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David De Roure

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Long Tail Research and the Rise of Social Machines

Created: 2012-07-30 07:26:22 | Last updated: 2012-07-30 15:14:48

Word doc and PDF of blog post "Long Tail Research and the Rise of Social Machines" posted 27 July 2012 by David De Roure on http://www.scilogs.com/eresearch/social-machines/ This is a position piece for the "Big Data and Long Tails" workshop organised by the Institute for Computing in Science, July 29 2012, Park city, Utah.

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social machines

Taverna 2

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Helen Hulme

Genome variant to Protein change (1)

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Reports protein change, given a genomic variant, using mutalyzer

Created: 2012-07-27 | Last updated: 2012-10-29

Credits: Helen Hulme

Taverna 2

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Susana

Extract SDSS field information and PSF (5)

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This workflow gathers information needed by the execution of Sextractor, Galfit and Ellipse, from the SDSS VO service. It receives two inputs: 1) An ascii table with information about the image such as data of the field, name of the fits file or if it is barred or not. 2) A configuration file with the paths where the files needed by the workflow can be found and other paths where to store the files generated by the workflow This workflow extracts the band from the image header, and the info...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Susana

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Cherian Mathew

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Data Refinement Workflow Utility Jar (Current Version)

Created: 2012-07-26 14:56:42 | Last updated: 2012-11-07 08:48:49

Credits: Cherian Mathew

License: Creative Commons Attribution-Share Alike 3.0 Unported License

jar which includes all utility classes with functionality used in the Data Refeinement workflow

File type: Trident (Package)

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Taverna 2

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Anja Le Blanc

Check the content of the Registry for mism... (1)

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This workflow check for tables which are registered in the HELIO registry but not available in the HFC and for tables which are in the UOC but which are not registred.

Created: 2012-07-26

Credits: Anja Le Blanc

Taverna 2

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Julian Garrido

Adjusting galaxy parameters using galfit (4)

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This workflow creates galfit configuration files using data from a votable, it runs galfit, its results is added to the votable, it creates new config files for galfit using the previous results, it runs galfit a second time considering galaxies that have and do not have bars in order to adjust the objective parameters and it finally includes the results into the votable. It requires the specification of the columns that contain file names (these files should be accesibles from taverna). If t...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run galfit using a votable Create votable from galfit results Create votable from different galfit paramenter adjustments Create galfit configuration files with partition criteria using votable

Taverna 2

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Julian Garrido

Create galfit configuration files with par... (1)

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This workflow creates galfit configuration files using a partition criteria. The resulting configuration files are different depending on whether the galaxy has o doesn't have a bar. They are created (one for every row in the votable) using a template whose keys are replaced by data from a votable. Keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file. This workflow uses astrotaverna ...

Created: 2012-07-26 | Last updated: 2012-07-26

Credits: Julian Garrido

Taverna 2

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Julian Garrido

Create votable from galfit results (4)

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/).

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Taverna 2

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Julian Garrido

Run galfit using a votable (2)

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It runs galfit and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Galfit is called by a bash script as 'galfit'. Galfit is called for every row in the votable. Columns where the result file name and the configuration file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain references to o...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Taverna 2

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Julian Garrido

Ajusting galaxy paramenters using sextractor (5)

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This workflow creates configuration files for sextractor, it runs sextractor using this configuration files, it adds sextractor results to the input votable and adds new calculated columns. This task requires a votable as input, a template, a vocabulary and the specification of the column names that contain some required files (configuration files, image files, ...). These files must be accesible from taverna. Sextractor is called by an bash script as 'sex'. Every row in the votable cotains ...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run sextractor using a votable Create votable from sextractor results Add columns to a votable resulting from executing sextractor.

Taverna 2

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Julian Garrido

Create votable from sextractor results (2)

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The workflow creates a votable from the results provided by sextractor (votables). It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running sextractor and such files accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-07-26 | Last updated: 2012-08-21

Credits: Julian Garrido

Taverna 2

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Julian Garrido

Run sextractor using a votable (2)

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It runs sextractor and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Sextractor is called by an bash script as 'sex'. Sextractor is called for every row in the votable. Columns where the configuration file and the image file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain refer...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

KNIME

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Ldpf

13C NMR spectra prediction (2)

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This workflow can be used to predict the 13C NMR spectra of a molecule. The generation of the structure of the molecule is done using the IUPAC to Structure node that uses OPSIN to convert the name of the molecule to a structure. Alternativelly, one can read the structure from a file. The spectra prediction is based on the NMRShiftDB implementation and the data used is also from NMRShiftDB. The atom topological environments were represented as Atom Signatures and used to calculate the checmia...

