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Items tagged with "genes" (29)

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Files (2)
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Blob Gene Cosine Scores

Created: 10/08/09 @ 16:00:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

File type: Excel workbook

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 18 times | Downloaded: 0 times

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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 35 times | Downloaded: 25 times

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Workflows (24)
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Workflow omim and pathways (2)

Created: 03/03/09 @ 13:17:27 | Last updated: 02/11/09 @ 10:13:38

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches OMIM for entries associated with a particular disease in OMIM, returns the IDs and maps them to Kegg Gene IDs. For each gene, it then gets the description and any corresponding pathways those genes are involved with

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 105 times | Downloaded: 41 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathways (1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 260 times | Downloaded: 159 times

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Original Uploader

Workflow Rank Phenotype Terms (1)

Created: 10/08/09 @ 15:43:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 139 times | Downloaded: 0 times

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Original Uploader

Workflow Arabidopsis thaliana Microarray Analysis (1)

Created: 08/07/09 @ 16:28:34

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 163 times | Downloaded: 35 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (2)

Created: 20/11/09 @ 14:04:37 | Last updated: 20/11/09 @ 14:04:39

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 142 times | Downloaded: 23 times

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Original Uploader

Workflow Get Kegg Pathway information (1)

Created: 10/03/10 @ 17:15:47 | Last updated: 10/03/10 @ 17:18:47

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 101 times | Downloaded: 44 times

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Original Uploader

Workflow Kegg pathway diagrams (3)

Created: 19/03/10 @ 12:41:27 | Last updated: 19/03/10 @ 12:41:28

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - ...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 64 times | Downloaded: 64 times

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Original Uploader

Workflow microRNA to KEGG Pathways and Abstracts (1)

Created: 17/03/10 @ 10:53:02

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 163 times | Downloaded: 2 times

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Original Uploader

Workflow Get KEGG gene descriptions and pathways (1)

Created: 30/04/10 @ 16:09:29 | Last updated: 30/04/10 @ 16:12:02

Credits: User Nadia Cerezo User Paul Fisher

Attributions: Workflow Get Kegg Gene information

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 852 times | Downloaded: 33 times

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Original Uploader

Workflow Gene to Pubmed (3)

Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 55 times | Downloaded: 32 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 15/11/10 @ 12:08:18 | Last updated: 16/11/10 @ 16:07:49

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 43 times | Downloaded: 14 times

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Original Uploader

Workflow Pathways and Gene annotations for RefSeq ids (1)

Created: 15/11/10 @ 12:25:01 | Last updated: 15/11/10 @ 12:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 85 times | Downloaded: 36 times

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Original Uploader

Workflow Pathways and Gene annotations forQTL region (1)

Created: 21/01/11 @ 16:56:47 | Last updated: 21/01/11 @ 16:58:50

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 16 times

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Original Uploader

Workflow BiomartAndEMBOSSDisease (4)

Created: 27/01/11 @ 17:03:03 | Last updated: 04/09/12 @ 09:32:08

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 131 times | Downloaded: 74 times

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Original Uploader

Workflow Pathways and Gene annotations forQTL region (2)

Created: 17/03/11 @ 11:10:28 | Last updated: 30/08/11 @ 10:40:14

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 32 times | Downloaded: 16 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (1)

Created: 27/05/11 @ 11:06:11 | Last updated: 27/05/11 @ 11:06:52

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 12 times

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Original Uploader

Workflow Pathways and Gene annotations for QTL region (7)

Created: 19/11/09 @ 18:18:52 | Last updated: 07/09/12 @ 18:23:36

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Rating: 4.6 / 5 (10 ratings) | Versions: 7 | Reviews: 1 | Comments: 7 | Citations: 1

Viewed: 6121 times | Downloaded: 1014 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathway Images (2)

Created: 12/01/12 @ 09:38:10 | Last updated: 12/01/12 @ 15:04:00

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 21 times

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Workflow NCBI Gi to Kegg Pathway Descriptions (2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: User Katy Wolstencroft

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 21 times | Downloaded: 19 times

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Workflow geneID to KEGG Pathways (2)

Created: 16/01/12 @ 10:54:39 | Last updated: 21/08/12 @ 12:18:19

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database. It also displays each pathway diagram.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 86 times | Downloaded: 158 times

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Workflow Define Associated Regions and Genes (2)

Created: 08/02/12 @ 16:08:08 | Last updated: 09/05/12 @ 09:52:18

Credits: User Paul martin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow SNP Position Information (1)

Created: 17/04/12 @ 10:10:59 | Last updated: 17/04/12 @ 10:15:57

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow extracts information about the position of SNPs and the genes they are associated with, using BioMart (ENSEMBL Variation 66).

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow ImportRefSeqtoKegg (1)

Created: 12/11/12 @ 14:31:05

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Packs (3)
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Pack Genotype to Pathway


Created: 11/08/09 @ 14:44:16 | Last updated: 11/08/09 @ 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

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Pack Text Mining Workflows


Created: 08/12/10 @ 11:55:03 | Last updated: 01/02/11 @ 11:33:11

This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.

0 items in this pack

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Pack wf4ever Deliverable 6.3 Pack


Created: 02/12/11 @ 09:31:26 | Last updated: 02/12/11 @ 10:21:03

This pack contains (references to) the workflows for GWAS analysis by workflows that perform pathway and GO analysis and biosemantics data interpretation (a special form of text mining). This pack aggregates the deliverable materials for month 8 for Work Package 6. The workflows have not been published in the scientific domain yet, so its content cannot yet be made public. They are available upon request, in particular for reviewers. Please contact Kristina Hettne or Marco Roos (see credit...

2 items in this pack

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