Workflows

Microarray CEL file to candidate pathways (2)

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Created: 2007-10-03

querySWS_minimalQuery (2)

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SRS by WS (SWS) is a set of Web Services allowing to retrieve database entries from libraries included in public SRS sites. The querySWS service implement a search on the basis of the database name (lib) and the term to be searched (query). It automatically identifies the best site to query. Additional parameters include in_fields (in which part of the record the terms are searched), out_fields (which information is returned) and site (the SRS site). This workflow is just a demonstration ...

Created: 2007-10-03

Fetch Dragon images from BioMoby v2 (2)

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demonstration to ISSGC07

Created: 2007-10-03

XSTAR (3)

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This is a simple workflow designed to run XSTAR with an user selected input. XSTAR is a computer program for calculating the physical conditions and emission spectra of photoionized gases. More information can be found here: - XSTAR home page: http://heasarc.nasa.gov/lheasoft/xstar/xstar.html - XSTAR on the Spinet client (Soaplab2): http://caoba.ivic.ve:8180/soaplab2-axis/

Created: 2010-04-02 | Last updated: 2011-02-27

Kegg pathway diagrams (3)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - ...

Created: 2010-03-19 | Last updated: 2010-03-19

BlastandParse2 (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

BlastandParse1 (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

Uczenie z macierza kosztow (1)

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Przeplyw pokazuje wykorzystanie operatora MetaCost, umozliwiajacego wprowadzenie macierzy kosztow do procesu uczenia klasyfikatora na przykladzie naiwnego klasyfikatora Bayesa.

Created: 2011-05-25 | Last updated: 2014-03-23

Algorytmy k-Means i k-Medoids (1)

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Przeplyw pokazuje zastosowanie algorytmow k-Means i k-Medoids do przeprowadzenia analizy skupien. Analizie podlega zbiór danych Iris, przy czym oryginalne dane zostaly przetransformowane z przestrzeni 4-wymiarowej do przestrzeni 2-wymiarowej za pomoca operatora Singular Value Decomposition. Redukcja liczby wymiarow ma na celu uproszczenie wizualizacji wynikowych modeli.

Created: 2011-05-11 | Last updated: 2013-08-19

Odkrywanie regul asocjacyjnych za pomoca a... (1)

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Workflow pokazuje sposób wykorzystania operatorow Apriori i PredictiveApriori (z narzedzia Weka) do odkrywania regul‚ asocjacyjnych. Operator Set Role zostal wykorzystany do tego, aby atrybut Play (który w oryginale jest zmienna celu) byl potraktowany jak zwyczajny atrybut.

Created: 2011-03-31 | Last updated: 2013-05-30