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Showing 4527 results. Use the filters on the left and the search box below to refine the results.
Taverna 2
Uploader
2820?size=60x60 Gb Kalai

Workflow Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

RapidMiner
Uploader
2640?size=60x60 Pl Mikolaj Morzy

Workflow Algorytm EM (1)

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Proces pokazuje przypadek wykorzystania algorytmu analizy skupien dzialajacego wedlug zasady expectation maximization (EM), czyli dopasowywania rozkladow do obserwowanego zbioru danych.

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

RapidMiner
Uploader
2640?size=60x60 Pl Mikolaj Morzy

Workflow Algorytm DBScan (1)

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Przeplyw ilustruje sposob wykorzystania algorytmu DBScan do znalezienia modelu skupien. Algorytm DBScan jest przykladem algorytmu bazujacego na gestosci, parametr epsilon wskazuje na promien sasiedztwa, a parametr min points wskazuje na minimalna liczbe punktow, jakie musza sie znalezc w sasiedztwie punktu aby kontynuowac rozrastanie sie skupienia.

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

RapidMiner
Uploader
2640?size=60x60 Pl Mikolaj Morzy

Workflow Wybor parametru k dla algorytmu k-Means (1)

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Proces pokazuje, w jaki sposob mozna eksperymentalnie dobrac wlasciwe wartosci parametru k (liczba poszukiwanych skupien) dla algorytmow k-Means i k-Medoids. Jako miary oceny podzialu wykorzystano srednia odleglosc od centroidu oraz indeks Daviesa-Bouldina

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

RapidMiner
Uploader
2640?size=60x60 Pl Mikolaj Morzy

Workflow Wybor poczatkowego podzialu dla algorytmu ... (1)

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Proces pokazuje, w jaki sposob mozna zautomatyzowac proces znajdowania najlepszego poczatkowego wyboru centroidow uniezalezniajac sie (do pewnego stopnia) od wplywu losowania.

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

Taverna 2
Uploader
1253?size=60x60 Gb Anja Le Blanc

Workflow MDES simple execution (2)

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workflow to query MDES, obtaining the DES results and from it extracting the VOTable and the PNG plot for the time range queried.

Created: 2011-03-02 | Last updated: 2014-03-12

Credits: User Anja Le Blanc

Taverna 2
Uploader
1253?size=60x60 Gb Anja Le Blanc

Workflow Extract content of columns from VOTables (3)

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Extracts all values from all columns which are passed from the input ColumnNames

Created: 2011-02-24 | Last updated: 2012-08-20

Credits: User Anja Le Blanc

Taverna 2
Uploader
58?size=60x60 Simon Jupp

Workflow miRNA GFF to entrez gene (1)

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This workflow reads a GFF file of miRNA cooridinates and uses BioMart to search human ensemble genes for the gene that codes for the miRNA. The workflow returns a list of miRNAid, chromosome, start, stop, strand, entrez gene id, gene name, gene strand. Example input file here: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff

Created: 2011-01-26 | Last updated: 2012-01-11

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow EMBL-EBI ClustalW2_SOAP (2)

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Perform a ClustalW2 alignment of protein sequences using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2011-01-17 | Last updated: 2013-01-30

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EMBL-EBI ClustalW2 (SOAP) Workflow EBI_ClustalW2

Taverna 2
Uploader
Avatar De Andreas Truszkowski

Workflow Weka Clustering With Silhouette Analysis A... (2)

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This workflow clusters given QSAR CSV file and performs a silhouette analysis which is visualised in a PDF file. The QSAR data is loaded from a CSV file and converted into a Weka dataset. After that the data is clustered and the results are visualised in a PDF file.

