All content

AlitoraKDAInputModule test workflow (1)

 This workflow calls the AlitoraKDAInputModule service from the test GenePattern server.

Created: 2010-07-07 | Last updated: 2010-07-07

Credits: Peter Li

Pivoting with Consideration of Example Wei... (1)

• Download

This process shows how the Pivoting operator can also consider example weights encoded by a special attribute with the role 'weight'. The first operators only create a demo data set for this purpose, the actual pivoting is performed by the last operator only. I recommend to place a breakpoint before the Pivoting and check the data (structure) in order to see how the Pivoting handles the weights.

Created: 2010-07-07

View Download

NCBI Entrez Utilities Web service set description file

Created: 2010-07-06 14:40:27 | Last updated: 2010-07-06 14:42:59

Credits: Alex Nenadic

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: XML

Comments: 0 | Viewed: 28 times | Downloaded: 83 times

View Download

NCBI Entrez Utilities Web service set

Created: 2010-07-06 14:17:35 | Last updated: 2010-07-22 13:17:33

2 items in this pack

Comments: 0 | Viewed: 129 times | Downloaded: 78 times

CTF - MEG Event Averager (1)

• Download

This workflow applies parametrs in a user-specified processing.cfg file to a set of MEG data files. The datasets must be in CTF-format, such as those produced by Omega275 systems. The processing.cfg file and datasets are selected at the initialization of the workflow.  processing.cfg can be created by the data inspection tool DataEditor, and contains desired filter settings etc. This file can also be edited easily with a text editor to tweak settings. The workflow identifies all the trig...

Created: 2010-07-06 | Last updated: 2010-07-06

Credits: Lakelander

View Download

Presentation - Repositories and Linked Open Data: th...

Created: 2010-07-06 08:05:27 | Last updated: 2010-07-06 11:41:18

2 items in this pack

Comments: 0 | Viewed: 115 times | Downloaded: 11 times

This Pack has no tags!

A template example workflow using U-Compar... (2)

• Download

An example workflow using the U-Compare text mining system inside embedded. Users can easily make their own workflow with U-Compare reusing this workflow. This workflow retrieves abstract texts from Pubmed with user specified query, inputs the texts to U-Compare, interprets the output of U-Compare. You have to download and store the UIMA CPE XML descriptor file (StdinPPIExtraction-CPE-EventMine.xml) to run the default setting, which runs a event extraction text mining workflow by U-Compare. S...

Created: 2010-07-05 | Last updated: 2010-09-02

Credits: Yoshinobu Kano

Phenotype to pubmed (3)

• Download

This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: Paul Fisher

Gene to Pubmed (3)

• Download

This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: Paul Fisher

Perfrom a text based search through PubMed (1)

• Download

This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Created: 2010-07-05 | Last updated: 2010-07-05

Credits: Paul Fisher

Retrieve sequence in EMBL format (1)

• Download

This workflow retrieves a sequence associated with its features in embl format

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Pipelined list iteration (1)

• Download

Perform multiple iterations of services in order to show pipelining

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Ian Dunlop Stian Soiland-Reyes

GBSeq test (1)

• Download

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Fetch today's xkcd comic (1)

• Download

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn Stian Soiland-Reyes

Fetch PDB flatfile from RCSB server (1)

• Download

Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

EBI_InterProScan for Taverna 2 (1)

• Download

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

Demonstration of configurable iteration (1)

• Download

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

BioMoby tutorial workflow (1)

• Download

A workflow from part of the BioMoby tutorial

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: EdwardKawas

BiomartAndEMBOSSAnalysis (1)

• Download

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Alan Williams

A workflow version of the EMBOSS tutorial (1)

• Download

Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Tomoinn

Extracting data from VOTable format by usi... (1)

• Download

Input VOTable and 'name' of a Output corrosponding data of that field in an arrayInput VOTable and 'name' of a Field

Created: 2010-07-01 | Last updated: 2010-07-01

Credits: Anja Le Blanc Donal Fellows

Holograph Reduced Representation (1)

• Download

After Kanerwa

Created: 2010-06-29

Workflow for Automated Comparative Protein... (2)

• Download

This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

Created: 2010-06-29 | Last updated: 2010-08-31

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree

Macro Propagation into Subprocesses and Ex... (1)

• Download

<p> This small process demonstrates how to propagate macros into a subprocess or Execute Process operator </p> <p> When macros are set once, they are available in subprocesses imediatly (see Generate Attributes in the seconde Subprocess operator) </p> <p> If someone wants to propagate a macro into a Excecute Process operator one need to edit the "macros" parameter in the Parameters list of the Execute Process operator. </p> Tags: Subprocess, Execute Proc...

Created: 2010-06-25

View Download

OPM graph in RDF format for PC1_B workflow with same...

Created: 2010-06-25 01:10:59

Credits: Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: RDF data

Comments: 0 | Viewed: 47 times | Downloaded: 38 times

This File has no tags!