Created: 2012-07-26 | Last updated: 2012-08-10

Credits: Ldpf

Taverna 2

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Julian Garrido

Create configuration files from a template... (1)

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This workflow uses astrotaverna artifacts. It creates files by using a template whose keys are replaced by data from a votable. A configuration file is created for every row in the votable. The keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file.

Created: 2012-07-26 | Last updated: 2012-09-04

Credits: Julian Garrido

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Bamdad Dashtban

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Task Data

Created: 2012-07-25 15:40:43 | Last updated: 2012-07-25 15:41:08

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component family

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David De Roure

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Presentation - Advances in Digital Scholarship

Created: 2012-07-25 10:29:46 | Last updated: 2012-07-25 13:12:21

Title: Advances in Digital Scholarship Speaker: David De Roure Event: DIGITAL RESEARCH RESOURCES IN THE ARTS AND HUMANITIES - Achievements and Prospects for Future Collaboration Location: King’s College London Date: 25 July 2012 Formats: .pptx

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Taverna 2

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Anja Le Blanc

Check the content of the Registry for mism... (1)

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This workflow check for tables which are registered in the HELIO registry but not available in the UOC and for tables which are in the UOC but which are not registred.

Created: 2012-07-25

Credits: Anja Le Blanc

Taverna 2

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Anja Le Blanc

Check registry for wrongly registed and un... (2)

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HELIO registry contains a list of tables available in the HEC. The HEC contains a table with available talbes itself. This workflow shows the differences between these two lists.

Created: 2012-07-24 | Last updated: 2012-07-24

Credits: Anja Le Blanc

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Drkrish...

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Process for the preparation of amorphous atorvastati...

Created: 2012-07-24 12:07:03

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Atorvastatin calcium is a drug compound that is used as a lipid-lowering agent, fortreating hypercholesterolemia. The compound has the chemical name[R-(R*,R*)]-2-(4-fluorophenyl)-3,ö-dihydroxy-5-(1-methylethyl)-3-phenyl-4-{(phenylamino)carbonyl}-1H-pyrolle-1-hepatonic acid, calcium salt (2:1) trihydrate. Pharmaceutical productscontaining crystalline atorvastatin calcium trihydrate are sold using the trademarkLIPITOR.

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Drkrish...

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Novel polymorph of 5-cyanopthalide high purity inter...

Created: 2012-07-24 12:02:16

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The present invention relates to obtaining a new polymorph of 5-Cyanophthalide in highly pure form (99.5 to 99.99%), which is an intermediate used forthe synthesis of citalopram& escitalopram both of which are potent antidepressant drugs.Moreover this new polymorph of 5-cyanophthalide does not contain impurities liketerephthalic acid & diphthalide derivatives.

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Drkrish...

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Enantioselective method of synthesizing methylphenid...

Created: 2012-07-24 11:51:52

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Process for the preparation of enantioselective method of making methylphenidate and derivatives . The method involves use of a rhodium catalyst, and selectively produces the D-enantiomer of the methylphenidate derivative in excess of the L-enantiomer . Furthermore, the method selectively produces the threo-diastereomer in excess of the erythro-diastereomer. The method is thus suitable for synthesis of D-threo-methylphenidate (the biologically active form of this compound) and derivatives &...

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Drkrish...

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Quality Assurance and GMP and ICH

Created: 2012-07-24 11:46:03

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Quality Assurance is a planned and systematic approach to generate enough confidence in the quality of the product and processes in the long run as per the specifications." In this biog you will find post related to ICH, GMP and Quality related matters.

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Drkrish...

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GLIBENCLAMIDE Complexes ( Complexes of Mg,Cr,Ni,Zn a...

Created: 2012-07-24 11:33:50 | Last updated: 2012-07-24 11:33:51

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The N-acetyl derivative of β-phenethylamine is reacted with chlorosulfonic acid to form the para sulfonyl chloride derivative. This is then subjected to ammonolysis, followed by base-catalyzed removal of the acetamide. This is then acylated with 2-methoxy-5-chlorobenzoic acid chloride to give the amide intermediate. This is then reacted with cyclohexyl isocyanate to yield the sulfonylurea glibenclamide

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Drkrish...

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HOW TO START ANALYTICAL METHOD DEVELOPMENT

Created: 2012-07-24 11:28:31

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A bulk drug during its production process, after its scale up, it is necessary to analyse for the presence of any impurities or related substances in it. This is to ensure the impurities and related substances are within their limits as per ICH Guidelines.The impurities and related substances are defined as; Impurity: Any component present in the drug substance or drug product which is not the desired product, a product-related substance, or excipient including buffer components. I...

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Drkrish...

