myExperiment - Content

Taverna 2

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Kasikrit Damkliang

8_nested_workflows (1)

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8_nested_workflows

Created: 2017-09-11

Credits: Kasikrit Damkliang

Taverna 2

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Kasikrit Damkliang

H1-2-H4-SLEEPDEMO (1)

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H1-2-H4-SLEEPDEMO

Created: 2017-09-11

Credits: Kasikrit Damkliang

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Pablo Carbonell

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Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example of an input file containing information about a metabolic pathway to query the KNIME workflow for Selenzyme, an enzyme selection tool for pathway design.The file contains a list of reactions or generic reactions expressed in SMILES or SMARTS (SMIRKS) format. In the example, the list of reactions correspond to the different steps of a biosynthetic pathway.

File type: text/csv

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Pablo Carbonell

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Selenzyme

Created: 2017-08-18 08:23:47 | Last updated: 2017-08-23 11:12:00

Enzyme selection workflow for pathway design

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Thomas Duigou

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Aminoglycosides-Data

Created: 2017-06-30 17:09:48 | Last updated: 2017-07-03 08:19:12

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-iQSAR

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-iQSAR and QSAR-model-aminoglycosides workflows for the "search for molecules maximizing biological activities" use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the antibacterial activity.

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KNIME

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Thomas Duigou

QSAR-model-aminoglycosides (2)

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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

KNIME

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Thomas Duigou

RetroPath2.0-Mods-iQSAR (2)

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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

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Thomas Duigou

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Monomers-Data

Created: 2017-06-30 17:01:24 | Last updated: 2017-10-12 13:47:22

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-transformation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-augmentation and QSAR-model-Tg-prediction workflows for the monomer enumeration use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the glass transition temperature.

File type: application/x-zip-compressed

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Thomas Duigou

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Alkane-Enumeration-Data

Created: 2017-06-30 16:57:41 | Last updated: 2017-10-12 13:45:28

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-transformation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-transformation workflow for the alkane enumeration use case:- Source and Rules input.- Pre-generated Results.

File type: application/x-zip-compressed

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KNIME

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Thomas Duigou

QSAR-model-Tg-prediction (2)

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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

KNIME

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Thomas Duigou

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

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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

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Thomas Duigou

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Isomer-augmentation-Data

Created: 2017-06-30 16:49:46 | Last updated: 2017-06-30 17:12:54

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-augmentation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-augmentation workflow:- Source and Rules input.- Pre-generated Results.

File type: application/x-zip-compressed

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KNIME

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Thomas Duigou

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

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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

KNIME

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Barbara Zdrazil

Scaffolds_trends_workflow_2 (1)

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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

KNIME

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Barbara Zdrazil

Scaffolds_trends_workflow_1 (1)

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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

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Barbara Zdrazil

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Workflows for scaffold trend analyses

Created: 2017-06-22 13:01:47 | Last updated: 2018-06-14 09:37:37

These two KNIME workflows were used to process the raw data (retrieved via sql query from ChEMBL) in order to retrieve the final data for scaffold trend analyses as described in the paper: "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. Guha, Journal of Medicinal Chemistry, 2018, 61 (11), pp 4688-4703.

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Taverna 2

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Christian S.

Color auto balancing (1)

Color auto balancing of RGB image

Created: 2017-05-02

Credits: Christian S.

Taverna 2

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Magnus Palmblad

searchPublications_and_MapAffil (1)

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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

Taverna 2

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Magnus Palmblad

profilePublications_over_time (1)

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This workflow takes a list of arbitrary Europe PMC search queries and generates the corresponding profiles of the number of matching publications per publication year.

Created: 2017-04-19

Credits: Magnus Palmblad

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Drkrish...

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Oxcarbazepine by HPLC Method

Created: 2017-04-12 10:18:08

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

~Oxcarbazepine is in a class of drug called anticonvulsants. It inhibits unusual electrical activity in the brain. Oxcarbazepine may help control seizures, but it does not cure the disease. However, this medication is also used for treatment of epilepsy. Oxcarbazepine HPLC chromatography determination method was developed to quantify the quality of the synthesized drug. The developed method was then validated for the determination of Oxcarbazepine The separation was achieved in a octylsilyl s...

