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Modified: websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
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<li><a href="/documentation/#tools">Tools and Services</a></li>
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- <h1>Chemistry Web Services</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>This document describes a set of chemistry services provided by <a href="#chemspider">ChemSpider</a>, <a href="#chebi">ChEBI</a> and <a href="#pubchem">PubChem</a>
- that can be used for the construction of chemistry workflows from the Taverna Workbench.</p>
-<p>Example workflows contained in the document show how some of the operations from the services in the set can
- be invoked.
-They can also be downloaded as part of the <a href="http://www.myexperiment.org/packs/136">Chemistry Workflows pack</a> at myExperiment.</p>
-<p><a name="chemspider"></a></p>
-<h2 id="wzxhzdk2chemspider"><h2>ChemSpider</h2>
-<p><a href="http://www.chemspider.com/">ChemSpider</a> is a chemistry search engine that has been built with the intention of aggregating and indexing
- chemical structures and their associated information into a single searchable repository and making it
- freely available to everybody.</p>
-<p>ChemSpider provides several Web services, and these are listed below together with their WSDL locations.</p>
-<h3 id="inchi-web-service">InChi Web service</h3>
-<p>WSDL: <a href="http://www.chemspider.com/InChI.asmx?WSDL">http://www.chemspider.com/InChI.asmx?WSDL</a></p>
-<p><img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16" height="16" />
-In BioCatalogue: <a href="http://www.biocatalogue.org/services/2164">http://www.biocatalogue.org/services/2164</a></p>
-<p>The InChI Web service provides operations to manipulate InChI Strings and InChIKeys,
- including the conversion to and from the MOL file format, validity checking of InChI identifiers,
- and searching ChemSpider using InChI inputs.</p>
-<p>Some of the Web service’s operations listed below require a “security token”.
-A security token can be obtained by completing the registration process for ChemSpider at
-<a href="http://www.chemspider.com/Register.aspx">http://www.chemspider.com/Register.aspx</a>.</p>
-<p>The following operations are contained within the InChI Web service:</p>
-<ul>
-<li>
-<p>CSIDToMol <br />
- Converts a ChemSpider identifier to a MOL file. A security token is required to get access to this
- service. <br />
-<a href="http://www.myexperiment.org/workflows/1418">Example workflow</a></p>
-</li>
-<li>
-<p>GenerateInChI <br />
- Generates an InChI string for a given chemical represented by its SMILES string, SDF or MOL file. <br />
-<a href="http://www.myexperiment.org/workflows/1387">Example workflow</a></p>
-</li>
-<li>
-<p>GenerateInChIInfo <br />
- Returns information relating to the InChI string for a given chemical compound. <br />
-<a href="http://www.myexperiment.org/workflows/1388">Example workflow</a></p>
-</li>
-<li>
-<p>GenerateInChIKey <br />
- Returns a hashed InChI key which is a fixed length (25 character) condensed digital representation of
- the input InChI string that is not human-understandable. <br />
-<a href="http://www.myexperiment.org/workflows/1389">Example workflow</a></p>
-</li>
-<li>
-<p>InChIKeyToCSID <br />
- Converts an InChI key to a ChemSpider identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1390">Example workflow</a></p>
-</li>
-<li>
-<p>InChIKeyToInChI <br />
- Converts an InChI key to an InChI string. <br />
-<a href="http://www.myexperiment.org/workflows/1391">Example workflow</a></p>
-</li>
-<li>
-<p>InChIKeyToMol <br />
- Converts an InChI key to a MOL file. <br />
-<a href="http://www.myexperiment.org/workflows/1392">Example workflow</a></p>
-</li>
-<li>
-<p>InChIToCSID <br />
- Convets an InChI string to a ChemSpider identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1393">Example workflow</a></p>
-</li>
-<li>
-<p>InChIToInChIKey <br />
- Converts an InChI string to an InChI key. This only works for 1.02b InChI strings. <br />
-<a href="http://www.myexperiment.org/workflows/1394">Example workflow</a></p>
-</li>
-<li>
-<p>InChIToMol <br />
- Converts an InChI string to a MOL file. Uses <a href="http://openbabel.org/wiki/Main_Page">OpenBabel</a> internally to perform this operation. <br />
-<a href="http://www.myexperiment.org/workflows/1395">Example workflow</a></p>
-</li>
-<li>
-<p>InChIToSMILES <br />
- Converts an InChI string to a SMILES string. Uses <a href="http://openbabel.org/wiki/Main_Page">OpenBabel</a></a> internally to perform this operation. <br />
-<a href="http://www.myexperiment.org/workflows/1396">Example workflow</a></p>
-</li>
-<li>
-<p>IsValidInChIKey <br />
- Checks that an InChI key is valid. Works only for v1.02b InChI keys. <br />
-<a href="http://www.myexperiment.org/workflows/1397">Example workflow</a></p>
-</li>
-<li>
-<p>MolToInChI <br />
- Converts a MOL file into an InChI string (v1.02s). <br />
-<a href="http://www.myexperiment.org/workflows/1398">Example workflow</a></p>
-</li>
-<li>
-<p>MolToInChIKey <br />
- Converts a MOL file into an v1.02s InChI key. <br />
-<a href="http://www.myexperiment.org/workflows/1399">Example workflow</a></p>
-</li>
-<li>
-<p>ResolveInChIKey <br />
- This operation does not work at the moment. ChemSpider have been notified of the problem.</p>
-</li>
-<li>
-<p>SMILESToInChI <br />
- Converts a SMILES string to an InChI string. The result is returned as a v1.02s InChI string. <br />
-<a href="http://www.myexperiment.org/workflows/1400">Example workflow</a></p>
-</li>
-</ul>
-<h3 id="openbabel-web-service">OpenBabel Web service</h3>
-<p>WSDL: <a href="http://www.chemspider.com/OpenBabel.asmx?WSDL">http://www.chemspider.com/OpenBabel.asmx?WSDL</a></p>
-<ul>
-<li>convert <br />
- Converts a molecule represented in one format to another.
- For a list of valid format values, please visit <a href="http://openbabel.org/wiki/Category:Formats">openbabel</a>.
- An empty string is returned in case of failure. <br />
-<a href="http://www.myexperiment.org/workflows/1401">Example workflow</a></li>
-</ul>
-<h3 id="mass-spec-api-web-service">Mass spec API Web service</h3>
-<p>WSDL: <a href="http://www.chemspider.com/MassSpecAPI.asmx?WSDL">http://www.chemspider.com/MassSpecAPI.asmx?WSDL</a> <br />
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16" height="16" />
-In BioCatalogue: <a href="http://www.biocatalogue.org/services/2040">http://www.biocatalogue.org/services/2040</a></p>
-<ul>
-<li>
-<p>GetCompressedRecordsSdf <br />
- Returns a SDF file containing records of compounds found by an asynchronous search operation.
- A security token associated with ‘Service Subscriber’
- role is required to access this operation. <br />
- Example workflow not available since a ‘Service Subscriber’ role is required by the user.</p>
-</li>
-<li>
-<p>GetDatabases <br />
- Returns a list of datasources in ChemSpider. <br />
-<a href="http://www.myexperiment.org/workflows/1404">Example workflow</a></p>
-</li>
-<li>
-<p>GetExtendedCompoundInfo <br />
- Returns extended record details for a given ChemSpider identifier.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1405">Example workflow</a></p>
-</li>
-<li>
-<p>GetExtendedCompoundInfoArray <br />
- Returns an array of extended record details from an array of ChemSpider identifiers.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1406">Example workflow</a></p>
-</li>
-<li>
-<p>GetRecordMol <br />
- Returns a ChemSpider record in MOL format or an empty string in case of failure.
