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Former countries

Created: 2015-05-05 12:43:01

Credits: Magnus Palmblad Arzu Tugce Guler

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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ISO 3166-1 and ISO 3166-3

Created: 2015-05-05 12:39:15

Credits: Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Excel workbook

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compare_pubmed_results_geographically (1)

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This workflow analyzes the scientific output, as documented by PubMed, geographically. The workflow takes as input the PubMed data in XML and the ISO 3166-1 and ISO 3166-3 country lists. The XML file can contain any subset from a specific PubMed search. The XPath components extract author affiliations, and feed these to a series of Beanshell components that match these with countries in the ISO standard. This data is then fed to an Rshell using the rworldmap R package to map the affiliation ...

Created: 2015-05-05 | Last updated: 2015-05-05

Credits: Magnus Palmblad Arzu Tugce Guler Bibliometrics and Scientometrics

Attributions: ISO 3166-1 and ISO 3166-3 Former countries

Using Graph Kernels for Feature Generation... (1)

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This example shows how to use graph kernels for feature generation.In this example we use the Root RDF Walk Count Kernel, and the Fast RDF WL Sub Tree Kernel.The input data for the process can be found here.More information about the process can be found here.

Created: 2015-05-04 | Last updated: 2015-05-04

Prioritize gene list for the Cure game (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. Here we are prioritizing a gene list against breast cancer, in order to try to beat Barney in the game The Cure (http://genegames.org/cure/). Note: Before running this workflow the gene names supplied in the game first needs to be mapped to Entrez gene identifiers. This can be done using either this workflow http://www.myexperiment.org/workflows/3722 or a by performing a search in the NCBI Entrez gene d...

Created: 2015-04-29

Credits: Kristina Hettne Eleni

Attributions: Prioritize gene list

Answer to biostar https://www.biostars.org... (1)

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My answer to https://www.biostars.org/p/138848/ Question: How to replace a set of sequence ID's with another set of sequence ID's ?? Let us consider I have a file (Notepad or MS-doc) having 10 sequences with ID's A, B, C, D, E, F, G, H, I, J. I want to replace the ID's with K, L, M, N, O ,P, Q, R, S, T i.e., A to re replaced with K, B to be replaced with M and so on. How can I do this? I am a Biologist who have newly started analyzing Large data's and having this prob...

Created: 2015-04-20 | Last updated: 2015-04-20

Credits: PL

All-vs-All blastP commands (1)

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Creates all the necessary command-line commands to execute all-vs-all blastP from the given FASTA files. Includes making the necessary database. Does not execute the commands.  For OSX and UNIX/Linux only (due to path separator).

Created: 2015-04-17

Credits: Aurora Cain

Species of top BLAST hits (1)

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Galaxy workflow for counting species of top BLAST hits.This is an example workflow using the Galaxy wrappers for NCBI BLAST+, see https://github.com/peterjc/galaxy_blast and http://dx.doi.org/10.1101/014043This Galaxy workflow (file blast_top_hit_species.ga) is intended for an initial assessment of a transcriptome assembly to give a crude indication of any major contamination present based on the species of the top BLAST hit of 1000 representative sequences.Development of this workflow is und...

Created: 2015-04-08 | Last updated: 2015-04-08

Credits: Peter Cock

example if-the-else (1)

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Created: 2015-04-08

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Genotype-phenotype knowledge discovery using the Con...

Created: 2015-04-07 18:38:40 | Last updated: 2015-04-07 18:44:49

5 items in this pack

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Create nanopublications (1)

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This workflow creates nanopublications for a gene list that is associated to Huntington's Disease

Created: 2015-04-03

Credits: Eleni BioSemantics

Attributions: create nanopublications converter_nanopublications

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converter_nanopublications

Created: 2015-04-03 21:08:40

Credits: Eleni BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-ruby

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create nanopublications

Created: 2015-04-03 21:05:56

Credits: Eleni BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: application/x-ruby

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Prioritize gene list (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. In our example here we are prioritizing a gene list to obtain genes that are more closely associated to huntingtin, the cause of huntington's disease

Created: 2015-04-03

Credits: Eleni BioSemantics

List Concept Sets (1)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Created: 2015-04-03

Credits: Eleni BioSemantics

Explain score between two concepts (1)

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Purpose of workflow: This workflow takes two ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage...

Created: 2015-04-03

Credits: Eleni BioSemantics

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Multiple selection

Created: 2015-03-31 11:23:55 | Last updated: 2015-03-31 11:37:25

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: htm

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myExperiment.test

Created: 2015-03-20 19:45:13 | Last updated: 2015-03-20 20:15:02

Credits: Richard Marchese Robinson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

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Galaxy workflow for the identification of ... (1)

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This approach screens three proteins against a given genome sequence, leading to a genome position were all three genes are located nearby. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby

Created: 2015-03-17

Credits: Björn Grüning

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A Preliminary Study of Ichthyofauna of Kukulugala Fo...

Created: 2015-03-04 15:02:07 | Last updated: 2015-03-04 15:03:52

Credits: HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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A new record of endangered Jonklaas Loach Lepidoceph...

Created: 2015-03-04 14:57:16

Credits: HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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SOME OBSERVATIONS OF Cnemaspis podihuna DERANIYAGALA...

Created: 2015-03-04 14:50:51

Credits: HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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SOME OBSERVATIONS OF NESTING BEHAVIOR OF RUFOUS-BELL...

Created: 2015-03-04 14:47:35

Credits: HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2015-02-18

Credits: Eelke van der Horst Kristina Hettne Marco Roos Eleni

Attributions: Get concept suggestions from term

North - Chapter 11 process (1)

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Testing myExperiment.org

Created: 2015-02-11