Workflows

FInd/filter idA and idB from MITAB (1)

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A workflow to filter idA and idB out of a MITAB file.

Created: 2015-11-05 | Last updated: 2015-11-05

Get all PSICQUIC (1)

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Workflow to retrive all PSICQUIC services 

Created: 2015-11-04 | Last updated: 2015-11-04

Credits: Maximilian Koch

Pubmed -Google Tag Cloud (1)

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A simple workflow to query PubMed, Google and build a Tag Cloud after some preprocessing.

Created: 2015-11-01

Credits: Insilicoconsulting

Author Citation Network (1)

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Map citation/reference network for one author using Europe PMC Web services. This workflow was created during the Tavernathon exercise held at the LUMC on October 14, 2015 and is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete, resulting in the workflow producing a subset of the correct citation graph.

Created: 2015-10-20

Credits: Magnus Palmblad

RDKit Aggregator Advisor (1)

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A Knime (2.12.1) workflow that uses RDKit nodes for assessing the risk of a compound to form aggregates under biochemical assay conditions, inspired by the Aggregation Advisor paper of Irwin et al. While the Aggregator Advisor web tool allows for aggregation risk assessment of individual compounds, this Knime workflow can be used to quickly run through large compound collections.Query structures are loaded as an SD file (here a set of 1090 approved drugs), and are then compared for Tanimoto s...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: Evert Homan

RDKit PAINS 4 (1)

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Improved Knime (2.12.1) workflow for detection of Pan-Assay Interference Compounds (PAINS) using RDKit nodes. PAINS SMARTS curated by Greg Landrum are used for the substructure searches. These yield 753 hits among the WEHI set of 10,000 compounds. A Total Hits count column is added by the RDKit Substructure Counter node, so no additional aggregation is needed. Structures devoid of PAINS are separated out for further progression, while the PAINS hits can be visually inspected using the RDKit I...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: Evert Homan

Web Service sample in .NET (1)

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To run this sample, you should first set up a web service with the following C# code: using System; using System.Collections.Generic; using System.Linq; using System.Web; using System.Web.Services; namespace TrabsEsicnece { [WebService(Namespace = "http://trabsescience.org/")] [WebServiceBinding(ConformsTo = WsiProfiles.BasicProfile1_1)] [System.ComponentModel.ToolboxItem(false)] public class Service1 : System.Web.Services.WebService { [WebMethod] public...

Created: 2015-10-13

Create Local Citation Graph (1)

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This workflow demonstrates how to build a local citation/reference graph for a single pubilcation in PubMed. The id input is the PubMed id (pmid) for any publication in the PubMed or PMC Europe. The workflow then queries the PMC Europe Web services to get the citations and references for this publication. Two XPath parsers are used to extract the citation and reference ids, which are then combined and passed on to an Rshell that draws a Sugiyama style layered graph using the igraph package. T...

Created: 2015-10-11

Credits: Magnus Palmblad

Get_Weather (1)

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Modeal based on other models already hosted at myExperiment, but with small changes (changed input from static to input type).

Created: 2015-10-06 | Last updated: 2015-10-06

PW2ENS (2)

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This workflow uses the WikiPathways Webservice/API to query to retrieve all ENSEMBL identifers for the given pathway.

Created: 2015-10-02 | Last updated: 2015-10-12

Credits: Kristina Hettne Eleni