- The cacl3d parameter specifies whether 3D coordinates should be calculated before returning record data.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1407">Example workflow</a></p>
-</li>
-<li>
-<p>GetRecordsSdf <br />
- Returns a SDF file containing records found by an asynchronous search operation.<br />
- A security token associated with the ‘Service Subscriber’
- role is required to access this operation. <br />
- Example workflow not available since a Service Subscriber role is required by the user.</p>
-</li>
-<li>
-<p>SearchByFormula <br />
- Search ChemSpider compounds by molecular formula within a specified list of datasources.
- This operation is deprecated and will be removed soon – use SearchByFormulaAsync instead. <br />
- Example workflow not available since this operation is deprecated.</p>
-</li>
-<li>
-<p>SearchByFormula2 <br />
- Search ChemSpider compounds by molecular formula. <br />
- Example workflow not available since this operation is deprecated.</p>
-</li>
-<li>
-<p>SearchByFormulaAsync <br />
- Searches ChemSpider compounds by molecular formula within a specified datasources list.
- Security token is required to get access to this service. <br />
-<a href="http://www.myexperiment.org/workflows/1420">Example workflow</a></p>
-</li>
-<li>
-<p>SearchByMass <br />
- Searches ChemSpider compounds by mass +/- range within specified datasources list.
- This operation is deprecated and will be removed soon – use SearchByMassAsync instead. <br />
- Example workflow not available since this operation is deprecated.</p>
-</li>
-<li>
-<p>SearchByMass2 <br />
- Search ChemSpider compounds by mass +/- range. <br />
- Example workflow not available since this operation is deprecated.</p>
-</li>
-<li>
-<p>SearchByMassAsync <br />
- Searches ChemSpider compounds by mass +/- range within a specified datasources list.
- A security token is required to access this service.</p>
-</li>
-</ul>
-<h3 id="spectra-web-service">Spectra Web service</h3>
-<p>WSDL: <a href="http://www.chemspider.com/Spectra.asmx?WSDL">http://www.chemspider.com/Spectra.asmx?WSDL</a></p>
-<ul>
-<li>
-<p>GetAllSpectraInfo <br />
- Returns information for all open access spectra in ChemSpider <br />
-<a href="http://www.myexperiment.org/workflows/1408">Example workflow</a></p>
-</li>
-<li>
-<p>GetCompoundSpectraInfo <br />
- Returns information about spectra associated with a particular compound identified by the cmp_id parameter <br />
-<a href="http://www.myexperiment.org/workflows/1409">Example workflow</a></p>
-</li>
-<li>
-<p>GetSpectrumInfo <br />
- Returns information about a particular spectrum identified by its spc_id parameter <br />
-<a href="http://www.myexperiment.org/workflows/1410">Example workflow</a></p>
-</li>
-</ul>
-<h3 id="compound-search-web-service">Compound search Web service</h3>
-<p>WSDL: <a href="http://www.chemspider.com/Search.asmx?WSDL">http://www.chemspider.com/Search.asmx?WSDL</a> <br />
-<img src="/pages/wp-content/uploads/2010/07/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16" height="16" /> In BioCatalogue: </span><a href="http://www.biocatalogue.org/services/1932" target="_blank">http://www.biocatalogue.org/services/1932</a></p>
-<ul>
-<li>
-<p>AsyncSimpleSearch <br />
- Searches for molecules based on the entered search terms.
- The operation returns a transaction ID which can be used to access the status of the search and results.
- A security token is required to access this service. <br />
- The result of this operation is a hash number which can be used to retrieve the actual results using
- the GetAsyncSearchResult operation below. <br />
-<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
-</li>
-<li>
-<p>CSID2ExtRefs <br />
- Returns a list of external references (data sources) for a given compound.<br />
- A security token with the relevant role is required to access this service.</p>
-</li>
-<li>
-<p>GetAsyncSearchResult <br />
- Returns a list of identifiers found by the asynchronous search operation.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
-</li>
-<li>
-<p>GetAsyncSearchStatus <br />
- Queries the asynchronous operation status.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1411">Example workflow</a></p>
-</li>
-<li>
-<p>GetCompoundInfo <br />
- Returns the record details (CSID, InChIKey, InChI, SMILES) of a molecule by its ChemSpider identifier.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1412">Example workflow</a></p>
-</li>
-<li>
-<p>GetCompoundThumbnail <br />
- Returns an image of a molecule’s 2D structure in PNG format.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1414">Example workflow</a></p>
-</li>
-<li>
-<p>GetRecordDetails <br />
- Returns a record details: CSID, InChIKey, InChI, SMILES.
- This operation is deprecated and will be removed soon – use GetCompoundInfo instead. <br />
- No example workflow due to deprecation of this operation.</p>
-</li>
-<li>
-<p>GetRecordImage <br />
- Returns an image of a molecule’s structure in PNG format.
- This operation is deprecated and will be removed soon – use GetCompoundThumbnail instead. <br />
- No example workflow due to deprecation of this operation.</p>
-</li>
-<li>
-<p>Mol2CSID <br />
- Searches for structures matching a given MOL file within a given range.
- Returns a list of ChemSpider identifiers associated with matching structures.
- A security token with the ‘specific’ role is required to access this service. <br />
- No example workflow due to specific role required for the operation.</p>
-</li>
-<li>
-<p>MolAndDS2CSID <br />
- Searches for structures matching a given MOL file within the range specified by search options and
- within the specified list of datasources.<br />
- Returns a list of ChemSpider identifiers.
- A security token with the ‘specific’ role is required to access this service. <br />
- No example workflow due to specific role required for the operation.</p>
-</li>
-<li>
-<p>SimpleSearch <br />
- Performs a search using a given set of terms. Returns a list of ChemSpider identifiers.
- A security token is required to access this service. <br />
-<a href="http://www.myexperiment.org/workflows/1427">Example workflow</a></p>
-</li>
-<li>
-<p>SimpleSearch2IdList <br />
- Tries to find whatever is entered.
- Returns a list of ChemSpider IDs.
- This operation is deprecated and will be removed soon – use SimpleSearch instead. <br />
- No example workflow due to deprecation of this operation.</p>
-</li>
-</ul>
-<h3 id="synonyms">Synonyms</h3>
-<p>WSDL: <a href="http://www.chemspider.com/Synonyms.asmx?WSDL">http://www.chemspider.com/Synonyms.asmx?WSDL</a></p>
-<ul>
-<li>GetStructureSynonyms <br />
- Returns synonym names for a given compound represented by its MOL file. <br />
-<a href="http://www.myexperiment.org/workflows/1415">Example workflow</a></li>
-</ul>
-<p><a name="chebi"></a></p>
-<h2 id="chebi">ChEBI</h2>
-<p>Chemical Entities of Biological Interest (<a href="http://www.ebi.ac.uk/chebi/">ChEBI</a>) is a freely available database of molecular entities
- focused on ‘small’ chemical compounds.<br />
-The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule,
- ion, ion pair, radical, radical ion, complex or conformer, identifiable as a separately distinguishable
- entity.
-ChEBI incorporates an ontological classification, whereby the relationships between molecular entities or
- classes of entities and their parents and/or children are specified.</p>
-<p>ChEBI provides the following Web service with 7 operations.
-WSDL: <a href="http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl">http://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl</a> <br />
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16" height="16" />
-In BioCatalogue: <a href="http://www.biocatalogue.org/services/2174">http://www.biocatalogue.org/services/2174</a></p>
-<ul>
-<li>
-<p>getLiteEntity <br />
- Retrieves a list of “lite” entities containing only the ChEBI ASCII name and ChEBI identifier.
- The input parameters are a search string and a search category.
- If the search category is null then it will search under all fields.
- The search string accepts the wildcard character “*” and also unicode characters.
