Workflows

NCBI Protein Clustal Omega Alignment (1)

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

Created: 2012-08-31

Credits: Carol Lushbough

Match gene lists based on information in l... (7)

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[THIS WORKFLOW IS IN BETA STAGE] This workflow computes the match between two lists of Entrez Gene Identifiers by means of concept profile matching (Jelier et al., van Haagen et al.). The result of this is a list of concepts ordered by their matching score (the length of the list set by maxMatchNr). Of this list the summed scores are explained by computing the concepts that contribute most to the combination of the matching genes. Example to explain (by analogy): When a group of informatic...

Created: 2012-04-17 | Last updated: 2012-04-25

Credits: Marco Roos Reinout van Schouwen Eleni Kristina Hettne BioSemantics

Attributions: Match concept profiles Explain concept scores

Extract Gene Sequence with Kepler (1)

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This is a workflow which allows one to extract gene sequence information using the accession number as the input.  Multiple outputs include a file output of sequence header information, as well as one output window of base pair count, ratios and gene sequence.

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Wdsnellg

BATWING (1)

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Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei...

Created: 2011-08-25 | Last updated: 2011-08-25

Credits: Pipeline

NGS sample workflow with data (1)

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 Sample workflow for NGS data analysis This worklfow relies on community contributions that can be installed through the following update site: http://tech.knime.org/update/community-contributions/nightly specifically the  KNIME NGS tools and the KNIME R Scripting extensions.    

Created: 2011-06-24 | Last updated: 2011-06-24

Credits: Baj

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

Get names of proteins similar to RNA bindi... (1)

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A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: hindlem

Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

[untitled] (1)

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Dennis Leenheer