Ensure you enter your valid MODELLER key via the BioSerf tab.

You input looks like it may be a multiple sequence alignment, please ensure it is in valid fasta format and that all sequences are the same length

UCL Bioinformatics Group Asynchronous Web Services

Due to a recent server upgrade our SOAP API has changed. Largely it is somewhat more streamlined. The core functionality remains the same but some of the method paths have changed names. We lost the invoke page but the WSDL remains in the same place.

You can view a full list of available webservices via WSDL:
bioinf.cs.ucl.ac.uk/psipred_api/wsdl

All our services include a Submit() and Result() function. Use submit() to send jobs to a given method and use the server's Result() to poll the server to check job progress. We recommend that users only poll the server once every 5 minutes for a given job, users who effectively DOS our server will be banned. Please also be aware that, as with the html submission forms users are restricted to 20 concurrent jobs. We would also like to remind users to take the time to familiarise themselves with of our Acceptable Use Policy before using our webservices.

Obviously the most direct method to test a job's progress is with the result() function. Alternatively, if you submit an email address your code could receive/check for the email. This method would greatly reduce the load on our webserver and we would be immensely grateful to any programmers who choose this method. However this is obviously more complex to code so we do appreciate it if people choose not to go this route.

Example Scripts

We also provide the following scripts presenting simple examples for connect to our web services

Ruby Soap Client for PSIPRED

This short Ruby script shows how to use soap4r to bind to the PSIPRED secondary structure SOAP interface and submit a job, setting all the mandatory fields. Included is a short loop that will poll the server for results every 500 seconds. You can find examples of all the job submission types in the script, most of them are commented out but this should be fairly easy to understand.

For legacy purposes we also have a RESTful job submitter written in PERL

Perl Job submission script

This shows how to submit jobs directly as a URI POST request. Our REST API does not include an XML response type, this may make parsing the results more complex. We would recommend where possible that users migrate to the SOAP API.

Webservice Submission Notes

 

Job Submission

All jobs take two common mandatory fields email address and job name

string

email

string

name

All jobs return the same formatted SubmitMessage upon job submission with the following fields:

message

A short human readable message about the success or failure of the submission

job_id

The job ID on our server upon successful submission

state

A computer readable number indicating the success of the job submission

 The state codes are:

0

job submission failed, no job_id returned

1

job submission successful, job_id will be complete


Job results

Using the job_id obtained from the job submission the result() function can be called to poll the state of the running job. All result() functions return the following common fields:

message

A short human readable message about the current state of the job

job_id

The job_id being polled

state

A computer readable number indicating the state of the job

The state codes are

0

job has stopped in an error state, check the message field

1

job completed successfully, the appropriate results fields will contain data

2

job is still being processed

3

can not find a job with the given ID for that API



API specific notes

Listed below are the inputs and outputs that are not common between services

ApiBioserf

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
string modeller : Valid modeller licence key in ASCII format
BioserfResult Result()
mgenthreader_templates : URI to download list of putative templates found by mGenTHREADER
psiblast_templates : URI to download list of putative templates found by pdbaa blast
selected_templates : URI to download final set of templates used for modelling
model_pdb : URI to download the final homology model

ApiDisopred

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
string fpr : False positive rate. Accepted values 1|2|3|4|5|6|7|8|9|10; defaults to 2
string psiblast : Sets whether psiblast output is returned. Accepted values opnone|ophits|opaln; defaults to opnone
string psipred : Sets whether psipred is run. Accepted values true|false; defaults to true
DisopredResult Result()
prediction_text : URI to download the disopred prediction data
prediction_table : URI to download the disopred prediction in tabulated format
postscript_graph : URI to download the disopred graph
psiblast : URI to download the psiblast results if requested

ApiDomthreader

SubmitMessage Submit()
base64 sequence : A protein sequence or MSA in fasta format submitted in ASCII format
string complex : Masks low complexity sequence in the input sequence. Accepted values true|false; defaults to true
string membrane : Masks TM helices in the input sequence. Accepted values true|false; defaults to false
string coil : Masks coiled-coil in the input sequence. Accepted values true|false; defaults to false
msa_control : controls depth of homologue search when input is msa. Accepted values all|distant|no. Default is all.
DomthreaderResult Result() domthreader_data : URI to download domthreader data table

 

ApiDompred

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
string eval : parameter sets the psi-blast e-value to use; defaults to 0.01
int iterations : parameter sets the number of PSI-BLAST iterations to use; defaults to 5
string secpro : parameters sets whether psipred plot will be returned. Accepted values yes|no; defaults to yes
string pp : parameters sets whether psipred data will be returned. Accepted values yes|no; defaults to yes
DompredResult Result()
dompred_graph : URI to download graph of dompred prediction trace
dompred_output : URI to download dompred data in ascii format
psiblast_output : URI to download the PSIBLAST results
psiblast_table : URI to downloaded the parse PSIBLAST results table
domssea_table : URI to download the domssea data
psipred_ps : URI to download the psipred diagram in postscript format

