We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.
Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.
Each tool has at least 2 steps, but most of them have more:
The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
In the following steps, the user has the possibility to change the default tool parameters
And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server
Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.
Step 1 - Input Sequences
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sequence
sequence
Input Sequence
One or more sequences to be translated can be entered directly into this form. Sequences can be in GCG, FASTA, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. (See example input formats). Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.
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upload
upload
Sequence File Upload
A file containing one or more valid sequences in any format (GCG, FASTA, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be uploaded and used as input for the translation. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.
Step 2 - Select Parameters
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codontable
codontable
Codon Table
Which genetic code table to use. These are kept synchronised with those maintained at the NCBI's Taxonomy Browser.
Table name
Value
Standard Code
0
Vertebrate Mitochondrial
2
Yeast Mitochondrial
3
Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Email Notification
Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.
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email
email
Email Address
If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).
Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines.
For an introduction on how to run these clients and use them in workflows please see the webinar series.
REST API
The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.
params: (required) parameters for the tool. These are described by the InputParameters data structure.
a string containing the job identifier (jobId).
getStatus(jobId)
Get the status of a submitted job.
jobId: (required) job identifier.
a string containing the status.
The values for the status are:
RUNNING: the job is currently being processed.
FINISHED: job has finished, and the results can then be retrieved.
ERROR: an error occurred attempting to get the job status.
FAILURE: the job failed.
NOT_FOUND: the job cannot be found.
getResultTypes(jobId)
Get the available result types for a finished job.
jobId: (required) job identifier.
a list of wsResultType data structures describing the available result types.
getResult(jobId, type, parameters)
Get the result of a job of the specified type.
jobId: (required) job identifier.
type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.
Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.
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title
List Datatypes
InputParameters
The input parameters for the job:
Attribute
Type
Description
codontable
string
Genetic code table to use.
sequence
string
Input sequence.
More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.
wsParameterDetails
Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).
Attribute
Type
Description
name
string
Name of the parameter.
description
string
Description of the parameter, suitable for use in option help interfaces.
type
string
Data type of the parameter.
values
list of wsParameterValue
List of valid values for the option.
wsParameterValue
Description of a tool parameter value. Used in wsParameterDetails.
Attribute
Type
Description
label
string
Display name of the value, for use in interfaces.
value
string
String representation of the value to be passed to the tool parameter.
defaultValue
boolean
Flag indicating if this value is the default.
properties
list of wsProperty
List of key/value pairs providing further information.
wsProperty
Properties of a tool parameter value. Used in wsParameterValue.
Attribute
Type
Description
key
string
Property name
value
string
Property value
wsRawOutputParameter
Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).
Attribute
Type
Description
name
string
Parameter name
value
list of string
Parameter value
wsResultType
Description of a result type. Returned by getResultTypes(jobId).
Attribute
Type
Description
identifier
string
Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label
string
Display name for use in user interfaces.
description
string
Description of the result type, for use in help interfaces.
mediaType
string
MIME type of the returned data.
fileSuffix
string
Suggested suffix for file name, if writing data to disk.
type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.
Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.
CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl