UCL Bioinformatics Group Asynchronous Web Services#

A full list of available webservices are available these URLs
http://bioinfdev.cs.ucl.ac.uk/psipred_api/wsdl
http://bioinfdev.cs.ucl.ac.uk/psipred_api/invoke

All services include a submit and results function. Use submit to send jobs to a given method and use 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.

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

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 results function can be called to poll the state of the running job. All functions return the following common fields:

message: A short human readable message about the current state of the job
job_id : The job_id
state : A computer readable number indicating the success of the job

0 - job has stopped in an error state, check the message field.
1 - job completed successfully, the results fields will be filled out
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

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

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

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

ApiMemsatsvm#

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
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

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

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

ApiMgenthreader#

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

ApiPsipred#

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

PsipredResult Result()
psipred_postscript : URI to download the Psipred diagram in postscript format
psipred_results : URI to download the psipred results in ascci format

ApiDomthreader#

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

DomthreaderResult Result() domthreader_data : URI to download domthreader data table

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

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

ApiMempack#

SubmitMessage Submit()
string sequence : A protein sequence in ASCII format
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

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

ApiMakeTdb#

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

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« This page (revision-1) was last changed on 10-Nov-2011 15:00 by UnknownAuthor