Created: 2011-01-13 | Last updated: 2011-07-21

Taverna 1
Uploader
394?size=60x60 Gb Hamish McWilliam

Workflow InterProScan (SOAP) (1)

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

Created: 2010-12-03 | Last updated: 2013-03-28

Credits: User Hamish McWilliam

Attributions: Workflow EBI_InterProScan Workflow InterProScan (SOAP)

Taverna 2
Uploader
394?size=60x60 Gb Hamish McWilliam

Workflow InterProScan (SOAP) (1)

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

Created: 2010-12-03 | Last updated: 2013-03-28

Attributions: Workflow EBI_InterProScan

Taverna 1
Uploader
394?size=60x60 Gb Hamish McWilliam

Workflow NCBI BLAST (SOAP) (1)

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Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Created: 2010-11-29 | Last updated: 2013-03-28

Credits: User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST Workflow NCBI BLAST (SOAP)

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Get image URLs from HTTP document and outp... (2)

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Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

Created: 2010-10-29 | Last updated: 2014-02-12

RapidMiner
Uploader
1069?size=60x60 De Sebastian land

Workflow Using Remember / Recall for "tunneling" re... (1)

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This process shows how Remeber and Recall operators can be used for passing results from one position to another position in the process, when it's impossible to make a direct connection. This process introduces another advanced RapidMiner technique: The macro handling. We have used the predefined macro a, accessed by %{a}, that gives the apply count of the operator. So we are remembering each application of the models that are generated in the learning subprocess of the Split validation. Af...

Created: 2010-04-29 | Last updated: 2012-01-16

Uploader
688?size=60x60 Us M. Kirsh
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Blob The Path of Knowledge ; The Knowledge of Path - New ...

Created: 2010-03-31 05:35:36

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract   An unwitnessible silence is suggested to accompany all change. Conceptual paradox involving mind and matter, contrasting mind as an enduring state of the becoming of energy into a state of matter, and matter as the constantly becoming environment, is tested against criteria of witnessibility with respect to criteria for the existence of entities and phenomenon for consistency to capture an acceptably reasoned description, from a modern perspective, of cultural evolution....

File type: Adobe PDF

Comments: 0 | Viewed: 55 times | Downloaded: 42 times

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Uploader
469?size=60x60 Gb Paolo
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Blob EDBT Provenance talk presentation - PFD version

Created: 2010-03-26 14:01:00 | Last updated: 2010-03-26 14:02:09

Credits: User Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

PDF version -- see related pack for Native Keynote link to paper link to conference proceedings  

File type: application/unknown

Comments: 0 | Viewed: 52 times | Downloaded: 27 times

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Taverna 2
Uploader
Avatar Gb Andrew David King

Workflow Test for Orthologues (1)

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Warning: The files are hardcoded in to the beanshell of this workflow. Given an orthlog file for an organism from http://www.ebi.ac.uk/integr8/FtpSearch.do? orgProteomeId=22602, find proteins that are orthologous to proteins in another oragnsims, e.g., B.subtils. Outputs percent.

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Taverna 2
Uploader
Avatar Gb Andrew David King

Workflow Fetch Fasta and Genbank files (1)

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Fetches fasta and genbank files for a given identifier., e.g., CP000256

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Taverna 2
Uploader
Avatar Gb Andrew David King

Workflow Fetch EMBL File (1)

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Fetches an EMBL file using the EMBL id. Creates file to a specified location.

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Taverna 2
Uploader
Avatar Paul Miller

Workflow Square A List Of Numbers (1)

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Simple workflow which squares a list of numbers.

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

Credits: User Paul Miller

Uploader
Avatar Architpuri
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Blob test

Created: 2010-03-08 14:43:10

Credits: User Architpuri

License: Creative Commons Attribution-Share Alike 3.0 Unported License

test

File type: Plain text

Comments: 8 | Viewed: 32 times | Downloaded: 21 times

This File has no tags!

Uploader
688?size=60x60 Us M. Kirsh
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Blob THE PATH OF KNOWLEDGE : KNOWLEDGE OF THE PATH

Created: 2010-02-22 00:21:43

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract       The philosophies of Parmenides, Socrates, Aristotle, the science of Einstein is discussed with respect to a division of the empirical and abstracted as they refer to the universe and universals. Methodologies of the natural and anthropological sciences are contrasted  in order to discuss validity in the representation of nature. A physical model for the evolution of knowledge is presented that distinguishes both the conceptual and physical in terms of...