Resolve an InChIKey on ChemSpider (1)

• Download

 Resolves an InChIKey on ChemSpider and opens the search results in a molecules table.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Downloads all Bioclipse Scripting Language... (1)

• Download

 Downloads all Bioclipse Scripting Language scripts uploaded to MyExperiment into the Bioclipse workspace, and opens them in JavaScript editors.

Created: 2010-06-23 | Last updated: 2010-06-23

Credits: Egon Willighagen

Syntetic population mapper (3)

• Download

This workflow creates individual-level population from census data and then joins with the BHPS (British Household Panel Survey) and reaggregates. In the last stage it maps the chosen BHPS field.

Created: 2010-06-23 | Last updated: 2010-12-09

Credits: Alex Nenadic

Pre process data per group using recall re... (1)

• Download

This process takes as input a dataset with different groups. For each group it discretises attributes into High, Medium, Low. This creates a group invariant representation.

Created: 2010-06-23 | Last updated: 2010-06-23

Discretization into Deviation Interval aro... (1)

• Download

This process shows how numerical attributes can be discretized into intervals based on the standard deviation for each attribute around their mean values.

Created: 2010-06-22 | Last updated: 2010-06-22

View Download

test

Created: 2010-06-22 14:27:37 | Last updated: 2010-08-18 16:46:31

2 items in this pack

Comments: 0 | Viewed: 21 times | Downloaded: 11 times

View Download

PC1 mockup part A

Created: 2010-06-21 09:42:44 | Last updated: 2010-06-21 16:17:25

2 items in this pack

Comments: 0 | Viewed: 40 times | Downloaded: 43 times

This Pack has no tags!

Finding all Examples that have duplicate v... (1)

• Download

This process will retrieve all examples, who have identical values in a specific attribute. For testing, the following data can be writen into the file, that will be read by the Read CSV operator: CID,Value 3596,X 4054,X 4054,X 3000,S 3000,T 3000,U 32135,S The target of this process is to return the two examples having the same value in the CID column. To achieve this, first a real id is generated by the generate id. After this, we have to find all duplicates: For this we first remove dupl...

Created: 2010-06-18

Optimizing Discretization (1)

• Download

This process generates a decision tree on the Iris data set. Before the decision tree is generated, the input attributes are discretised so we only work on nominal attributes. We use a combination of "Select Subprocess" and "Optimize Parameters" to select the best out of five different discretizazion methods independently for each of the attributes. The process shows, that the resulting accuracy heavily depends on the choice of the method. It varies between 64% and 94%.

Created: 2010-06-18 | Last updated: 2010-06-18

Phylogenetic Study Using the Bio Extract S... (2)

• Download

This workflow, created using the BioExtract Server, contains a nucleotide query (using the NCBI Core Nucleotide Database), Blastn (against the Homo sapiens genome), Blastn (against the Mus musculus genome), the Format Conversion tool, the Fetch Translator Tool, and ClustalW. This workflow was created following the analytical steps described in the journal article "Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced the...

Created: 2010-06-17 | Last updated: 2010-07-19

Credits: Kendra Giesey BioExtract Server for Genomics

SDS-Page Gel (1)

• Download

Created: 2010-06-17 | Last updated: 2010-06-17

Credits: http://thebluerhino.myopenid.com/

View Download

COMAD20_API_Specification

Created: 2010-06-17 06:41:56 | Last updated: 2010-06-17 06:41:57

Credits: Leidou

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-zip-compressed

Comments: 0 | Viewed: 64 times | Downloaded: 72 times

View Download

Comad20_User_Manual

Created: 2010-06-16 22:30:44 | Last updated: 2010-06-16 22:40:19

Credits: Leidou

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 48 times | Downloaded: 82 times

Unbiasing procedure (1)

• Download

It is a workflow for description of our unbiasing procedure that is used in LiquidPub project,  "Peer Review and Reviewer Behavior" branch. The procedure is used  for conducting experiments on conference data.

Created: 2010-06-16 | Last updated: 2010-06-16

Credits: Katsiaryna Mirylenka

Preprocessing nominal data for frequent it... (1)

• Download

This process will first create artificial data that can be compared to usual data loaded for frequent item set mining: Nominal Data with a true and false value, but differently mapped to internal indices. For ItemSet Mining these must be preprocessed to avoid problems: First they have to be transformed to Binominal Attributes, then it has to be defined, which is the positive and the negative value.

Created: 2010-06-16 | Last updated: 2010-06-16

PI_Calculation (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

View Download

comad biomoby demo workflow

Created: 2010-06-15 19:48:35 | Last updated: 2010-06-15 19:48:51

2 items in this pack

Comments: 0 | Viewed: 39 times | Downloaded: 22 times

BioMoby_PhylogeneticTree (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

BioMoby_Blast (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

View Download

comad simple demo workflow

Created: 2010-06-15 19:40:19 | Last updated: 2010-06-15 19:41:35

8 items in this pack

Comments: 0 | Viewed: 43 times | Downloaded: 28 times

Statistic_XmlInputFormat (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

Statistic_UserDefinedType (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

Statistic_TypeAlias (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

Statistic_portReference (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou

Statistic_filter (1)

• Download

Created: 2010-06-15 | Last updated: 2010-06-15

Credits: Leidou