- A maximum 5000 entries can be retrieved at a time. <br />
-<a href="http://www.myexperiment.org/workflows/1419">Example workflow</a></p>
-</li>
-<li>
-<p>getCompleteEntity <br />
- Retrieves the complete record of a molecule including synonyms, database links and chemical structures,
- using the ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1421">Example workflow</a></p>
-</li>
-<li>
-<p>getCompleteEntityByList <br />
- Given a list of ChEBI accession numbers,
- retrieves the complete entity record associated with each accession number.<br />
- The maximum size of a given list is 50. <br />
-<a href="http://www.myexperiment.org/workflows/1422">Example workflow</a></p>
-</li>
-<li>
-<p>getOntologyParents <br />
- Retrieves the ontology parents of an entity including the relationship type, using a ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1423">Example workflow</a></p>
-</li>
-<li>
-<p>getOntologyChildren <br />
- Retrieves the ontology children of an entity including the relationship type, using a ChEBI identifier. <br />
-<a href="http://www.myexperiment.org/workflows/1424">Example workflow</a></p>
-</li>
-<li>
-<p>getAllOntologyChildrenInPath <br />
- Retrieves the ontology children of an entity including the relationship type, using a ChEBI identifier. <br />
- No example workflow available.</p>
-</li>
-<li>
-<p>getStructureSearch <br />
- Does a substructure, similarity or identity search using a query structure. <br />
-<a href="http://www.myexperiment.org/workflows/1426">Example workflow</a></p>
-</li>
-</ul>
-<p><a name="pubchem"></a></p>
-<h2 id="pubchem">PubChem</h2>
-<p><a href="http://pubchem.ncbi.nlm.nih.gov/">PubChem</a> is a free database of chemical structures of small organic molecules and information on
- their biological activities provided by the National Center for Biotechnology Information (<a href="http://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information">NCBI</a>),
- part of the United States National Institutes of Health (<a href="http://en.wikipedia.org/wiki/National_Institutes_of_Health">NIH</a>).</p>
-<p>PubChem provides the following Web service with 28 operations.
-WSDL: <a href="http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl">http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl</a>
-<img src="/img/biocatalogue-smallcog.png" alt="BioCatalogue icon" width="16" height="16" />
-In BioCatalogue: <a href="http://www.biocatalogue.org/services/2176">http://www.biocatalogue.org/services/2176</a></p>
-<ul>
-<li>
-<p>AssayDownload <br />
- Given an assay key, prepares a file for download which contains an assay data table in the selected format.
- See the assay query section of the PUG service documentation
- (<a href="http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html">http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html</a>) for more details on the supported formats.
- Compression is optional and defaults to gzip (.gz). Returns a download key. Asynchronous.</p>
-</li>
-<li>
-<p>Download <br />
- Given a list key, prepares a file for downloading which contains those records in the selected format.
- See the web download service documentation
- (<a href="http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html">http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html</a>)
- for more detail on the supported formats and file types.
- Returns a download key. Asynchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1435">Example workflow</a></p>
-</li>
-<li>
-<p>GetAssayColumnDescription <br />
- Returns the description of a column (readout) in a BioAssay, which may be the outcome, score,
- or a TID from the given AID. Synchronous.</p>
-</li>
-<li>
-<p>GetAssayColumnDescriptions <br />
- Returns the description of all columns (readouts) in a BioAssay. Synchronous.</p>
-</li>
-<li>
-<p>GetAssayDescription <br />
- Returns the descriptive information for a BioAssay, including the number of user-specified readouts (TIDs)
- and whether a score readout is present.<br />
- Optionally get version information. Synchronous.</p>
-</li>
-<li>
-<p>GetDownloadUrl <br />
- Given a download key, returns an FTP URL that may be used to download the requested file. Synchronous.</p>
-</li>
-<li>
-<p>GetEntrezKey <br />
- Given a list key, returns an Entrez history key (db, query key, and WebEnv) corresponding to that list.
- Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
-</li>
-<li>
-<p>GetEntrezUrl <br />
- Given an Entrez history key (db, query key, and WebEnv), returns an HTTP URL that may be used to view the
- list in Entrez. Synchronous.
- <a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
-</li>
-<li>
-<p>GetIDList <br />
- Given a list key, returns the identifiers as an array of integers. Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
-</li>
-<li>
-<p>GetListItemsCount <br />
- Returns the number of IDs in the set represented by a given list key. Synchronous.</p>
-</li>
-<li>
-<p>GetOperationStatus <br />
- Given a key for any asynchronous operation, returns the status of that operation.
- Possible return values are: Success, the operation completed normally; HitLimit, TimeLimit: the operation
- finished normally, but one of the limits was reached (e.g. before the entire database was searched);
- ServerError, InputError, DataError, Stopped: there was a problem with the input or on the server,
- and the job has died; Queued: the operation is waiting its turn in the public queue; Running:
- the operation is in progress. Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
-</li>
-<li>
-<p>GetStandardizedCID <br />
- Given a structure key that has been processed by Standardize, returns the corresponding PubChem Compound
- database CID, or an empty value if the structure is not present in PubChem. Synchronous.</p>
-</li>
-<li>
-<p>GetStandardizedStructure <br />
- Given a structure key that has been processed by Standardize, returns the chemical structure in as SMILES
- or InChI strings. Synchronous.</p>
-</li>
-<li>
-<p>GetStandardizedStructureBase64 <br />
- Given a structure key that has been processed by Standardize, returns the chemical structure as ASN, XML,
- or SDF, returned as a Base64-encoded string. Synchronous.</p>
-</li>
-<li>
-<p>GetStatusMessage <br />
- Given a key for any asynchronous operation, returns any system messages (error messages, job info, etc.)
- associated with the operation, if any. Synchronous.</p>
-</li>
-<li>
-<p>IdentitySearch <br />
- Searches PubChem Compound for structures identical to the one given by the structure key input based on
- a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc.
- The search may be limited by elapsed time or number of records found, or restricted to search only within
- a previous result set (given by a list key).
- Returns a list key. Asynchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
-</li>
-<li>
-<p>InputAssay <br />
- Specifies an assay table from a BioAssay AID.
- The table may be complete, concise, or include a ListKey-specified set of readouts (TIDs).
- By default, all tested substances are included, but can be restricted to a ListKey-specified set of SIDs
- or CIDs. Returns an assay key. Synchronous.</p>
-</li>
-<li>
-<p>InputEntrez <br />
- Configures an Entrez history key (db, query key, and WebEnv).
- Returns a list key. Synchronous.</p>
-</li>
-<li>
-<p>InputList <br />
- Configures a set of identifiers for a PubChem database, as an array of integers.
- Returns a list key. Synchronous.</p>
-</li>
-<li>
-<p>InputListText <br />
- Configures a set of identifiers for a PubChem database, as a simple string of integer values separated
- by commas and/or whitespace. Returns a list key. Synchronous.</p>
-</li>
-<li>
-<p>InputStructure
- Configures a chemical structure as a simple (one-line) string, either SMILES or InChI.
- Returns a structure key. Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1433">Example workflow</a></p>
-</li>
-<li>
-<p>InputStructureBase64 <br />
- Configures a chemical structure in ASN.1 (text or binary), XML, or SDF format.
- The structure must be encoded as a Base64 string.
- Currently only single structures are supported.
- Returns a structure key. Synchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
-</li>
-<li>
-<p>MFSearch <br />
- Searches PubChem Compound for structures of a given molecular formula,<br />
- optionally allowing elements not specified to be present.
- The search may be limited by elapsed time or number of records found, or restricted to search only
- within a previous result set (given by a list key). Returns a list key. Asynchronous.</p>
-</li>
-<li>
-<p>ScoreMatrix <br />
- Computes a matrix of scores from one or two lists of IDs (if one, the IDs will be self-scored),
- of the selected type and in the selected format.<br />
- Compression is optional and defaults to gzip (.gz). Returns a download key. Asynchronous.</p>
-</li>
-<li>
-<p>SimilaritySearch2D <br />
- Searches PubChem Compound for structures similar to the one given by the structure key input,
- based on the given Tanimoto-based similarity score.<br />
- The search may be limited by elapsed time or number of records found,<br />
- or restricted to search only within a previous result set (given by a list key).