File type: Adobe PDF

Comments: 0 | Viewed: 68 times | Downloaded: 67 times

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688?size=60x60 Us M. Kirsh
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Blob Introduction to My Presented Works-Marvin E. Kirsh

Created: 2010-02-15 01:10:45 | Last updated: 2010-02-15 04:40:32

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

    An introductory  background and stated approach with initial assumptions employed towards the creation of my manuscripts and ideas.  My notions reflect a naturalism,  with a slant oriented from the realism of perception, away from abstracted theory that is given its' only validity from empirical test rather than direct first person witness. I began this project as a graduate student in the biological sciences with a statement from a professor of classical g...

File type: Adobe PDF

Comments: 0 | Viewed: 49 times | Downloaded: 21 times

This File has no tags!

Uploader
688?size=60x60 Us M. Kirsh
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Blob Physical Contiguity of "The Concept" : The Concept o...

Created: 2010-02-05 03:37:55 | Last updated: 2010-02-05 19:31:11

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract It is an entity of nature,  the human conceiver that emerges ?the concept?. It might be conjectured that in order for  a human  conceiver to conceive a concept of ?the concept?, as a subset of nature, first he must have a concept of nature with which to commence investigation into the nature of ?the  concept?.  Second,  the nature of ?the concept? might be expected to be an emergence from the individuals? concept of nature; in essence to reflect a conce...

File type: Adobe PDF

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Taverna 1
Uploader
Avatar It Achille Zappa

Workflow Search TP53 Somatic Mutation catalogue by ... (1)

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This workflow takes the intron, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs: - first output: a TP53 somatic mutation database unique IDs list associated with the input intron (done via a call to the getP53MutationIdsByIntron web service) - second otput: a TP53 somatic mutation database unique IDs list associated with the input effect (done via a call to the getP53MutationIdsB...

Created: 2010-01-15

Credits: User Achille Zappa

Taverna 1
Uploader
Avatar It Achille Zappa

Workflow Get TP53 Mutations By Intron (1)

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This workflow takes the intron and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByIntron web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Special requirements on input data are: - The intron range of numb...

Created: 2010-01-15

Credits: User Achille Zappa

Taverna 1
Uploader
Avatar It Achille Zappa

Workflow Get TP53 Mutations By Exon (1)

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This workflow takes the exon and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByExon web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Special requirements on input data are: - The exon range of numbers is...

Created: 2010-01-15

Credits: User Achille Zappa

Taverna 1
Uploader
Avatar It Achille Zappa

Workflow Get TP53 Mutation Function Entries And TP... (1)

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This workflow retrieves from two different databases two distinct set of entries starting from the same inputs data (i.e. the Mutated Aminoacid encoded at the codon in which the mutation occurred, and the Codon Number where the mutation occurs). Input data: Mutant Amino Acid encoded at the codon in which the mutation occurred and Codon Number where the mutation is located. Special requirements on input data are: - the MutAA (Mutated Amino Acid) in three letters code (Gly, Ala, Trp, Phe etc.)...

Created: 2010-01-15 | Last updated: 2010-01-15

Credits: User Achille Zappa

Uploader
688?size=60x60 Us M. Kirsh
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Blob Uniqueness, Self Belonging and Intercourse in Nature...

Created: 2010-01-09 04:42:06

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract Biological organization is discussed within a holistic framework . A new orientation is presented of natural processes with  an approach in model construction that is focused strictly on physical form and centered away from abstractions that escape the perceptual senses,  lead towards the postulation of non-verifiable and non-witnessible  entities.  A universal construction composed of first perspective representations of path, witness as unique loci in volumes o...

File type: Adobe PDF

Comments: 0 | Viewed: 76 times | Downloaded: 59 times

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688?size=60x60 Us M. Kirsh
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Blob What Happened? Are We Asking or Telling?

Created: 2010-01-02 04:12:38

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract      A conceptual parallel is created between studies in anthropology and natural science.  A  space occupied by “the conceptualization”  is argued to not only parallel  symbolically the scientifically conceived value of volume as space, but to have an equal meaning- the spaces of the conceptual ordering of nature as manifestations of energy are held to be paralleling  manifestations of the same energies that mold the environm...

