the number of applications and databases providing tools to perform computations on dna , rna and proteins are rapidly growing .
however , the lack of communication between such tools in molecular biology is commonly a barrier to extracting new knowledge using these resources .
many tools and databases already communicate using the web , as shown by the ever - growing list of servers in this issue of nucleic acids research .
currently , integrating tools and databases available on the web frequently involves either  screen - scraping web pages using scripting languages like perl or manual cut - and - paste of data between applications .
screen - scraping is notoriously fragile , because the integrating script is prone to break when the web page or form changes , and for this reason has been likened to  medieval torture ( 1 ) . cutting and pasting data between applications is another common way to quickly achieve interoperation .
in addition to providing form - based interfaces , tool and database providers can describe their application or database using the standard web services description language ( wsdl ) .
these wsdl descriptions can then be indexed to build a searchable and browsable registry of operations for end - users .
applications can then exchange data , typically using soap , a protocol for exchanging xml - based messages over a network , normally using http . for a full description of web service technology ,
has several advantages : 
 tools and databases do not need to be installed locally on the users machine or laboratory server , as they are programmatically accessible over the web.tools created using different programming languages ( e.g. python , perl , java , etc . ) and platforms ( e.g. unix , windows , etc . ) can be accessed through the same web service interface .
this removes the need for the user to know about all the different platforms and programming languages underneath.the need for fragile screen - scraping integration scripts is reduced.it provides an alternative to time - consuming and laborious  cut - and - paste integration between web applications.workflows , or pipelines , of web services can be built to provide high - level descriptions of analyses .
these can be created and tested relatively quickly to integrate many different tools and applications in a single analysishowever , there are also several limitations of using web services : 
 since services are provided by autonomous third - parties around the world , they frequently have insufficient or non - existent metadata . where metadata exists it often provides little indication of the purpose of a service .
string which hide complex legacy flat - file formats , and have no immediately obvious function . in the worst case , the only way to work out what task a service performs is to invoke it with some data and examine what comes back from the service .
invoking services relies on knowing exactly what data a service takes as input , information which is not always available .
an important consequence of poor service metadata is that many services can be difficult to find in a registry ( 3).joining services together into pipelines is frequently problematic , as the inputs and outputs are not directly compatible .
consequently , many one - off  shim services ( 4 ) are required to align closely - related data and enable services to interoperate.the web services stack ( 2 ) can be difficult to debug .
standard open - source libraries that taverna uses for creating , documenting and invoking services like wsif ( ) , wsdl4j and axis ( ) can provide poor documentation by default , and cryptic error messages when services fail.services accessed over a network can have unpredictable performance and reliability ( ) . some services , particularly the more specialist and obscure tools provided by smaller laboratories , can be unreliable , unstable or have licensing issues . such services are often the  weakest link in the chain . when individual services fail , for whatever reason , the whole workflow can not be run .
mirrored replica or redundant services are not always available to address this problem through failover .
tools and databases do not need to be installed locally on the users machine or laboratory server , as they are programmatically accessible over the web .
tools created using different programming languages ( e.g. python , perl , java , etc . ) and platforms ( e.g. unix , windows , etc . ) can be accessed through the same web service interface .
this removes the need for the user to know about all the different platforms and programming languages underneath .
it provides an alternative to time - consuming and laborious  cut - and - paste integration between web applications .
workflows , or pipelines , of web services can be built to provide high - level descriptions of analyses .
these can be created and tested relatively quickly to integrate many different tools and applications in a single analysis since services are provided by autonomous third - parties around the world , they frequently have insufficient or non - existent metadata . where metadata exists it often provides little indication of the purpose of a service .
string which hide complex legacy flat - file formats , and have no immediately obvious function . in the worst case , the only way to work out what task a service performs is to invoke it with some data and examine what comes back from the service .
invoking services relies on knowing exactly what data a service takes as input , information which is not always available .
an important consequence of poor service metadata is that many services can be difficult to find in a registry ( 3 ) .
joining services together into pipelines is frequently problematic , as the inputs and outputs are not directly compatible .
consequently , many one - off  shim services ( 4 ) are required to align closely - related data and enable services to interoperate .
standard open - source libraries that taverna uses for creating , documenting and invoking services like wsif ( ) , wsdl4j and axis ( ) can provide poor documentation by default , and cryptic error messages when services fail .
services accessed over a network can have unpredictable performance and reliability ( ) . some services , particularly the more specialist and obscure tools provided by smaller laboratories , can be unreliable , unstable or have licensing issues . such services are often the  weakest link in the chain .