- Returns a list key. Asynchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1431">Example workflow</a></p>
-</li>
-<li>
-<p>Standardize <br />
- Standardizes the structure given by the structure key input,
- using the same algorithm PubChem uses to construct the Compound database.
- Returns a structure key. Asynchronous.</p>
-</li>
-<li>
-<p>SubstructureSearch <br />
- Searches PubChem Compound for structures containing the one given by the structure key input,
- based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc.
- The search may be limited by elapsed time or number of records found,
- or restricted to search only within a previous result set (given by a list key).
- Returns a list key. Asynchronous. <br />
-<a href="http://www.myexperiment.org/workflows/1434">Example workflow</a></p>
-</li>
-<li>
-<p>SuperstructureSearch <br />
- Searches PubChem Compound for structures contained within the one given by the structure key input,
- based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The search may be limited by elapsed time or number of records found, or restricted to search only within a previous result set (given by a list key). Returns a list key. Asynchronous.</li></p>
-</li>
-</ul></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation, Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/how-can-taverna-help-me.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/how-can-taverna-help-me.html (original)
+++ websites/staging/taverna/trunk/content/introduction/how-can-taverna-help-me.html Wed Mar 11 08:37:10 2015
@@ -104,126 +104,3 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna to use</a></li>
- <li><a href="/download/workbench">TavernaWorkbench</a></li>
- <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a href="/download/server">Taverna Server</a></li>
- <li><a href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source Code</a></li>
- <li><a href="/download/maven">Maven Repository</a></li>
- <li><a href="/download/system-requirements">System Requirements</a></li>
- <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search" action="http://www.google.com/search" method="get">
- <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query" placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ASF<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/">Apache Software Foundation</a></li>
- <li><a href="http://www.apache.org/foundation/how-it-works.html">How it works</a></li>
- <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
- <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
- <li><a href="http://incubator.apache.org/projects/taverna.html">Taverna Incubation Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>How can Taverna help me?</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>If you need to perform multi-step or repetitive analysis that involves invoking several services,
- or if you find yourself copying and pasting results between different Web pages or services,
- and would like to automate this process, then Taverna could be suitable for you.</p>
-<p>Taverna allows you to define how your data flows between the services,
- without having to worry how you are going to invoke these services.
-It will automate and pipeline processing of your data.</p>
-<p>Taverna can help you convert data from one format to another in cases when the services you are using are not 100% compatible
- and shied you from servicesâ (non-)interoperability horror.</p>
-<p>Taverna allows for rapid incorporation of new â©serviceâ©s without â©coding.â© It is not â©restricted â©to â©predetermined â©services; it provides access â©to â©local â©and â©remoteâ© resources â©and â©analysis â©tools â 3500+ services available on startâ©up.</p>
-<p>Taverna will provide you with trackable results of your experiments using the OPM (Open Provenance Model) standard. Workflow provenance gives a detailed trace of workflow execution: which services were executed, when, which inputs were used and what outputs were produced.</p>
-<p>Taverna lets you do collaborative science â share your workflows on myExperiment through the Taverna Workbench and search and download workflows from your fellow scientists.</p>
-<p>Read more about the <a href="/introduction/taverna-features">characteristics and features of Taverna</a>.</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation, Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/index.html (original)
+++ websites/staging/taverna/trunk/content/introduction/index.html Wed Mar 11 08:37:10 2015
@@ -104,200 +104,3 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna to use</a></li>
- <li><a href="/download/workbench">TavernaWorkbench</a></li>
- <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a href="/download/server">Taverna Server</a></li>
- <li><a href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source Code</a></li>
- <li><a href="/download/maven">Maven Repository</a></li>
- <li><a href="/download/system-requirements">System Requirements</a></li>
- <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search" action="http://www.google.com/search" method="get">
- <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query" placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ASF<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/">Apache Software Foundation</a></li>
- <li><a href="http://www.apache.org/foundation/how-it-works.html">How it works</a></li>
- <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
- <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
- <li><a href="http://incubator.apache.org/projects/taverna.html">Taverna Incubation Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Introduction</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><h2 id="what-is-taverna">What is Taverna?</h2>
-<p>Taverna is an open source domain independent
- <a href="/introduction/what-is-a-workflow-management-system">Workflow Management System</a> -
- a suite of tools used to design and execute
- <a href="/introduction/why-use-workflows">scientific workflows</a>.
-Taverna was started by the <a href="http://www.mygrid.org.uk">myGrid project</a>.</p>
-<p class="row text-center">
-<a href="/img/Taverna_Intro_slide1.png">
- <img width="680" height="382" title="Taverna_Intro_slide1" src="/img/Taverna_Intro_slide1.png"
- alt="" usemap="#tavernamap" /></a></p>
-
-<p><map name="tavernamap">
-<area shape="rect" coords="200,100,300,193"
- href="http://www.taverna.org.uk/download/workbench/" alt="Taverna Workbench" />
-<area shape="rect" coords="316,102,415,196"
- href="http://www.taverna.org.uk/developers/work-in-progress/taverna-lite/" alt="Taverna Lite" />
-<area shape="rect" coords="100,143,184,188" href="http://www.panacea-lr.eu/" alt="Panacea" />
-<area shape="rect" coords="3,137,98,177" href="http://www.biocatalogue.org/" alt="Biocatalogue" />
-<area shape="rect" coords="14,184,169,218"
- href="https://www.biodiversitycatalogue.org/" alt="Bio Diversity Catalogue" />
-<area shape="rect" coords="26,69,181,107" href="http://www.myexperiment.org/" alt="My Experiment" />
-<area shape="rect" coords="28,264,86,308" href="http://soaplab.sourceforge.net/soaplab1/" alt="SoapLab" />
-<area shape="rect" coords="84,268,177,301" href="http://www.unicore.eu/" alt="UNICORE" />
-<area shape="rect" coords="29,300,80,335" href="http://www.r-project.org/" alt="R Project" />
-<area shape="rect" coords="80,300,131,335" href="http://www.biomart.org/" alt="Biomart" />
-<area shape="rect" coords="131,300,182,335" href="http://www.beanshell.org/" alt="BeanShell" />
-<area shape="rect" coords="38,337,101,379" href="http://sadiframework.org/content/" alt="SADI" />
-<area shape="rect" coords="120,332,166,374" href="http://office.microsoft.com/en-gb/excel/" alt="Excel" />
-<area shape="rect" coords="632,165,678,207" href="http://office.microsoft.com/en-gb/excel/" alt="Excel" />
-<area shape="rect" coords="478,87,554,145" href="http://www.biovel.eu/" alt="Biovel" />
-<area shape="rect" coords="584,83,646,138" href="http://www.evo-uk.org/" alt="EVO" />
-<area shape="rect" coords="436,164,537,209" href="https://main.g2.bx.psu.edu/" alt="Galaxy" />
-<area shape="rect" coords="536,161,637,206"
- href="http://code.google.com/p/google-refine/" alt="Google Refine" />
-<area shape="rect" coords="194,216,313,285"
- href="/documentation/taverna-2-x/provenance/" alt="Provenance" />
-<area shape="rect" coords="194,279,313,341"
- href="http://www.taverna.org.uk/developers/work-in-progress/components/" alt="Taverna Components" />
-<area shape="rect" coords="321,215,427,292"
- href="/documentation/taverna-2-x/server/" alt="Taverna Server" />
-<area shape="rect" coords="319,283,425,341"
- href="/developers/work-in-progress/interaction/" alt="Interaction Server" />
-<area shape="rect" coords="434,221,552,288"
- href="/developers/work-in-progress/taverna-player/" alt="Taverna Player" />
-<area shape="rect" coords="554,222,678,290"
- href="download/server/2-2/" alt="Taverna Virtual Machine" />
-<area shape="rect" coords="434,284,558,352"
- href="/download/command-line-tool/" alt="Command Line Tool" />
-<area shape="rect" coords="560,290,678,358"
- href="http://www.osgi.org/Main/HomePage" alt="OSGi Alliance" />
-<area shape="rect" coords="200,344,422,380"
- href="/documentation/faq/security/" alt="Security" />
-</map>
-</p>
-<p class="row text-center">
-<a href="http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/Taverna-Intro-slide1.pptx">Download a (Non Apache) presentation slide of the above</a>
- </p></p>
-<p>The Taverna suite is written in Java and includes the Taverna Engine
- (used for enacting workflows) that powers both
- [Taverna Workbench][/download/workbench/] (the desktop client application) and
- <a href="/documentation/server/">Taverna Server</a>
- (which executes remote workflows).