File type: Adobe PDF

Comments: 0 | Viewed: 51 times | Downloaded: 31 times

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Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch Dragon images from BioMoby (2)

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Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: User EdwardKawas

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow GBSeq test (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch today's xkcd comic (1)

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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: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch PDB flatfile from RCSB server (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Demonstration of configurable iteration (1)

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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: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow BiomartAndEMBOSSAnalysis (1)

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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: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow A workflow version of the EMBOSS tutorial (1)

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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: 2009-12-15

Credits: User Alan Williams

Creator
3791?size=60x60 Gb David De Roure
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Pack Presentation - Socialising e-Science


Created: 2009-12-13 11:01:20 | Last updated: 2011-06-28 17:27:44

Title: Socialising e-Science Speaker: David De Roure Event: IEEE e-Science 2009 Event URL: http://www.escience2009.org/ Location: Oxford, UK Date: Tuesday December 8, 2009 Formats: .ppt and .pptx

3 items in this pack

Comments: 0 | Viewed: 83 times | Downloaded: 18 times

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Creator
3791?size=60x60 Gb David De Roure
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Pack Presentation - Lessons from myExperiment: Two insigh...


Created: 2009-12-13 10:58:37 | Last updated: 2009-12-13 11:06:19

Title: Lessons from myExperiment: Two insights into emerging e-Research practice Speaker: David De Roure Event: UK e-Science All Hands Meeting 2009 Event URL: http://www.allhands.org.uk/ Location: Oxford, UK Date: Monday December 7, 2009 Formats: .ppt and .pptx

2 items in this pack

Comments: 0 | Viewed: 78 times | Downloaded: 19 times

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45?size=60x60 Gb David R Newman
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Blob NeuroHub Presentation to Southampton Neuroscientists

Created: 2009-11-26 11:59:43

Credits: User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This presentation was given on 19th November 2009 to allow the the neuroscientists in Southampton to get an overview of what we NeuroHub intended to do and get feedback to find out what they would and wouldn't find useful.

File type: PowerPoint presentation

Comments: 0 | Viewed: 85 times | Downloaded: 63 times

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Taverna 2
Uploader
Avatar Jorgep

Workflow workflow1 (1)

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blast dando o ID de uma proteinablast dando o ID de uma proteina ex: database is ‘SWISS’, for program, ‘blastp’, and for ID ‘1220173blast dando o ID de uma proteina ex: database is SWISS’, for program, blastp, and for ID 1220173

Created: 2009-11-16

Credits: User Jorgep

Uploader
688?size=60x60 Us M. Kirsh
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Blob Anthropology and Parallelism: The Individual as a Un...

Created: 2009-11-15 19:52:10

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract It is difficult to define perspective within sets that are self belonging. For example in the study of man­kind, anthropology, both men and their studies fall into the same category that contains the topic out­line. This situation entails a universal quality of uniqueness, an instance of it, to the topic of anthropo­logy that may be viewed in parallel with the topic of nature as the set of unique particulars. Yet one might assent to the notion in the inclusive study of m...

File type: Adobe PDF

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324?size=60x60 Gb George
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Pack Portugal Tutorial November 2009


Created: 2009-11-14 17:14:46 | Last updated: 2009-11-16 14:09:29

This is a pack containing all files for the collaborative team-building workflow exercise. 

8 items in this pack

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324?size=60x60 Gb George
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Blob Kegg Gene Identifiers

Created: 2009-11-14 16:29:01

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An example file of a list of Kegg gene identifiers used to test searching the Kegg database.

File type: Plain text

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324?size=60x60 Gb George
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Blob Pubmed Identifiers

Created: 2009-11-14 16:23:47

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A list of example pubmed identifers to use when testing abstract retrieval and text-mining workflows

File type: Plain text

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Taverna 2
Uploader
Avatar Nl Bas Vroling

Workflow blastp using the MRS system (1)

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database. Databases that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb".

Created: 2009-11-10

Credits: User Bas Vroling

Uploader
Avatar Gb Andrea
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Blob Very simple script to fix pathway commons biopax files

Created: 2009-11-04 11:05:46

Credits: User Andrea

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This very simple script (it only replace one type of ID!) will fix BioPAX files coming from PathwayCommons. In this files, rdf:ID is used instead of rdf:about, and since these files contains repetition, this results in an error in strict parsers. This error gets undetected in many system as they disable replicated ID checking for performance, but it's still a problem in some.

File type: application/x-perl

Comments: 0 | Viewed: 39 times | Downloaded: 33 times

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