Workflows

Find master regulators in networks (GeneWays) (1)

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This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.At the first step, the input table is converted into a table with Entrez Gene IDs.At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.The annotated gene table is subjected to master regulator search in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated....

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze promoters (GTRD) (1)

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This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set.At the first step, the input table is converted into a table with Ensembl Gene IDs.At the next step, promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 ...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence for site enrichment (1)

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This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Mapping to ontologies (Gene table) (1)

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This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Compute differentially expressed genes (1)

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This workflow is designed to identify up-regulated, down-regulated and non-changed genes for experimental data with three and more data points for each experiment and control.  As input, normalized data with any types of IDs (Ensembl, gene symbols, EMBL, RefSeq) can be submitted.In the next step, p-values for up- and down-regulated probes are calculated for all probes using the “Up and Down Identification” analysis. This analysis applies Student’s T-test for p-value cal...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

ChIP-Seq - Identify and classify target genes (1)

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This workflow identifies and classifies target genes using positional information of peaks found by ChiP-Seq approach. As input, the peak regions in BED format, can be submitted. Actually, any dataset in BED format can be submitted as input track for this workflow.First, the track file is converted into a gene set using Track to gene set analysis. The Ensembl gene list is then annotated with additional information, gene descriptions and chromosomal location.The annotated Ensembl genes are sub...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, GeneBank (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in GeneBank format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individua...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, Fasta (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in Fasta format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual w...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, EMBL (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in EMBL format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual wo...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Imagemagick convert - tiff2tiff - compression (1)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-11-08

Credits: Markus Plangg

MatchboxHadoopAPI (1)

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The workflow MatchboxHadoopApi.t2flow enables using of matchbox tool on Hadoop with Taverna. This workflow is based on Python scripts and Hadoop Streaming API included in"pythonwf" folder of pc-qa-matchbox project on github (https://github.com/openplanets/scape/tree/master/pc-qa-matchbox/hadoop/pythonwf).For this workflow we assume that digital collection is located on HDFS and we have a list of input files in format "hdfs:///user/training/collection/00000032.jp2" - one ro...

Created: 2013-11-05

Credits: Roman SCAPE

Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Map genes to chromosomal location (1)

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This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

nested_echo (2)

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Just calls the echoer

Created: 2013-10-30 | Last updated: 2013-10-30

echoer (6)

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Renamed beanshell

Created: 2013-10-25 | Last updated: 2014-05-07

blast (1)

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This is a demo workflow to run BLAST program. It has multiple executionchoices: local execution, Map only, Map Reduce, Cross Reduce, and JobSubmission.NOTE: The Map only, Map Reduce and Cross Reduce choices only workwith the tabular output format (namely -m8). Also, Map Reduce andCross Reduce choices have scripts that only work on Mac and Linux.  bioKepler team (www.biokepler.org)Aug-24-2012 

Created: 2013-10-24

Credits: bioKepler

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2013-10-15

Credits: Stian Soiland-Reyes