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RapidMiner

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Afzal Muhammad

Quality Recognition Model (QRM) (1)

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Quality Recognition Model (QRM) is a SVM-based Machine Learning supervised classification model that assigns label to the evidentiary documents on the basis of rigorousness of the contents. It assigns the label Rigor if the document is of quality otherwise assigns the Non-Rigor. It uses two type of features: data and metadata. Data features include title and abstract while the metadata features include MeSH terms and publication type.

Created: 2017-03-11

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Pharmnography PIS

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Circle of Hygeia Meets Innovation For the Millennial...

Created: 2017-03-01 12:54:26

Credits: Pharmnography PIS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

It is an interactive and innovative, easy access and official website of the Circle of Hygeia suitable for the aspiring millennial pharmacy students of the University of Makati.

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Pharmnography PIS

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Phytochemical Screening of Rain Tree

Created: 2017-03-01 10:36:56

Credits: Pharmnography PIS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The objective of this study is to know the active constituent of Albizia saman and to knowwhat are the indications or uses by phytochemical screening. Before our study began we didsome researches about our plant sample, Albizia saman.First we do the authentication to know the scientific name of the plant. And we do themoisture determination to determine the moisture content of the plant drugs sample andunderstand it’s significant. Also we did drug extraction; we use the maceration metho...

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DATAVIEW

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Shiyong Lu

A Montage workflow in DATAVIEW. (1)

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A sample workflow that implements the Montage workflow in DATAVIEW.

Created: 2017-02-22 | Last updated: 2017-02-22

Credits: Shiyong Lu

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Yaroslav Zaitsev

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Superlight synthetic cannabinoids.

Created: 2017-02-20 18:34:05

Credits: Yaroslav Zaitsev

License: No license

Superlight sinthetic cannabinoids, design of cannabinoid terpenes nature.

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Dr Kaveh Ostad Ali Askari

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The Evaluation of the Usage of the Fuzzy Algorithms ...

Created: 2017-02-05 13:58:44

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Abstract:This study aimed to evaluate the accuracy of object-oriented classification with and without the use of fuzzy algorithms, compared with pixel based algorithm in land use/ land cover classification. In order to compare different methods, AVNIR2 sensor images obtained from ALOS satellite were used to classify land use in Maragheh County. The results indicated that object-oriented classification approach produced more accurate results than pixel-based, So that the fuzzy knowledge based ...

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Dr Kaveh Ostad Ali Askari

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Determination of the height of vertical filter in he...

Created: 2017-02-05 13:55:51

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In order to determine the height of the filter in heterogeneous earth dam, three embankment models were provided in a flume laboratory, with the length of 4.2 m at the base of dam, the width of 60 cm and the height of 1 m and body slope 1H: 2V. For embankment of model, two types of fine and coarse grained soils were used. The texture of the soil was made using hydrometer method. In the first model, the fine-grained and coarse-grained soils were used in downstream and upstream of the dam crest...

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Dr Kaveh Ostad Ali Askari

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SHORT CURRICULUM VITAE OF Dr Kaveh Ostad-Ali-Askari

Created: 2017-02-05 13:51:03

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

SHORT CURRICULUM VITAE OF Dr Kaveh Ostad-Ali-Askari ,29 May 2016

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Dr Kaveh Ostad Ali Askari

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Comparison of solution of Saint-Venant equations by ...

Created: 2017-02-05 13:43:09

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The unsteady flow can be analyzed by Saint-Venant equations. These equations can be solved by characteristics and finite difference methods. The Saint-Venant equations are changed into four complete differential equations in characteristics method and these equation are solved by drawing two characteristics lines. The Saint-Venant equations are changed into a set non-linear equations and are solved using Preissman scheme in finite difference method. This set equation are changed into linear e...

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Dr Kaveh Ostad Ali Askari

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Engineering Operations Research (Linear Planning, Op...

Created: 2017-02-05 13:42:18

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Operational Research is the discipline of applying advanced analytical methods to help make better decisions.A branch of Applied Mathematics, Operational Research deals with real world problems. This requires a close collaboration among the clients (enterprises, entrepreneurs, companies, firms, organizations, etc.) who apply the advice of Operational Research, the specialists in Operational Research giving the advice, and everyone who will be influenced by the better decision. The clients may...

