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GT: Database - Master SNP Call Table (1)

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Either load new Master SNP call data into the database (from an Excel file) or export the master SNP data from the database into an Excel file. NOTE: Running this workflow will take a couple of minutes. If loading excel data into database, make sure the file is located in the correct directory: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/

Created: 2011-09-10

Credits: Chengc

The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: PL

GT: Genotyping Comparison Analysis and Clu... (7)

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Creates a genotyping comparison analysis Excel file and heatmap image given final report and gender call input files. User provides either plate numbers, CLID/BIOIDs, cNames, etc. and can choose to either load the data into the database or not. Note that if user chooses to load data into database, script may take longer (few minutes) to run. Before running, make sure the final report and gender call text files are correctly named and that they are in the correct directory under: /gne/researc...

Created: 2011-09-01 | Last updated: 2011-09-10

Credits: Chengc

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Ondex Workflows

Created: 2011-09-01 17:17:57 | Last updated: 2011-09-01 17:18:05

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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GT: Sample Sheet Generation (7)

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Creates a sample sheet from a SAMid exported file. User provides a plate number. Before running, make sure the SAMid exported file is in the correct directory under: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/Plate_# Results will be stored under this directory: /gne/research/data/bioinfo/gcell/genotype/prd/Plate_#

Created: 2011-08-31 | Last updated: 2011-09-08

Credits: Chengc

Convert GML to SVG (1)

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This workflow can convert the GML (Geography Markup Language) file to SVG image.

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

TIFF to PNG (1)

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This workflow can convert Image format from TIFF to PNG. This workflow is one of the example for GENESI-DEC ontology.

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

Image metadata extraction (1)

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This workflow invokes the gdalinfo service and will list various information about a GDAL supported raster dataset of the image ( GeoTIFF, PNG, JPEG and GIF.).

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

BATWING (1)

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Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei...

Created: 2011-08-25 | Last updated: 2011-08-25

Credits: Pipeline

Find instruments of a special type in a se... (1)

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This workflow takes a type of isnstrument as input and the minimum and maxium coordinates in HCI as input. Cadence for the location service is for defining the 'continues' presence. Output is a VOTable based on the ICS return where two columns are added for the time this instrument has entered and exited the Region of Interest.

Created: 2011-08-24 | Last updated: 2011-08-24

Credits: Anja Le Blanc

Attributions: Find instruments of a special type in a section of space described in HCI coordinates

Find instruments of a special type in a se... (1)

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This workflow takes a type of isnstrument as input and the minimum and maxium coordinates in HCI as input. Cadence for the location service is for defining the 'continues' presence. Output is a VOTable based on the ICS return where two columns are added for the time this instrument has entered and exited the Region of Interest.

Created: 2011-08-24 | Last updated: 2011-08-24

Credits: Anja Le Blanc

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A sample pack

Created: 2011-08-22 10:42:16 | Last updated: 2011-08-22 10:43:06

4 items in this pack

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BLAST your sequences against the NucleaRDB (1)

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BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc)

Created: 2011-08-19 | Last updated: 2011-08-19

Credits: Bas Vroling

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Test file for dLibra import

Created: 2011-08-17 15:35:06

Credits: Piotr Hołubowicz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JPEG image

Comments: 0 | Viewed: 27 times | Downloaded: 21 times

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Presentation - The Execution of Dave 2.0

Created: 2011-08-17 13:07:06 | Last updated: 2011-08-17 13:17:43

3 items in this pack

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Rave Usability Lab Workflow (1)

Created: 2011-08-16 | Last updated: 2011-11-10

Credits: Liz Masterman

Split string into string list, new line se... (1)

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Split string into string list using new line as separator. Should work in Linux, Mac and Windows.

Created: 2011-08-15 | Last updated: 2014-02-26

Credits: Rafael C. Jimenez

Difference: Query - Reference (1)

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Difference bettwen the query list and the reference list. Things that are in the query and not in the reference.

Created: 2011-08-15 | Last updated: 2011-08-15

Credits: Rafael C. Jimenez

Plotting Training vs Testing Error (Loop +... (1)

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This process increases the parameter C of a support vector machine and hence also the risk for overfitting. It uses an outer loop operator for increasing the parameter value and an inner log operator for storing the current number of applications together with the current errors on the training and the testing data set. At the end of the process, the log data can be plotted (for example with the plotter "Scatter Multiple" with "Count" on the x-axis and both "Training Error" and "Testing Error...

Created: 2011-08-15

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Scientific Social Objects

Created: 2011-08-14 23:54:47 | Last updated: 2011-08-14 23:58:12

2 items in this pack

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Towards the Preservation of Scientific Workflows

Created: 2011-08-12 23:18:58 | Last updated: 2011-08-12 23:25:32

7 items in this pack

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XML-RPC example current time (1)

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Using Apache ws-xmlrpc from Beanshell scripts to call time.xmlrpc.com - see http://www.xmlrpc.com/currentTime To use, download the JARs from http://ws.apache.org/xmlrpc/download.html (ie. http://apache.mirror.anlx.net//ws/xmlrpc/apache-xmlrpc-current-bin.zip ) - unzip and put into Taverna's home directory lib/ folder. Right-click on the Beanshell script and check the "Dependencies" tab to check that all JARs have been ticked off (minimum required: ws-common-util.jar, xmlrpc-client.jar and x...

Created: 2011-08-11 | Last updated: 2011-08-11

Credits: Stian Soiland-Reyes

OpenTox Learn and evaluate model (1)

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Learns a LoMoGraph model on the TUM servers and evaluates it using 10 fold cross validation.

Created: 2011-08-09

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Rave in Context project - test pack

Created: 2011-08-08 14:13:04 | Last updated: 2011-11-10 16:07:29

6 items in this pack

Comments: 0 | Viewed: 37 times | Downloaded: 11 times

OpenTox Upload and merge data sets (1)

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Uploads 2 data sets to OpenTox, merges them and returns the merged data set.

Created: 2011-08-08 | Last updated: 2011-08-08