Workflows

EDPS 6571 Week 1 Introduction (1)

• Download

Week 1 Introduction

Created: 2018-04-25

EDPS 6751 Week 2 Problem Definition (1)

• Download

Week 2: Problem Definition

Created: 2018-04-25

EDPS 6751 Week 3 Data Exploration (1)

• Download

Week 3: Data Exploration

Created: 2018-04-25

List_CorrData (1)

• Download

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)

• Download

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)

• Download

Created: 2017-12-01

Credits: Barry Mitchell

demo-01 (1)

• Download

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

Created: 2017-11-27

Credits: Barry Mitchell

zetasizer2excel (2)

• Download

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)

• Download

Puts a message into a file using echo

Created: 2017-11-03

Credits: Stian Soiland-Reyes

Predador Presa v1 (1)

• Download

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

Tratamento de erro para WSDL (1)

• Download

Verifica se web service está ativo antes de propriamente executá-lo, como forma de tratamento de erro, enviando mensagem de alerta caso erro ocorra.

Created: 2017-10-30

Credits: Johnathan Melo Neto

Variant Annotation with VEP (Variant Effec... (1)

• Download

Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2017-10-19

Credits: alabarga

RetroPath2.0-Mods-isomer-transformation-queue (2)

• Download

The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.4.1 of Kni...

Created: 2017-10-12 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data RetroPath2.0-Mods-isomer-transformation

WSDL Calculator (1)

• Download

Utiliza uma calculadora com métodos disponíveis via WSDL para somar dois números.

Created: 2017-10-10

Credits: Johnathan Melo Neto

8_nested_workflows (1)

• Download

8_nested_workflows

Created: 2017-09-11

Credits: Kasikrit Damkliang

H1-2-H4-SLEEPDEMO (1)

• Download

H1-2-H4-SLEEPDEMO

Created: 2017-09-11

Credits: Kasikrit Damkliang

QSAR-model-aminoglycosides (2)

• Download

The workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-iQSAR (2)

• Download

The workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

QSAR-model-Tg-prediction (2)

• Download

The workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. T...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-isomer-transformation (2)

• Download

The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licen...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

RetroPath2.0-Mods-isomer-augmentation (2)

• Download

The workflow allows one to enumerate isomers using the isomer augmentation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.Koch M, D...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

Scaffolds_trends_workflow_2 (1)

• Download

Second part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes grouping and filtering steps to retrieve the summary data needed for performing the scaffold trend, bioactivity, and liability analyses.

Created: 2017-06-22

Credits: Barbara Zdrazil

Scaffolds_trends_workflow_1 (1)

• Download

First part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes initial filtering steps, extraction of Murcko frameworks, inclusion of journal Impact Factors, and calculation of Z-Scores. The example of oxetane substructure search is also included.

Created: 2017-06-22 | Last updated: 2017-06-22

Credits: Barbara Zdrazil

Color auto balancing (1)

Color auto balancing of RGB image

Created: 2017-05-02

Credits: Christian S.

searchPublications_and_MapAffil (1)

• Download

This is a workflow for spatiotemporal analysis of literature indexed in PubMed. The workflow takes an arbitrary Europe PMC search query, calls the Europe PMC Web service searchPublications and extracts the publication year and PubMed ID from the results. The first author affiliation is then geoparsed by the MapAffil Web server to get latitude and longitudes. The coordinates are then concatenated together with the publication year, to produce a single list of publication years, latitudes and ...

Created: 2017-04-19

Credits: Magnus Palmblad