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Dr Kaveh Ostad Ali Askari

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FLOOD ROUTING IN RIVERS BY MUSKINGUM’S METHOD WITH N...

Created: 2017-02-05 13:40:41

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

For determining of Muskingum model coefficients, requires to an output hydrograph. Such hydrograph is not available in most rivers. In this research, the Muskingum's new coefficients are determined by the method that which is not require to output hydrograph and its accuracy is high. This coefficient is determined based on kinematic wave model with suitable scheme. The comparison between results of Muskingum model with new coefficients and dynamic wave model, showed that the new coefficie...

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Dr Kaveh Ostad Ali Askari

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Water in Literature Aspects (Social and Cultural Asp...

Created: 2017-02-05 13:39:27

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The type of water in a story or novel is just as important as the fact that water is used as a symbol. Rivers often represent the flow of life or fertility. Rivers are typically used as symbols by authors because rivers flow; they are constantly moving and they follow a distinct path. Oceans, on the other hand, because of their scope in relation to the earth, often represent obstacles or abysses from which things emerge or that characters must journey across to reach a destination. Oceans are...

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Dr Kaveh Ostad Ali Askari

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Artificial neural network for modeling nitrate pollu...

Created: 2017-02-05 12:18:50

Credits: Dr Kaveh Ostad Ali Askari

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Excessive use of chemical fertilizers, especially nitrogen fertilizers to increase crop and improper purification, and delivery of municipal and industrial wastewater are proposed as factors that increase the amount of nitrate in groundwater in this area. Thus, investigation of nitrate contamination as one of the most important environmental problems in groundwater is necessary. In the present study, modeling and estimation of nitrate pollution in groundwater of marginal area of Zayandeh-rood...

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Taverna 2

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Brayan S. Zapata-Impatá

recommenderSystem (1)

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Complementary workflow for the modelBuild. It can read the trained model parameters in order to classify samples in another dataset.

Created: 2017-01-20 | Last updated: 2017-01-20

Taverna 2

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Brayan S. Zapata-Impatá

modelBuild (1)

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Using this workflow one can train a softmax regression model (a machine learning algorithm) and the learnt parameters are exported to files.

Created: 2017-01-20 | Last updated: 2017-01-20

Taverna 2

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Brayan S. Zapata-Impatá

dataExploration (1)

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This workflow allows the user to explore and process a dataset file.

Created: 2017-01-20 | Last updated: 2017-01-20

Taverna 2

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Brayan S. Zapata-Impatá

repoRead (1)

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Workflow created to perform a search over the Harvard Dataverse. It can also download datasets linked files.

Created: 2017-01-20 | Last updated: 2017-01-20

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Brayan S. Zapata-Impatá

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Open research data reutilization tool

Created: 2017-01-20 16:44:15 | Last updated: 2017-03-15 07:30:53

Workflows created in order to perform a machine learning project using open research data from the Harvard Dataverse. This work is the result of my master's thesis and you are very welcome to collaborate!

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Analytics Workbench

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Sittisak Krotasuwan

SNPs@PSU (1)

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Example file test workflows.

Created: 2016-12-03 | Last updated: 2016-12-03

Credits: Sittisak Krotasuwan

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Sittisak Krotasuwan

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SNPs@PSU_Service

Created: 2016-12-03 17:04:31

Credits: Sittisak Krotasuwan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example test workflows.

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William Senior

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Growth of the tropical scallop, Euvola (Pecten) zicz...

Created: 2016-11-25 16:26:20

Credits: William Senior

License: Creative Commons Attribution-Share Alike 3.0 Unported License

We compared the growth of the scallop Euuolu (Pecten) ziczuc (L.) in three situations whichpotentially could be used for commercial culture, in cages maintained in suspension, in cages on thebottom and in cages partly buried in a sediment bottom. The latter permitted the scallops to burythemselves as in their natural habitat. Throughout the 7-month study, growth, as measured by shelllength and muscle mass, was by far superior for scallops in the partly buried cages. Possible explanationsfor t...

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William Senior

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PRINCIPALES FUENTES DE CONTAMINACIÓN DEL RIO MANZANA...