-Taverna is also available as a <a href="/documentation/command-line-tool/">Command Line Tool</a>
- for faster execution of workflows from a terminal without the overhead of a GUI.
-Taverna automates experimental methods through the use of a number of different (local or remote) services from
- a diverse set of domains – biology, chemistry and medicine to music, meteorology and social sciences.</p>
-<p>Effectively, Taverna enables a scientist who has a limited background in computing,
- limited technical resources and support,
- to construct highly complex analyses over data and computational resources that are both public and private,
- all from a standard PC, UNIX box or Apple computer.</p>
-<p class="row text-center">
-<a href="/img/Taverna_Spectrum_Slide.png">
- <img title="Taverna_Spectrum_Slide" src="/img/Taverna_Spectrum_Slide.png" alt="" width="680" height="400" />
- </a>
-</p>
-
-<p class="row text-center">
-<a href="http://www.taverna.org.uk/pages/wp-content/uploads/2013/05/Taverna_Spectrum_Slide.pptx">Download a (Non Apache) presentation slide of the above</a>
-</p>
-
-<p>See a full list of <a href="/introduction/taverna-features">Taverna's features</a> or
- <a href="/documentation/videos/">videos</a> of Taverna in action. <br />
-The screenshot shown below shows the Taverna Workbench 2.x during the design of a workflow.</p>
-<p class="row text-center">
-<img src="/img/Taverna_Workbench.png" alt="Taverna 2.1 Workbench Design Perspective" width="606" height="392" />
-</p></div>
-
- </div>
-
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- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation, Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
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Modified: websites/staging/taverna/trunk/content/introduction/related-projects.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/related-projects.html (original)
+++ websites/staging/taverna/trunk/content/introduction/related-projects.html Wed Mar 11 08:37:10 2015
@@ -104,446 +104,3 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna to use</a></li>
- <li><a href="/download/workbench">TavernaWorkbench</a></li>
- <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a href="/download/server">Taverna Server</a></li>
- <li><a href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source Code</a></li>
- <li><a href="/download/maven">Maven Repository</a></li>
- <li><a href="/download/system-requirements">System Requirements</a></li>
- <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
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- name="search" id="search" action="http://www.google.com/search" method="get">
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- <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
- <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
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- </nav>
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- <div id="page" class="container">
- <h1>Related projects</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>The Taverna team are currently involved or collaborating on several projects sponsoring the development
- of new tools and the improvement of Taverna:</p>
-<ul>
-<li><a href="#biovel">BioVeL</a> â establishing an international e-Laboratory to allow biodiversity scientists to jointly tackle
- diverse research challenges using Taverna, myExperiment and BioCatalogue</li>
-<li><a href="http://www.wf4ever-project.org/home">Wf4Ever</a> â providing methods and tools required to ensure the long-term preservation of
- scientific workflows</li>
-<li><a href="#scape">SCAPE</a> â large scale and computation intense automated digital preservation and quality assurance
- workflows on a cloud infrastructure</li>
-</ul>
-<p>We are also involved in various projects set out to solve particular e-Science problems using Taverna:</p>
-<ul>
-<li><a href="#ChemTaverna">ChemTaverna</a> â workflows for chemoinformatics</li>
-<li><a href="#ondex">ONDEX</a> â integration of biological data</li>
-<li><a href="#shared-genomics">Shared Genomics</a> â the use of the <a href="/documentation/server">Taverna Server</a> to run genetic data workflows</li>
-<li><a href="#refine">REFINE</a> â text mining and visualisation</li>
-<li><a href="#helio">HELIO</a> â services and workflows for HelioPhysics</li>
-</ul>
-<p>An outreach project designed to expose scientists to the possible uses of e-Science and to aid them in
- adopting the available tools and techniques:</p>
-<ul>
-<li><a href="#engage">ENGAGE</a> â JISC initiative for exploiting the benefits of e-Infrastructure by developing and deploying
- new software solutions on available UK e-Infrastructure; funded a development project to facilitate
- the use of Taverna for <a href="#shared-genomics">Shared Genomics</a></li>
-</ul>
-<p>There are also a large number of Taverna-related projects that the team have been involved with in the past:</p>
-<ul>
-<li><a href="#helio">HELIO</a> â the Heliophysics Integrated Observatory</li>
-<li><a href="#tsb">TSB grant</a> â to address NHS requirements for accessing and comparing large amounts of information and
- find common genetic links when testing new treatments (in partnership with Eagle Genomics)</li>
-<li><a href="#taverna-galaxy">Taverna-Galaxy</a> â a tool for automatic generation and exposure of Taverna workflows as Galaxy tools.
- Galaxy is an open, web-based platform for data intensive biomedical research</li>
-<li><a href="#e-lico">e-LICO</a> â a virtual laboratory for interdisciplinary collaborative workflows in data mining and
- data-intensive sciences</li>
-<li><a href="#neiss">NeISS</a> â Taverna workflows for social (population and traffic) simulations in portals</li>
-<li><a href="#cagrid">caGrid project</a> â support for running cancer-research workflows</li>
-<li><a href="#e-fungi">e-Fungi</a> â Web services for comparative genomics</li>
-<li><a href="#ispider">ISpider</a> â proteomics workflows</li>
-<li><a href="#miasgrid">MIASGrid</a> â medical imaging</li>
-</ul>
-<p><a name="biovel"></a></p>
-<h2 id="biovel">BioVeL</h2>
-<p>The Biodiversity Virtual eâLaboratory (BioVeL) project,
- led by the School of Computer Science and Informatics at Cardiff University,
- has â¬5 million in funding and is seeking to provide a vital service that will improve the way scientists share,
- analyse and present information in the growing area of biodiversity science.
-The project includes the application of Taverna, <a href="http://www.myexperiment.org/">myExperiment</a> and the <a href="http://www.biocatalogue.org/">BioCatalogue</a>.</p>
-<p>Biodiversity science is the study of plants and animals that inhabit our planet and the environments they
- live in.
-Amid growing concerns over the extinction rate of certain species as their natural habitats are increasingly
- destroyed, and with biodiversity becoming as important as climate change on the political agenda,
-this new research project could not be more timely.</p>
-<p>Biodiversity Virtual eâLaboratory (BioVeL) will establish an international e-Laboratory â
- the first of its kind in Europe â that will allow biodiversity scientists to jointly tackle diverse
- research challenges.</p>
-<p>Experts from Cardiff University along with 15 partners from institutions across Europe,
- hope that when completed, the BioVeL e-Laboratory will, for the first time,
- give scientists access to multiple data, analysis and computing resources for biodiversity science through
- a robust e-Science infrastructure.</p>
-<p>Ranked by the European Commission (EC) as top of its class from more than 60 proposals,
- BioVeL is funded under the ECâs FP7 e-Infrastructures programme to support the creation of the
- European Research Area.</p>
-<p>For further information on the BioVeL project, visit <a href="http://www.biovel.eu/">http://www.biovel.eu/</a></p>
-<p><a name="scape"></a></p>
-<h2 id="scape">SCAPE</h2>
-<p><a href="http://www.scape-project.eu/">SCAPE</a> (SCAlable Preservation Environments) is an EU-funded FP7 project aimed at building a scalable
- platform for planning and execution of computation intensive processes for ingestion or migration of
- large data sets in order to help automate digital preservation.</p>
-<p>The data sets involved are either heterogeneous data collections (collections of objects of different type),
- contain data objects that are themselves large or complex in structure or contain a huge amount of digital
- objects.