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DEFINITION â€œIMPURITYâ€

Created: 2012-07-24 11:18:54

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Impurities are normally generated during the formation of Active PharmaceuticalIngredients and their intermediates. Chances of their generation during Drug Productsformation are less as formulation is a physical blending process. Care is taken that theseexcipients do not react with each other to produce the degradants. They may consist oforganic and inorganic, and define levels at which impurities/degradants should beidentified.ICH Q3A covers drug substances and Q3B covers drug products. Th...

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Drkrish...

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Improved process for preparing L-phenylephrine hydro...

Created: 2012-07-24 11:12:15

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The present invention relates to an improved process for preparing L-phenylephrinehydrochloride on an industrial scale

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Drkrish...

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PROCESS FOR PREPARATIN OF VITAMIN-C-Dr.krishnasarma ...

Created: 2012-07-24 11:03:13

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ascorbic acid (vitamin C) is a water-soluble vitamin. It occurs as a white or slightly yellowcrystal or powder with a slight acidic taste. It is an antiscorbutic product. On exposure to light, itgradually darkens. In the dry state, it is reasonably stable in air, but in solution it rapidlyoxidizes. Ascorbic acid (vitamin c) is freely soluble in water; sparingly soluble in alcohol;insoluble in chloroform, in ether, and in benzene. The chemical name of ascorbic acid (vitaminc) is L-ascorbic a...

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Drkrish...

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Industrial process for preparation of Levetiracetam....

Created: 2012-07-24 10:59:51

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Levetiracetam belongs to the class of compounds used in the treatment of epilepsy so it.has huge demand in market and it is worth to develop the product.

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Drkrish...

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solid-state forms of celecoxib andAN IMPROVED PROCE...

Created: 2012-07-24 10:54:47

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The present application provides an improved process for the preparation of 4-[5-(4-methylphenyl)-3- (trifluoromethyl)-1H-pyrazol-1-yl] benzenesulfonamide (Celecoxib) and its purification and crystallisation to produce polymorph .

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Drkrish...

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A Primer on Intellectual Property Rights-Dr.krishnas...

Created: 2012-07-24 10:39:44

Credits: Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

nTypes of Intellectual Property nWhat is a Patent , its requirements & specification nPatent claims nCriteria for claiming inventors nTypes of patents nInfringement & validity of patent nIndian patent scenario nPatent Cooperation Treaty (PCT) nDifferences in patent Laws nPatent Resources

File type: PowerPoint presentation

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Mohd Saberi

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Using A Dynamic Bayesian Network-based Model for Inf...

Created: 2012-07-24 04:51:56

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Largely due to the technological advances in bioinformatics, researchers are now garnering interests in inferring gene regulatory networks (GRNs) from gene expression data which is otherwise unfeasible in the past. This is because of the need of researchers to uncover the potentially vast information and understand the dynamic behavior of the GRNs. In this regard, dynamic Bayesian network (DBN) has been broadly utilized for the inference of GRNs thanks to its ability to handle time-seri...

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Mohd Saberi

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Aspartate Biosynthesis Pathway Simulation Using an I...

Created: 2012-07-24 04:49:23

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An improved Differential Evolution algorithm (IDE) is proposed in this paper. It is aimed at enhancing its efficiency in estimating the relevant kinetic parameters for metabolic pathway data to simulate aspartate biosynthesis pathway for plant model Arabidopsis. Metabolic pathway data are anticipated to be of vital help in the development of effectual tools in parameter estimation and kinetic modeling platforms. However, a number of computation algorithms face difficulty, produces low a...

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Mohd Saberi

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Gene Knockout Strategies Identification by Using a H...

Created: 2012-07-24 04:48:16

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

By optimizing microbial strains it is possible to improve product yield or improve growth characteristics. Microbial strains can be optimized through genetic engineering. It is proven that through genetic engineering it is able to obtain the desirable phenotypes. However, it is difficult to predict the effects of genetic modifications on the resulting phenotype due to the complexity of the networks. Optimization algorithms are implemented in previous works in order to identify the effec...

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Mohd Saberi

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Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-07-24 04:46:49

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data to simulate glycolysis pathway for Saccharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testifying to be supreme to the others estimation algorithms. The outcomes from this study promote estimating ...

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Mohd Saberi

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Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-07-24 04:45:28

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extracting metabolic pathway that dictates a specific biological response is currently one of the important disciplines in metabolic system biology research. Previous methods have successfully identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structure is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identifying the significant pathwa...

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Mohd Saberi

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Random Forest for Gene Selection and Microarray Data...

Created: 2012-07-24 04:44:00

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A random forest method has been selected to perform both gene selection and classification of the microarray data. The goal of this research is to develop and improve the random forest gene selection method. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. In this research, ten datasets that consists of different classes are used, which are Adenocarcinoma, ...

