Workflows

Find Orthologs for proteins in Ensembl (1)

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Find Orthologs for proteins in Ensembl using biomart.

Created: 2011-10-03 | Last updated: 2011-10-03

Credits: Rafael C. Jimenez

[untitled] (1)

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 æˆ‘的第一个工作流，测试

Created: 2011-10-03 | Last updated: 2011-10-03

Credits: Zhaoyingguang

Comparing Quantities using HyperLEDA (1)

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This workflow receives the name of the property to compare, a file with a list of names of galaxies, and a file with the list of original values of that property. The property name must be typed in the same way used in the HTML returned by HyperLEDA The workflow calls to HyperLEDA using the names of the galaxies as input, and it returns a HTML file with information about the galaxy. This file is parsed by the python tool "ExtractPropertyValues", that extracts the value of the property introdu...

Created: 2011-10-03

Retrieve Molecular Interactions from PSICQ... (1)

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Retrieve Molecular Interactions from PSICQUIC Services for a list of Protein Accessions in PSI-MITAB format

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Rafael C. Jimenez

What's the Season? (1)

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When given a list of astronomical object names, this workflow will check them against a simple Excel spreadsheet and return which season the object is best observed in. It will also compare the distances to the objects in a Google Charts bar chart. A later version of this may switch to a scatter plot, depending on whether or not this works with the Google Chart API. Running this workflow requires Python. Sys and string should be bundled in Python, but the numpy module will need to be downloa...

Created: 2011-10-05 | Last updated: 2011-10-05

Attributions: Spreadsheet Import Example

Extracting Quantities from HyperLEDA (1)

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This workflow receives the name of the property to compare and a file with a list of names of galaxies. The property name must be the same used in the HTML file returned by the HyperLEDA service. The workflow calls to HyperLEda service, using as input the names of the galaxies in order to get a HTML file with information about each galaxy. From each HTML file, it extracts the value of the property selected by the user. The workflow uses a python tool to parse the HTML file (one for each gala...

Created: 2011-10-05 | Last updated: 2011-10-05

HTML Citation Extraction (1)

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 This workflow is a beanshell script that locates and extracts text within an html page.  It was designed to pull citation information from the website http://robjhyndman.com/TSDL/.

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Jeff adamus

Current Date Output (1)

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Returns the Current Date optionally Formatted by input. Free to copy and use by all!.

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Jeff adamus

Time Series Data Graphed and Cited (1)

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This workflow uses time series data from Rob Hyndman's Time Series Data Library (TSDL) and graphs it with Google charts. It also provides the citation information with the current date. The outputs are a Google Chart and the corresponding citation information. The inputs are URL strings for two datasets provided by Rob Hyndman under the subject of Ecology. These datasets include the annual number of lynx pelts and the annual unit price of lynx pelts during the year range 1857 -1911. This...

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Trisha Adamus Alan Williams Jeff adamus

Attributions: Fetch today's xkcd comic Spreadsheed Data Import Example HTML Citation Extraction Current Date Output

[untitled] (1)

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This workflow ...tbc img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; } .cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; } .cubbies-selected:active{ box-shadow: 2px 2px 5px -1px darkblue !important; margin: -1px 1px 1px -1px; } #cubbies-overlay{ positio...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Get Element ID from Gzipped GenBank file (1)

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This workflow gunzips a *.gbk.gz file, converts it to XML (via agavewriter) and finds the Element ID. Does not work on *.gz files larger than 10MB. I upped the JVM settings on Taverna to:         <key>VMOptions</key>         <string>-Xmx4096m -XX:MaxPermSize=1024m</string> Created my own agave.dtd to get the XPath service to work the XML file generated from the Read_GenBank_File service. You will need to ...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Mutanthumb Alan Williams

Elevation plot v.2 (2)

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Functionally identical to the original. I tried to upload a version with annotation, but somehow the notes didn't make it to myExperiment. From the prior verion: This workflow accepts city and country names as user-supplied input. These value are supplied to the GetWeather webservice (http://www.webservicex.net/globalweather.asmx?WSDL), which returns an XML record of location and weather info for each recognized city. (See the uploaded photo "weather example") The XML returned fr...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Latitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out latitude coordinates formatted as ##-##(N or S) using the following regular expression: \d\d-\d\d(N|S). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow contains primarily string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatting I requi...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Longitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out longitude coordinates formatted as ###-##(N or S) using the following regular expression: \d\d\d-\d\d(E|W). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow primarily contains string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatti...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Mapping Workflow - Attempt (1)

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PLEASE NOTE: This is an early variation of http://www.myexperiment.org/workflows/2474.html. This workflow was abandoned as the above mentioned workflow is more streamlined. This workflow may or may not work successfully.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: tpacurtis

Mapping Service (2)

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This service generates a google map of a group of place names and coordinates. The workflow will accept both coordinates and place names. This workflow takes place names/coordinates from both a spreadsheet, as well as on-the-fly input of a list of coordinates or place names (please note, if no supplemental data is desired, an empty link will allow the workflow to function). The Mapping Service workflow was created to assist in generating a map of where a series of interviews took p...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: tpacurtis

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Alan Williams

Average and Standard Deviation (1)

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This workflow takes in a list of values and a list name, and returns the list name, average, and standard deviation of the values.

Created: 2011-10-07 | Last updated: 2011-10-07

Credits: Atminer

Population Plot with R (1)

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This script pulls the population of every country and creates a plot of them. This is based on the script at http://www.myexperiment.org/workflows/1728.html , with a few modifications for labelling axes and the title.

Created: 2011-10-08

Credits: Atminer

Broccoli Production New York State, 1960-1965 (1)

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This workflow takes data about agricultural production in New Jersey and New York from 1960 -1965, to compare productivity in broccoli growing.

Created: 2011-10-09 | Last updated: 2011-10-09

Credits: Atminer Alan Williams

Attributions: Spreadsheet Import Example

Spreadsheet Import - Fertilizer Use (1)

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This workflow takes data from a spreadsheet and creates a graph of fertilizer use in NY state from 1960-1965.

Created: 2011-10-09 | Last updated: 2011-10-09

Credits: Atminer

Attributions: Spreadsheet Import Example

WPS-GRASS-Bridge r.los example (1)

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r.los generates a raster output map in which the cells that are visible from a user-specified observer position are marked with the vertical angle (in degrees) required to see those cells (viewshed). A value of 0 is directly below the specified viewing position, 90 is due horizontal, and 180 is directly above the observer. The angle to the cell containing the viewing position is undefined and set to 180. http://grass.fbk.eu/grass62/manuals/html62_user/r.los.html

Created: 2011-10-13

Credits: Jorgejesus

Get homologous from NCBI homoloGene (1)

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Get homologous from NCBI homoloGene for a list of Refseq protein accessions. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Created: 2011-10-13 | Last updated: 2011-10-13

Credits: Rafael C. Jimenez

Find orthologs using a uniprot accession (1)

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Find orthologs based on ensembl information using as input/output uniprot accession

Created: 2011-10-14 | Last updated: 2011-10-14

Credits: Rafael C. Jimenez

Find orthologs using a list of uniprot acc... (2)

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Find orthologs based on ensembl information using as input/output uniprot accessions

Created: 2011-10-14 | Last updated: 2014-06-03

Credits: Rafael C. Jimenez