-The sheer volume of data archives makes it impossible to use the current service-oriented architectures to
- ensure access to digital information over time.</p>
-<p>In this project, preservation processes will be realised as data pipelines and described formally as automated,
- quality-assured preservation Taverna workflows. The workflows will invoke various services for planning
- and execution of institutional preservation and quality assurance strategies.
-The workflows will be deployed on a large scale (using Hadoop MapReduce clouds) and executed over large,
- distributed and heterogeneous collections of complex digital objects.</p>
-<p>The workflows will enable reproducibility of preservation processes and collect provenance data over the
- entire digital objectâs lifecycle.</p>
-<p>The execution of workflows will be controlled by a policy-based âplanning and watchâ system, which will
- ensure the workflows are in line with state-of-the art in digital object representation, file formats,
- rendering tools, etc. and detect and report any errors in a preservation process.</p>
-<h3 id="scape-and-taverna-in-use">SCAPE and Taverna in use</h3>
-<p>by Schlarb Sven, sven.schlarb@onb.ac.at, Austrian National Library</p>
-<p>SCAPE consists of testbeds that have three application areas: Digital Repositories,
- from the library community, Web Content, from the web archiving community, and Research Data Sets,
- from the scientific community.
-The testbeds are used to evaluate solutions developed by the SCAPE project against defined institutional
- data sets in order to validate their applicability to real life application scenarios,
- such as large scale data repository ingest-workflows or data archive maintenance.</p>
-<p>Taverna is being used to develop concept workflows locally, to study the feasibility of differing approaches.
-Taverna server is used for remote execution of workflows,
- with the Tool service in use as the main integration pattern.</p>
-<p>In the context of how Taverna technology is currently used from a research perspective it is being used
- as a tool for ETL (Extraction/Transform/Load) and creating query-able data tables from large
- digital object collections. Content analysis and quality assurance are also performed using Taverna.</p>
-<p>Austrian National Library</p>
-<p>Max Kaiser, Head of Department of Research and Development
-Bettina Kann, Head of Digital Library</p>
-<p><a name="ChemTaverna"></a></p>
-<h2 id="chemtaverna">ChemTaverna</h2>
-<p>ChemTaverna is a pilot project currently being undertaken to investigate the application of Taverna in
- cheminformatics by scientists at the School of Chemistry, University of Southampton in collaboration
- with developers at the <a href="http://www.mib.ac.uk/">Manchester Interdisciplinary Biocentre</a> (MIB).</p>
-<p>A range of cheminformatics services are available for use in the Taverna Workbench â
- their <a href="/introduction/chemistry-web-services">descriptions and example workflows</a> showing how they can be used in data analyses are available
- on-line.
-All cheminformatics services can be imported to the Workbench in one go in the form of the
- <a href="http://www.myexperiment.org/packs/135.html">Chemistry Service Set</a> , which is available from myExperiment as a Service Set Pack.</p>
-<p>The results from cheminformatics workflows will be shared by means of blogs to provide a notebook record
- of data analyses.
-The ChemTaverna project will also investigate how laboratory instrumentation can be controlled in workflows
- for use in closed-loop optimization experiments to enhance the performance of analytical instruments.</p>
-<p><a href="http://usefulchem.wikispaces.com/">UsefulChem</a> project, an Open Notebook Science project in chemistry led by the Bradley Laboratory at
- Drexel University, have created many useful chemistry workflows using Taverna.
-The workflows are described at Jean-Claude Bradleyâs <a href="http://usefulchem.blogspot.com/">UsefulChem blog</a>.</p>
-<p><a name="ondex"></a></p>
-<h2 id="ondex">ONDEX</h2>
-<p><a href="http://www.ondex.org/">ONDEX</a> is currently an opensource suite of software that âenables data from diverse biological data sets
- to be linked, integrated and visualisedâ.
-This <a href="http://www.bbsrc.ac.uk/">BBSRC</a> funded project aims to support ONDEX and its integration with more general bioinformatics
- tools, such as those developed by the myGrid team.</p>
-<p>The existing ONDEX functionality is being exposed as Web services.
-These may then be used in workflow systems such as Taverna. Taverna workflows are also used to increase the
- functionality of ONDEX.</p>
-<p>The partners are the <a href="http://www.manchester.ac.uk/">University of Manchester</a> (<a href="https://sites.google.com/site/carolegoble/">Carole Goble</a> and Robert Stevens),
-<a href="http://www.ncl.ac.uk/">University of Newcastle</a> (Anil Wipat), <a href="http://www.rothamsted.ac.uk/">Rothamsted Research</a> (C Rawlings),
-<a href="http://www.nactem.ac.uk/">the National Centre for Text Mining</a> and <a href="http://www.mcisb.org/">Manchester Centre of Integrative Systems Biology</a>.
-The project runs from April 2008 to March 2011.</p>
-<p><a name="shared-genomics"></a></p>
-<h2 id="shared-genomics">Shared Genomics</h2>
-<p>Shared Genomics project, in partnership with Microsoft, aims to develop accessible High Power Computing
- infrastructure to support the analysis of large genetic data. An essential part of the work is the
- integration of results with metadata retrieved from knowledge repositories.
-This work will build upon the myGrid achievements in the association of metadata with data and the description
- of the semantics of services.</p>
-<p>The project is based at the North West Institute for BioHealth Informatics (NIBHI),
- a collaborative venture between the major universities in the North West of England,
- industrial partners such as Astra Zeneca, and the North West Development Agency.
-The principal investigator is Iain Buchan. The project is funded for £600k and runs from March 2008 to
- February 2010.
-Enable Taverna workflows in a Shared Genomics causality workbench</p>
-<p>This is an ENGAGE funded project to enable Taverna workflows using Shared Genomics services to be called
- in a more efficient manner. This work builds on the Taverna Server.</p>
-<p><a name="refine"></a></p>
-<h2 id="refine">REFINE</h2>
-<p><a href="http://www.nactem.ac.uk/pathtext/">REFINE</a>, Tools for the text mining-based visualisation of the provenance of
- biochemical networks, is a BBSRC funded project to find solutions for the terminology
- problem in systems biology, by developing techniques for recognising synonym terms.</p>
-<p>The REFINE project involves the use of text mining tools.
-Their application will be influenced by the experience of the myGrid team and Taverna Workbench users in
- this area.</p>
-<p>The principal investigator is <a href="http://www.nactem.ac.uk/staff/sophia.ananiadou/">Sophia Ananiadou</a>, Director of the National Centre for Text Mining
- (<a href="http://www.nactem.ac.uk/">NaCTeM</a>) at the <a href="http://www.manchester.ac.uk/">University of Manchester</a>.
-The project runs from January 2007 to June 2010.</p>
-<p><a name="helio"></a></p>
-<h2 id="helio">HELIO</h2>
-<p><a href="http://www.helio-vo.eu/">HELIO</a>, the Heliophysics Integrated Observatory, is a three year EU funded project that started in
- June 2009.</p>
-<blockquote>
-<p>The Heliophysics Integrated Observatory, HELIO, will deploy a
-distributed network of services that will address the needs of a broad
-community of researchers in heliophysics. HELIO will provide the most
-comprehensive integrated information system in this domain; it will
-coordinate access to the resources needed by the community, and will
-provide access to services to mine and analyse the data.</p>
-</blockquote>
-<p>The project <a href="http://www.helio-vo.eu/aboutus/helio_consortium.php">partners</a> include institutions from France, Ireland, Italy, Switzerland, the UK and the USA.
