat...

No description specified

Submitter: Dorothee Houry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Manuscript: structural determinants of substrat...

No description specified

Submitter: Dorothee Houry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Manuscript: structural determinants of substrat...

No description specified

Submitter: Dorothee Houry

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: Manuscript: structural determinants of substrat...

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

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

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

This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.

Submitter: Gudrun Gygli

Biological problem addressed: Model Analysis Type

Investigation: Deep Eutectic Solvents

Study: Choline chloride:glycerol:water mixtures in CML

Data digitized from publication.

Spigset1999a Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Jeppesen1996 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Oh2012 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Healy1991 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Akinyinka2000 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Kakuda2014 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Haller2002 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Amchin1999 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

Data digitized from publication.

Kaplan1997 Description

Submitter: Matthias König

Assay type:

Technology type:

Investigation: MM-PLF: Multiscale modeling for personalized li...

Study: PKDB Caffeine Study

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