Workflows

Genetic Algorithms for BIOISOSTERIC Struct... (1)

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Genetic algorithm workflow to generate novel structures by recombination and mutation and that uses an ML model as a fitness function. Both the fitness function and the fingerprints modified in the model should be the same. ML model cannot have any descriptors other than given fingerprint.Reverse molecular mapping/generation is not part of this workflow and can be done by creating a large Structure-FP database.

Created: 2018-11-06

Credits: Insilicoconsulting

Substructure querying | R-group decomposit... (1)

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This workflow creates maximum common substructure (MCS) out of the provided structures and then substructure mining using MCS as a structural query is performed. Obtained hits are then subjected to R-group decomposition to explore their functional groups. Optionally, physicochemical descriptors for individual functional groups can be calculated.

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

Scaffold Analysis | Statistical analysis o... (1)

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This workflow performs an extraction and statistical analysis of Murcko scaffolds for compounds being active against (a) different target(s). Specifically, target-wise detection of Murcko Scaffolds in active versus inactive compounds, filtering steps by removing too generic scaffold (i.e., number of rings equals to one OR number of heteroatoms in a ring is zero or one), calculating the frequency of a particular scaffold which appears frequently in the active over inactive class, applying Fish...

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

Find concept-literature relationships and ... (1)

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This Bioclipse script (dev version) searches articles titles for the given concept and creates QuickStatements to create Wikidata statements that that article is about that concept.

Created: 2018-09-01

Credits: Egon Willighagen

Human MSH3 exon 1 variant genotyping (1)

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This workflow is designed to genotype 9 bp tandem repeat region in MSH3 exon 1 as well as flanking variants described in Flower and Lomeikaite et al. (2018). Detailed description as follows:1. Input files.Input files for the workflow are demultiplexed fastq files from MiSeq Illumina sequencing. 2. Read merging.To enable obtaining haplotype information, forward and reverse paired-end reads are merged using Pear with default settings. 3. Demultiplexing.Merged reads are demul...

Created: 2018-08-22 | Last updated: 2018-08-22

KNIME Workflow for RetroRules and Retropat... (3)

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Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

EDPS 6751 Week 6 Decision Tree Classifier (1)

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Week 6: Decision Tree Classifier

Created: 2018-04-26

EDPS 6751 Week 5 Unsupervised Learning (1)

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Week 5: Unsupervised Learning

Created: 2018-04-26

EDPS 6751 Week 4 Data Preparation (1)

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Week 4: Data Preparation

Created: 2018-04-25

EDPS 6571 Week 1 Introduction (1)

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Week 1 Introduction

Created: 2018-04-25

EDPS 6751 Week 2 Problem Definition (1)

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Week 2: Problem Definition

Created: 2018-04-25

EDPS 6751 Week 3 Data Exploration (1)

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Week 3: Data Exploration

Created: 2018-04-25

List_CorrData (1)

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This test workflow demonstrates the ability to read a file.

Created: 2018-03-07

Credits: Divya Karade

Search Europe PMC and get ChEBI annotations (3)

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This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: Magnus Palmblad

demo-02 (1)

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Created: 2017-12-01

Credits: Barry Mitchell

demo-01 (1)

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this is a demo on how to upload a keplar file to myexperiment.org

Created: 2017-11-27

Credits: Barry Mitchell

zetasizer2excel (2)

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Arrrgh! The exported data file format for the Malvern Zetasizer is insane!Row1, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row2, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row3, x1,x2,x3,x4,....,y1,y2,y3,y4,....This workflow imports the txt file, takes each row and reformats as table with 3 columns: Size, Intensity, Volume. Then exports the data for each row to a new tab in Excel. Or you can just use KNIME to plot and prepare reports (to do).The TableRow2Variable node allows you to name the tabs in Excel from a ...

Created: 2017-11-20 | Last updated: 2017-11-20

Credits: sauberns

Hello World in CWL (1)

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Puts a message into a file using echo

Created: 2017-11-03

Credits: Stian Soiland-Reyes

Predador Presa v1 (1)

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Envia dois textos e três parâmetros numéricos para um web service, e recebe um texto como saída. O web service implementa um modelo de predador-presa.

Created: 2017-10-30 | Last updated: 2017-10-30

Credits: Johnathan Melo Neto