-Publications</p>
-<p>Workflows for Heliophysics, Blanc, A., Brooke, J., Fellows, D., Soldati, M., Pérez-Suárez, D., Marassi, A.,
- Santin, A., <a href="http://link.springer.com/journal/10723">Journal of Grid Computing</a>.
-<a href="http://link.springer.com/article/10.1007%2Fs10723-013-9256-5">http://link.springer.com/article/10.1007%2Fs10723-013-9256-5</a></p>
-<p><a name = "engage"></a></p>
-<h2 id="engage">ENGAGE</h2>
-<p>The ENGage Academic Groups with E-infrastructure (<a href="http://www.engage.ac.uk/">ENGAGE</a>) project is a <a href="http://www.jisc.ac.uk/">JISC</a>
- funded initiative involving the
- <a href="http://www.ngs.ac.uk/">National Grid Service</a> (NGS) and the Universities of <a href="http://www.soton.ac.uk/">Southampton</a>,
- <a href="http://www.manchester.ac.uk/">Manchester</a> and <a href="http://www.edinburgh.ac.uk/">Edinburgh</a>.</p>
-<p>âThe overall aim of the project is to improve the experience of research users of UK e-Infrastructure,
- and promote the use of UK e-Infrastructure to a wider set of users by engaging with different research
- communities.â</p>
-<p>The principal investigator is David De Roure.</p>
-<p>ENGAGE funded a development project to facilitate the use of Taverna for <a href="#shared-genomics">Shared Genomics</a>.</p>
-<p><a name = "tsb"></a></p>
-<h2 id="tsb-grant">TSB grant</h2>
-<p>This £500,000 project is part-funded by the UKâs national innovation agency,
- the Technology Strategy Board (TSB) and is carried out by <a href="http://www.eaglegenomics.com/">Eagle Genomics</a>,
- a leading open-source bioinformatics service provider,
- in collaboration with the myGrid/Taverna team and Cytocell Ltd., with assistance from <a href="http://www.ngrl.org.uk/">NGRL</a>,
- based at the Central Manchester University Hospitals NHS Foundation Trust,
- and the <a href="http://www.manchesterbrc.org/index.php">NIHR Manchester Biomedical Research Centre</a>.</p>
-<p>The project will build upon the success of the Taverna Workflow Management System in next generation
- sequencing to enable medical researchers who are developing and testing new treatments to compare large
- amounts of information analysed and stored on a cloud and find common genetic links.</p>
-<p>The technology will also help clinicians to look at an individual patientâs genetic make-up to aid diagnosis
- and ongoing treatment.</p>
-<p>Rather than simply testing a patient for one suspected condition,
- using the cloud technology could allow clinicians to test for a much wider range of complaints.</p>
-<p>Currently, the NHS IT systems do not have the resources to cope with the huge demands required.
-The cloud system can be accessed from a separate site, away from hospitals, freeing up space.</p>
-<p>Eagle Genomics will work with the Taverna team to adapt Taverna to allow non-IT experts to easily add and
- extract information and share it with their colleagues.</p>
-<p><a href="http://www.eaglegenomics.com/genetics-cloud-to-create-new-opportunities-for-researchers-and-clinicians">Read mode about the project</a>.</p>
-<p><a name = "taverna-galaxy"></a></p>
-<h2 id="taverna-2-galaxy">Taverna 2-Galaxy</h2>
-<p><a href="http://galaxy.psu.edu/">Galaxy</a> is an open, Web-based platform for data intensive biomedical research.
-Taverna 2-Galaxy integration is a first step towards making Galaxy and Taverna 2 more interoperable.
-It allows the automatic generation of Galaxy tools from Taverna 2 workflows.
-The tools can then be installed as usual in a Galaxy server and allow the Taverna workflows to become part
- of a Galaxy pipeline. It has been developed by Kostas Karasavvas of <a href="http://www.nbic.nl/">NBIC</a>.</p>
-<p>Users do not need to install Taverna 2-Galaxy themselves.
-It is available as part of the myExperiment <a href="http://www.myexperiment.org/">Web site</a>.
-While browsing Taverna 2 workflows the user will see an additional link âDownload as Galaxy Toolâ in the
- download section of the workflow.
-The tool can then be installed into Galaxy in the usual manner by the Galaxy administrator.
-They will also need a <a href="/documentation/server">Taverna Server</a> that will run the Taverna 2-Galaxy tools.</p>
-<p>Also check out the Taverna-Galaxy <a href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">wiki</a>.
-For Taverna-Galaxy users</p>
-<ul>
-<li>You can now include Taverna workflows as part of your Galaxy workflows</li>
-<li>The Taverna workflow will be made available as a Galaxy tool</li>
-<li>You can <a href="http://www.myexperiment.org/workflows">search/browse</a> Taverna workflows from the <a href="http://www.myexperiment.org/">myExperiment</a> workflow repository, and</li>
-<li>Just let your Galaxy administrator know which Taverna workflows you want installed in Galaxy</li>
-</ul>
-<p>Try it out</p>
-<div class="codehilite"><pre><span class="n">The</span> <span class="p">[</span><span class="n">NBIC</span> <span class="n">Galaxy</span> <span class="n">Server</span><span class="p">][</span>65<span class="p">]</span> <span class="n">provides</span> <span class="n">a</span> <span class="n">demo</span> <span class="n">platform</span> <span class="n">to</span> <span class="n">run</span> <span class="n">some</span> <span class="n">pre</span><span class="o">-</span><span class="n">installed</span> <span class="n">Taverna</span> <span class="n">workflows</span> <span class="n">in</span> <span class="n">Galaxy</span>
-</pre></div>
-
-
-<p>Taverna-Galaxy in use</p>
-<p>Dr Casey Bergman and his group of Life Sciences researchers from the <a href="http://bergmanlab.smith.man.ac.uk/">Bergman Lab</a> @ University of Manchester
- working on eukaryotic genome biology have successfully installed and used the integrated Taverna-Galaxy tools.</p>
-<p>See <a href="http://bergmanlab.smith.man.ac.uk/?p=943">their blog</a> about their experiences in installing and running Taverna-Galaxy.</p>
-<p><a name = "e-lico"></a></p>
-<h2 id="e-lico">e-LICO</h2>
-<p>The goal of the <a href="http://www.e-lico.eu/">e-LICO project</a> is to build a virtual laboratory for interdisciplinary collaborative research in data mining and data-intensive sciences. The proposed e-lab will comprise three layers: the e-science and data mining layers will form a generic research environment that can be adapted to different scientific domains by customizing the application layer.</p>
-<p>The foundation of the e-science layer is a suite of open source components from the myGrid e-science platform (one of which is the next generation Taverna Workbench). To build the e-LICO infrastructure, these components will be extended with tools for content creation (e.g. semantic annotation, ontology engineering), as well as mechanisms for multiple levels and modes of collaboration in experimental research.</p>
-<p>A <a href="http://www.vimeo.com/10345778">video tutorial</a> explains how to build data mining workflows.</p>
-<p><a name = "neiss"></a></p>
-<h2 id="neiss">NeISS</h2>
-<p>The National e-Infrastructure for Social Simulation is a <a href="http://www.jisc.ac.uk/">JISC</a>-funded project to undertake a coordinated
- programme of producing services and furthering uptake through community engagement to create a sustainable,
- long-term platform for social simulation with potential for major strategic impact,
- both in the UK and internationally.