ApiFfpred

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
FfpredResult Result()
go_table : URI to download the final predicted GO terms
ffpred_data : URI to download the full output data
seq_feature_map : URI to download the sequence feature diagram
transmembrane_diagram : URI to download memsatsvm cartoon

ApiGenthreader

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
string complex : Masks low complexity sequence in the input sequence. Accepted values true|false; defaults to true
string membrane : Masks TM helices in the input sequence. Accepted values true|false; defaults to false
string coil : Masks coiled-coil in the input sequence. Accepted values true|false; defaults to false
GenthreaderResult Result()
genthreader_data : URI to download genthreader data table
contact_alignment : URI to download contacts alignments
cert_alignment : URI to download realignment of query and CERT hits
cert_high_alignment : URI to download realignment of query and CERT, HIGH hits
cert_high_med_alignment : URI to download realignment of query and CERT. HIGH, MED hits

ApiHspred

SubmitMessage Submit()
base64 pdb_file : uncompressed pdb file in ASCII format
string chainsa : a space separated string of the chains on one side of the interface
string chainsb : a space separated string of the chains on the other side of the interface
HspredResult Result()
annotated_pdb_a : URI to download the annotated pdb file for the initial side of the interface
annotated_pdb_b : URI to download the annotated pdb file for the other side of the interface
hspred_data : URI to download the HSPred output data

ApiMakeTdb

SubmitMessage Submit()
base64 pdb_file : uncompressed pdb file in ASCII format
MakeTdbResult Result()
tdb_file : URI to download the TDB calculated

ApiMemsatsvm

SubmitMessage Submit()
base64 sequence : A protein sequence or MSA in fasta format submitted in ASCII format 
msa_control : controls depth of homologue search when input is msa. Accepted values all|distant|no. Default is all.
MemsatsvmResult Result()
memsat3_data : URI to download memsat3 prediction data
memsat3_image : URI to download memsat3 cartoon
memsatsvm_data : URI to download memsatsvm prediction data
memsatsvm_image : URI to download memsatsvm cartoon
memsatsvm_schematic : URI to download memsatsvm summary schematic

ApiMgenthreader

SubmitMessage Submit()
base64 sequence : A protein sequence or MSA in fasta format in submitted ASCII format
string complex : Masks low complexity sequence in the input sequence. Accepted values true|false; defaults to true
string membrane : Masks TM helices in the input sequence. Accepted values true|false; defaults to false
string coil : Masks coiled-coil in the input sequence. Accepted values true|false; defaults to false
msa_control : controls depth of homologue search when input is msa. Accepted values all|distant|no. Default is all.
GenthreaderResult Result()
genthreader_data : URI to download genthreader data table
contact_alignment : URI to download contacts alignments
cert_alignment : URI to download realignment of query and CERT hits
cert_high_alignment : URI to download realignment of query and CERT, HIGH hits
cert_high_med_alignment : URI to download realignment of query and CERT. HIGH, MED hits

ApiMetsite

SubmitMessage Submit()
base64 pdb_file : uncompressed pdb file in ASCII format
string fpr : Sets the false positive rate. Accepted values are 1|5|10|20; defaults to 1%
string mettype : Sets the metal ion predicted. Accepted values are CA|ZN|MG|FE|CU|MN; defaults to CA
MetsiteResult Result()
annotated_pdb : URI to download a pdb with the metal contacts annotated
metsite_data : URI to download metsite SVM output data

ApiMempack

SubmitMessage Submit()
base64 sequence : A protein sequence or MSA in fasta format submitted in ASCII format
msa_control : controls depth of homologue search when input is msa. Accepted values all|distant|no. Default is all.
MempackResult Result()
memsat3_data : URI to download memsat3 prediction data
memsat3_image : URI to download memsat3 cartoon
memsatsvm_data : URI to download memsatsvm prediction data
memsatsvm_image : URI to download memsatsvm cartoon
memsatsvm_schematic : URI to download memsatsvm summary schematic
mempack_cartoon : URI to download the mempack cartoon
graph_results : URI to download the graph analysis data
lipid_results : URI to download the lipid analysis data
contact_results : URI to download the contact data

ApiPsipred

SubmitMessage Submit()
base64 sequence : A protein sequence or MSA in fasta format submitted in ASCII format
string complex : Masks low complexity sequence in the input sequence. Accepted values true|false; defaults to true
string membrane : Masks TM helices in the input sequence. Accepted values true|false; defaults to false
string coil : Masks coiled-coil in the input sequence. Accepted values true|false; defaults to false
msa_control : controls depth of homologue search when input is msa. Accepted values all|distant|no. Default is all.
PsipredResult Result()
psipred_postscript : URI to download the Psipred diagram in postscript format
psipred_results : URI to download the psipred results in ascci format

ApiSimpleModeller

SubmitMessage Submit()
base64 template_pdb : The template pdb file for modeller in uncompressed ascii format
base64 pir_alignment : The alignment for modeller in ascii format
string modeller : Your valid modeller licence key
SimpleModellerResult Result()
model_pdb : URI to download pdb file of the homology model built by modeller