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websites/staging/taverna/trunk/content/introduction/chemistry-web-services.html
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<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
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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>
-
- <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>
-
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- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
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- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
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- location.href = this.href;
- });
-
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- });
-</script>
-
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- </body>
-</html>
\ No newline at end of file
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>
- <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>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, [email protected], 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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