-The project involves <a href="http://www.leeds.ac.uk/">Leeds University</a>, <a href="http://www.manchester.ac.uk/">Manchester University</a>
- (including <a href="http://en.wikipedia.org/wiki/National_Centre_for_e-Social_Science">NCeSS</a>),
- <a href="http://www.stir.ac.uk/">Stirling University</a>, Glasgow University, UCL, Southampton University, STFC Daresbury Laboratory.</p>
-<p>Within the project, the Taverna team are working on:</p>
-<ul>
-<li>the integration of the Taverna functionality into a portal, i.e. providing JSR 168/286 compliant
- components that provide access to enactment, management, monitoring and creation of workflows.</li>
-<li>the re-purposing of services from <a href="http://www.myexperiment.org/">myExperiment</a>, facilitating their integration into a portal.
- An important focus will be the incorporation of social networking functionality to provide extended
- archiving and documentation capability for social simulations.</li>
-</ul>
-<p><a href="http://www.mygrid.org.uk/dev/wiki/display/portals/NeISS+Project">Documentation on wrapping Taverna workflows in a portal and the code</a> is available from our
- (Pre Apache) wiki.</p>
-<p><a name = "cagrid"></a></p>
-<h2 id="cagrid">caGrid</h2>
-<p><a href="http://www.cagrid.org/">caGrid</a> is part of <a href="http://cabig.cancer.gov/">caBIG</a> (cancer Biomedical Informatics Grid),
- a US project to carry out eScience and bioinformatics in cancer research.</p>
-<p>The Taverna team were funded by the US National Cancer Institute (NCI) to help integrate Taverna with caGrid,
- so that Taverna can find and use (secured and non-secured) caBIG data and analytical services found on caGrid.</p>
-<p>The team wrapped a selection of typical non-caBIG services used by Taverna users so that they are annotated
- and comply with caBIGâs Silver-level compatibility requirements.</p>
-<p>The team also implemented a plugin for Taverna 2.1.2 that enables semantic search for caGrid services
- described by the caGridâs Index Service and adding them as component to workflows.</p>
-<p>More details about the project and the deliverables can be found on the projectâs <a href="http://www.mygrid.org.uk/dev/wiki/display/caGrid/Home">Wiki pages</a> and
- NCIâs Gforge project pages. Source code of the Taverna plugins is available from the <a href="https://gforge.nci.nih.gov/svnroot/taverna-cagrid/">SVN repository</a>.
-The project ran from September 2008 to November 2009.</p>
-<p>The work on the caGrid project follows on from caGridâs previous adoption of Taverna when the Taverna and
- caGrid collaborated in 2007 to develop a Taverna 1.7.0 GT4 processor as a plugin based upon the
- Tavernaâs WSDL processor.
-This work has been updated for Taverna 2.x and there are two plugins available: <a href="http://www.taverna.org.uk/documentation/taverna-plugins/taverna-2-x-plugins#cagrid_plugin">caGrid plugin</a>
- (for invoking caGrid services) and <a href="http://www.taverna.org.uk/documentation/taverna-plugins/taverna-2-x-plugins#cagrid_remote_execution_plugin">caGrid remote execution plugin</a> (for remote execution of
- caGrid workflows on a server).</p>
-<p>The functionality of the Taverna 1.7.0 caGrid plugin was shown at a caGrid meeting in late 2008 where
- the associated poster won an outstanding poster <a href="http://www.mygrid.org.uk/2008/09/outstanding-poster-award-at-the-cabig-ncri-conference/">award</a>.</p>
-<p>The installation and use of the Taverna 1.7.0 caGrid plugin is described on the caGrid <a href="http://cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna">wiki</a>.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a href="http://dx.doi.org/10.1109/MIC.2008.120">paper</a> âCombining the Power of Taverna and caGrid: Scientific Workflows that Enable Web-Scale
- Collaborationâ has been written by Wei Tan, Ian Foster and Ravi Madduri to describe some of the work done on
- the project.</p>
-<p><a name = "e-fungi"></a></p>
-<h2 id="e-fungi">e-Fungi</h2>
-<p>e-Fungi was a BBSRC funded project to produce an e-Science infrastructure for comparative functional
- genomics in fungal species.
-Parts of the e-Fungi project include the development of a data warehouse and analysis libraries that are
- exposed as Web services.
-These Web services can be used within the Taverna Workbench for the creation of workflows.</p>
-<p>The principal investigators were Professor Norman Paton, Professor Oliver,
- Dr Rattray and Dr Hubbard of the University of Manchester.
-The project ran from October 2004 to June 2008.</p>
-<p><a name = "ispider"></a></p>
-<h2 id="ispider">iSpider</h2>
-<p><a href="http://www.ispider.manchester.ac.uk/">iSpider</a> was a <a href="http://www.bbsrc.ac.uk/">BBSRC</a> funded project to create an informatics platform for proteomics using Grid-based
- technologies, and to use this to address specific biological problems.
-The grantholders were Dr S. Hubbard, Dr Suzanne Embury, Professor <a href="https://sites.google.com/site/carolegoble/">Carole Goble</a> CBE,
- Professor Norman Paton, Dr Robert Stevens and Prof Oliver of the <a href="http://www.manchester.ac.uk/">University of Manchester</a>.
-The project ran from July 2004 to June 2007.</p>
-<p>The iSpider project developed three tools that make use of Tavernaâs functionality and plugability to
- support the development of workflows, in particular for proteomics.</p>
-<p>Much of the work has been done by Khalid Belhajjame and additional information can be found in his publications.
-A tool for the identification and the characterisation of mismatches in scientific workflows</p>
-<p>By using the <a href="http://www.mygrid.org.uk/tools/service-management/feta/">Feta</a> service registry and extending the capabilities of the Taverna Workbench,
- this tool provides a means for automatically identifying and characterising the mismatches that may
- arise between the constituent operations of an in silico experiments.
-A tool for automatically inferring service annotations</p>
-<p>This tool allows the derivation, in an automatic fashion,
- of information about the annotations of service parameters using existing tested-and-tried workflows.
-It has been evaluated using the workflow repository provided by <a href="http://www.myexperiment.org/">myExperiment</a> together with the
- <a href="http://www.mygrid.org.uk/tools/service-management/mygrid-ontology/">myGrid ontology</a>.
-A system for querying multiple proteomics data sources</p>
-<p>It supports the combined use of Grid data access (<a href="http://www.ogsadai.org.uk/">OGSA-DAI</a>), Grid distributed querying (<a href="http://link.springer.com/chapter/10.1007%2F978-3-540-24741-8_58">OGSA-DQP</a>) and
- data integration (<a href="http://www.doc.ic.ac.uk/automed/">AutoMed</a>) software tools to support distributed data analysis.
-This system has been used for providing an integrated access to four proteomics data sources, namely,
- <a href="http://gpmdb.thegpm.org/">gpmDB</a>, <a href="http://pedro.cs.manchester.ac.uk/">PedroDB</a>, PepSeeker and <a href="http://www.ebi.ac.uk/pride/">Pride</a>.</p>
-<p><a name = "miasgrid"></a></p>
-<h2 id="miasgrid">MIASGrid</h2>
-<p>The MIAS project examined the requirements of Medical Imaging and Signals.
-The <a href="http://www.robots.ox.ac.uk/~irc/grid_mias-grid.html">MIASGrid</a> sub-project, took examples of those requirements and investigated how e-Science and
- the myGrid tools in particular could satisfy them.
-The project was funded by the <a href="http://www.epsrc.ac.uk/">EPSRC</a> for £494k and ran until April 2006.</p>
-<p>The project produced several workflows that demonstrated the applicability of Taverna to the handling of
- large amounts of medical image data.
-The workflows made use of <a href="http://www.mathworks.com/products/matlab/">MATLAB</a> and also interaction with users.</p>
-<p>The workflows covered two domains:</p>
-<ul>
-<li>The analysis of MRI scans of knees to detect changes in cartilage</li>
-<li>The <a href="https://www.escholar.manchester.ac.uk/uk-ac-man-scw:1d33210">description and searching</a> of a database of mammograms</li>
-</ul></div>
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