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Pack #1 - Isomer enumeration (canonical augmentation...

Created: 2017-06-30 16:29:21 | Last updated: 2017-12-19 10:20:58

2 items in this pack

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Epitope-based Vaccine Design Workflow usin... (3)

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Population-based vaccine design workflow in KNIME. AlleleFrequency is used to specify the geographical region or population of interest and returns a tab-separated list of HLA alleles with their corresponding occurrence probability within the selected population. This file, together with a FASTA file containing protein sequences, or a file containing peptides is used as input to EpitopePrediction, which generates a file containing the predicted binding affinities of the (generated) peptides a...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Benjamin Schubert

HLA ligandomics workflow using OpenMS and ... (2)

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HLA ligandomics workflow combining native KNIME, OpenMS, and ImmunoNodes nodes. The workflow extracts MS data from PRIDE and performs mass spectra identification with X!Tandem, annotates the results with details of the given target/decoy database, calculates false discovery rates and filters for 5% FDR using OpenMS’ nodes. The identified peptides are annotated with their respective binding affinity predicted by NetMHC using the EpitopePrediction node. Finally, simple summary statistics ...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Mathias Walzer

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Tools to split spatial N-dimensional data in cells o...

Created: 2016-10-19 09:31:56 | Last updated: 2018-06-29 09:12:04

Credits: Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/x-python

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AmrPlusPlus Single Workflow (2)

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Created: 2016-08-12 | Last updated: 2017-01-05

Credits: Chris

Sequences Alignment and Sorting by Coordinate (1)

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We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz Alignment via Burrows-Wheeler transformation using BWA-MEM algorithm Sorts the input SAM or BAM Post Alignment File Processing We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz MarkDuplicates examines aligned records in the supplied SAM or BAM f...

Created: 2016-05-16 | Last updated: 2016-07-06

Variant Annotation with VEP (Variant Effec... (1)

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2016-05-16 | Last updated: 2016-07-06

Metavisitor: Workflow for Use Case 3-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 3-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 2-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedoc Mississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 2-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 1-2 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server

Created: 2016-05-13 | Last updated: 2017-04-17

Metavisitor: Workflow for Use Case 1-1 (2)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-05-13 | Last updated: 2017-04-17

Data Mining Recommender (4)

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Scientific workflow for the recommender construction 

Created: 2014-10-29 | Last updated: 2018-09-20

Credits: respinosa

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Multiplot

Created: 2014-10-05 11:04:30 | Last updated: 2018-03-12 15:20:56

Credits: Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/x-python

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MsaPAD: Multiple Sequence Alignment - Inpu... (2)

BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multip...

Created: 2014-07-30 | Last updated: 2015-06-12

Credits: Bachirb Giacinto Donvito Pasquale Notarangelo Saverio Vicario Graziano Pesole

Attributions:

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Taverna 2.5 Core Starter Pack

Created: 2014-04-02 11:32:18 | Last updated: 2017-01-09 13:09:40

14 items in this pack

Comments: 0 | Viewed: 106 times | Downloaded: 33 times

Imagemagick convert - tiff/png/bmp/jpeg2ti... (2)

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Converts tiff to tiff/png/bmp/jpeg using imagemagick convert with the provided compression

Created: 2014-02-14 | Last updated: 2014-11-06

Credits: Markus Plangg

MrBayes (10)

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using slow paced JSTasync 1

Created: 2013-12-11 | Last updated: 2014-06-19

JSTAsync1 (6)

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slow down job retrival to one every 60 sec

Created: 2013-12-11 | Last updated: 2014-06-19

JSTAsync2 (7)

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slow down loops to 60 sec

Created: 2013-12-11 | Last updated: 2014-06-19

Annotate gene list with top ranking concepts (4)

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This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The output provides us with the top (cutoff) concepts that describe our gene list of interest The workflow is using the anni web services .

Created: 2013-12-03 | Last updated: 2015-04-03

Credits: Eleni

RNA-Seq workflow with TopHat and Cufflinks... (1)

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Created: 2013-11-09 | Last updated: 2014-04-10

Credits: zohim Carol Lushbough Bioextract BioExtract Server for Genomics

Gene set enrichment analysis (Affymetrix p... (1)

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This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at http://www.broadinstitute.org/gsea/index.jsp. As input, the normalized data with Affymetrix probeset IDs can be submitted.First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene...

Created: 2013-10-29 | Last updated: 2015-04-17

Credits: geneXplain