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Mohd Saberi

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Optimized Local Protein Structure with Support Vecto...

Created: 2012-07-24 04:21:20

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact through complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental ...

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Mohd Saberi

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Prediction of Protein Residue Contact Using Support ...

Created: 2012-07-24 04:19:46

Credits: Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Prediction of protein residue contact is one of the important twodimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy of ...

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pinarpink

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eScience-WF-Motifs-Consolidated-DataSet

Created: 2012-07-18 23:58:01

Credits: pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The spreadsheet containing data consolidated by domain. Also contains al the charts that are generated over consolidated data.

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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pinarpink

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eSCience-WF-Motifs-Wings-DataSet

Created: 2012-07-18 23:56:30

Credits: pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The Dataset containing Wings workflows that are manually analyzed for the detection of motifs

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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pinarpink

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eScience-WF-Motifs-Taverna-DataSet

Created: 2012-07-18 23:55:17

Credits: pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The Dataset containing Taverna workflows that are manually analyzed for the detection of motifs

File type: Excel workbook

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David De Roure

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Presentation - Web Observatories

Created: 2012-07-18 19:52:23 | Last updated: 2012-07-18 20:14:36

Title: Web Observatories Speaker: David De Roure Event: Web Observatory and Discovery Informatics workshop Event URL: http://research.microsoft.com/en-us/events/wodi2012/ Location: Microsoft, Redmond, WA Date: Wednesday July 18, 2012 Formats: .pptx

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pinarpink

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eScience-2012-Workflow Motifs-Submission-Dataset

Created: 2012-07-18 12:36:14 | Last updated: 2012-07-18 23:58:59

The data sets that have been used for the manual analysis of motifs in Taverna-2 and Wings workflows.

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David De Roure

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SALAMI Ground Truth stats

Created: 2012-07-17 17:43:32 | Last updated: 2012-07-17 17:46:46

Galaxy workflow to plot song durations and also a scatterplot of human annotation time versus song duration. Tested only on Galaxy main server.

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Galaxy

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David De Roure

RTTS Mapper (1)

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Generates RTTS counts file from SAM file. Output consists of three columns: counts at given position;chromosome;position(0 based). Workflow removes untemplated nucleotides from 5' ends of the reads. Authors: Jeppe Vinther, Lukasz Kielpinski Workflow published by lukaszkielpinski on Galaxy Jun 26, 2012 imported to myExperiment Jul 17, 2012 during demonstration of Galaxy-myExperiment integration (specifically generating SVG and showing steps of more complex workflow).

Created: 2012-07-17 | Last updated: 2012-07-17

Galaxy

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David De Roure

Transform 'Stitch Gene blocks' FASTA block... (1)

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Converts FASTA blocks to a FASTA file. Workflow published by galaxyproject on Galaxy Jun 27, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration https://main.g2.bx.psu.edu/u/galaxyproject/w/transform-stitch-gene-blocks-fasta-blocks-to-standardized-fasta-file

Created: 2012-07-16 | Last updated: 2012-07-16

Galaxy

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David De Roure

Basic Illumina Reads Quality (Functional G... (1)

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From the RNA-Seq analysis tutorial during the Functional Genomics Workshop 2012 https://caps.osu.edu/pfg-workshop Workflow published by mejia-guerra on Galaxy Jun 22, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration

Created: 2012-07-16 | Last updated: 2012-07-16

Galaxy

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David De Roure

Basic RNA-Seq Analysis - Differential Expr... (1)

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From the RNA-Seq analysis tutorial during the Functional Genomics Workshop 2012 https://caps.osu.edu/pfg-workshop Workflow published by mejia-guerra on Galaxy Jun 22, 2012 imported to myExperiment Jul16, 2012 during demonstration of Galaxy-myExperiment integration

Created: 2012-07-16 | Last updated: 2012-07-16

Galaxy

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David De Roure

AnnotationTimes (1)

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This very simple workflow was used in the analysis of the metadata produced by the human annotation phase of the SALAMI (Strucural Analysis of Large Amounts of Music Inforamtion) project. The input data is the metadata available from http://ddmal.music.mcgill.ca/salami/annotations It produces a histogram of song durations and scatterplot of combined annotation time verus song duration. The fields are SONG_ID Un...

Created: 2012-07-16 | Last updated: 2012-07-16

Taverna 2

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Susana

Example of how to use Sesame service and V... (1)

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This workflow needs as input a list of names of galaxies. Then it queries Sesame services to get the coordinates of this galaxies, and finally with this coordinates queries a Virtual Observatory Services (a cone service).

Created: 2012-07-14

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