Workflows

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

• Download

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

Frequent Itemset and association rules ana... (1)

• Download

Generates frequent itemsets and association rules from the gene data. Frequent itemsets correspond to different gene characteristics (locations and functions) that frequently occur together across different genes. The quality of a frequent itemset is given by its support which is the fraction of genes for which a given combination of gene characteristics hold; the longer the itemset the lower its support. Based on the frequent itemset this WF also generates association rules which have some...

Created: 2011-05-23 | Last updated: 2011-05-24

Prepares data for gene correlation analysis (1)

• Download

Prepares data for gene correlation analysis.

Created: 2011-05-23 | Last updated: 2011-05-23

Prepares data for the analysis of fibrosis... (1)

• Download

Prepares gene data for fibrosis by joining datasets from different studies on fibrosis across various organs including the kidney.

Created: 2011-05-23 | Last updated: 2011-05-25

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

• Download

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

EBI PICR, find cross-references for protei... (2)

• Download

Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Created: 2011-05-18 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Example for external tools with gzip and g... (1)

• Download

This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.

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

Credits: Steffen Möller Alan Williams

Molecular Interactions from IntAct PSICQUI... (2)

• Download

Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

Created: 2011-05-17 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

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

• Download

 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)

• Download

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