Workflows

Metabolic differences in ripening of Solan... (2)

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Updated data processing workflow for metabolomics LC-MS/MS data. This workflow depends on the stable community plug-in MassCascade and KNIME plug-ins Base Chemistry, Chemistry Types & Nodes, Math Expression, and XLS Support. The workflow was run under KNIME version 2.9.2.

Created: 2013-10-16 | Last updated: 2014-07-04

Credits: SBeisken

Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: Insilicoconsulting

Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: Insilicoconsulting

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment13 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment12 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Untargeted metabolomics reveals molecular ... (1)

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Normal 0 false false false EN-US X-NONE AR-SA ...

Created: 2019-06-21

Credits: David_MTX

Integrative data mining of chemical compou... (1)

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This workflow downloads ligand data for hepatic Organic Anion Transporting Polypeptides (OATPs) from five different open sources (CHEMBL, Metrabase, USFC-FDA Transportal, IUPHAR, and Drugbank) in an semi-automatized fashion. This workflow can be adopted to any other ligand data showing an (in)activity against membrane transporter. If missing, structural file format is mapped via PubChem webservices. Pre-curated compounds are subjected to standardization procedure (Atkinson standardization scr...

Created: 2018-12-10 | Last updated: 2018-12-10

Credits: Alzbeta Tuerkova

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