when individual services fail , for whatever reason , the whole workflow can not be run .
mirrored replica or redundant services are not always available to address this problem through failover . working with both these strengths and limitations , taverna ( 5,6 ) , part of the grid project , is an application that makes building and executing workflows accessible to bioinformaticians who are not necessarily experts in web services and programming .
it provides a single point of access to a range of services with programmatic interfaces , primarly web services . as of march
2006 , there are around 3000 of these publicly available services in molecular biology , provided by range of third - parties around the world .
the potential set of services accessible in taverna is even larger , as more tool and database providers expose programmatic interfaces to their resources over the web .
currently , building workflows of these services in taverna , allows users glue these diverse resources together relatively quickly .
this can allow rapid exploration of data of hypothesis testing , e.g. on given gene(s ) or protein(s ) .
there are a wide range of services available in taverna , first those provided by insdc ( ) member organizations , embl - ebi provides standard services ( 7 ) , the ncbi entrez programming utilities ( ncbi services can only be used in taverna version 1.3.2-rc1 or later ) ( 8) and the dna databank of japan ( ddbj ) ( 9 ) . additional tools and databases are provided by the protein databank of japan ( pdbj ) ( 10 ) , kyoto encyclopedia of genes and genomes ( kegg ) ( 11 ) , biomart ( 12 ) , pathport / toolbus tools ( 13 ) , biomoby ( 14 ) , bind ( 15 ) , seqvista ( 16 ) and pfam ( 17 ) from the wellcome trust sanger institute
. a more comprehensive list and description of the services available can be found at the sourceforge website ( ) .
an important feature of taverna is that it can talk to many different kinds of service , so for example , different services can be added to the services panel . a workflow built from some of the services described above , which illustrates the capabilities of taverna
this workflow starts with an input genbank identifier ( gi number ) , to retrieve a draft dna sequence which is then fed into repeatmasker ( ) then genscan ( . )
the report output from genscan is split , and the part containing the peptide sequence is fed into blastp , hosted by the ddbj . although not shown in this workflow , the results of the blast analysis could be fed into further programs , provided that the user knows how to parse blast records and what services could follow . as the services have very little metadata , taverna can not currently guide the user during workflow construction .
the workflow shown here is a basic gene prediction and characterization pipeline that is part of many workflows created in taverna , e.g. workflows used inresearch of williams  beuren syndrome ( 19 ) and graves disease ( 20 ) .
the workflow shown in figure 1 can be downloaded from the grid workflow repository ( . ) in order to run this worklfow , which takes > 5 min to execute , download taverna and consult the user documentation ( ) under the heading  enacting a predefined workflow. other pre - defined workflows can be run by browsing the workflow repository or examples directory of taverna . alternatively
, arbitrary workflows can be constructed using the services described above , again see the user documentation for details .
each taverna workflow can have metadata stored inside it using the author and title tags .
additional workflow metadata can be stored seperately from the workflow and identified using a life science identifier ( lsid ) ( 21 ) .
all workflows have an lsid by default , although the user has to assign metadata to this lsid if they require it .
the current version of taverna , ( 1.x ) has been downloaded around 14  000 ( ) times and has an estimated user base of around 1500 installations .
taverna has been used several different areas of research throught europe , asia , australia and the usa for functional genomics ( 19,20 ) , metabolic and signalling pathway analysis ( 5 ) and chemoinformatics ( 22 ) .
based on the experiences of these users , requirements have been gathered for the next release of taverna , version 2.0 . this version is currently being developed and is scheduled for release in 2007 .
planned new features include the ability to support higher - throughput and longer - running workflows using grid technology , a semantically enabled registry with services annotated with terms from a standard ontology , facilities for provenance gathering and a repository of workflows that can be re - used and re - purposed .
taverna 2.0 will also have enhanced results browsing with the ability to incrementally execute workflows and use microarray tools like maxd ( 23 ) and the r library ( 24 ) .
we present here an application , taverna , that allow users who are not necessarily expert programmers to design , execute and share workflows of web services .
these workflows can be used to perform a range of different analyses in molecular biology and bioinformatics , accessing numerous different databases and tools using standard web protocols .
 taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web , especially web services . 
 it allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses , such as sequence analysis and genome annotation . 
 these high - level workflows can integrate many different resources into a single analysis . 
 taverna is available freely under the terms of the gnu lesser general public license ( lgpl ) from . 
INTRODUCTION
SERVICES AND WORKFLOWS TAVERNA
RUNNING WORKFLOWS
TAVERNA USERS AND FUTURE WORK
CONCLUSIONS
Figures and Tables