Created: 2016-11-25 15:45:27

Credits: William Senior

License: Creative Commons Attribution-Share Alike 3.0 Unported License

El río Manzanares es uno de los más importantes de Venezuela. Está ubicado en la región nor-oriental,en el Estado Sucre. Posee una cota máxima de 2.200,oo msnm, en el Cerro Las Peonias y una mínimade 00,oo msnm en el Golfo de Cariaco, con una longitud de cauce de 81 km, pendiente mínima de 15%y gasto medio de 1,23 m3/s. Existe una precipitación media anual de 1.328,10 mm, con evaporación de1.929,4 mm (MARNR, 1998). Según el...

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William Senior

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Especiación de metales en sedimentos del río Cuchive...

Created: 2016-11-25 14:51:19

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The total concentration and the chemical forms of heavy metals were determined insuperficial sediments of the Cuchivero river, Venezuela, using sequential extraction andatomic absorption spectrophotometry with flame. Pollution indices were used to study thedistribution, pollution and environmental risk in the sediments. Total values ranged from,394-457 mgkg-1 Fe, 46,87-74,82 Mn, 6,45-11,92 Zn, 1,70-5,75 Ni, 0,39-3,7 Cu, 1,25-3,63Cr, 0,37-1,82 Co, 0,10-0,30 Cd y <Ld-0,20 mgkg-1 Pb. The meta...

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Santanu Koley

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A Novel Approach of Secret Message Passing Through ...

Created: 2016-11-24 18:00:17

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Today’s internetworking globe is full of busy roads for transferring data. Challenges on sending or receiving various kinds of hidden data, messages or information especially using this public networks. Hackers took place to leak this surreptitious data. That's the reason behind the need of a cover media where the furtive message has been hiding our information securely...

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Santanu Koley

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Cloud Computing: A New Era of Saving Precious Lives...

Created: 2016-11-24 17:53:57

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cloud Computing, nowadays used for saving cost, space, computer hardware and software, can be implemented on a newly designed system with cloud computing approach is a solution for remote districts, villages in hilarious regions where mobile network exists. First it can be implemented on animals and then if successful can be implemented on human beings. It provides better so...

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Santanu Koley

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Present scenario of cybercrime in INDIA and its pre...

Created: 2016-11-24 17:50:34

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The internet in India is growing rapidly. It has given rise to new opportunity in every field like – entertainment, business, sports, education etc. It is universally true that every coin has 2 sides, same for the internet, it uses has both advantage and disadvantage, and one of the most disadvantage is Cyber-crime. We can say, cyber-crime is any illegal activity which is committed using a computer network (especially the internet). Also, cyber-crime involves the breakdow...

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Santanu Koley

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Particle Swarm Optimization for creating self organi...

Created: 2016-11-24 17:47:55 | Last updated: 2016-11-24 17:48:58

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A novel technique for developing a self organized Back Propagation Artificial Neural Networks (BPANNs) or simply Back Propagation Neural Network (BPN) with the help of swarm Intelligence (SI) technique. This paper proposes an overlapping swarm intelligence algorithm for training of neural networks in which a &...

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Santanu Koley

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The Art of Learning: Knowledge Comprehension and Imp...

Created: 2016-11-24 17:44:11

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The Learning concept can be categorized by supervised and unsupervised learning in a broad sense, where supervised learning model assumes the availability of a teacher or supervisor who classifies the training examples and unsupervised learning model identify the pattern classes by information heuristically or by experience. A novel concept of learning; Reflective Teaching-learning methodology is derived from reinforcement learning an accurate self-perception technique to promote learning pro...

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Santanu Koley

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A Life Saving Cloud Computing Architecture for Mobi...

Created: 2016-11-24 17:41:37

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

We have presented here a newly designed system with cloud computing approach is a solution for remote districts, villages in hilarious regions where mobile network exists. It can provide better solution for the patients admitted in a hospital or primary health center. The developing countrie...

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Santanu Koley

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Advanced Technique for best use of CDroid OS for Mob...

Created: 2016-11-24 17:00:10

Credits: Santanu Koley

License: Creative Commons Attribution-Share Alike 3.0 Unported License

CDroid is the next generation technology which will be used with clouds to get benefits from it. The twenty first century made us smart enough, it is now mandatory to save power consumption as much as for the sake of financial, environmental stability. &n...

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