- beg-bogas@psb.ugent.be - maillist.psb.ugent.be

[Beg-bogas] [BOGAS] #171: url security
by BOGAS 18 Jan '11

18 Jan '11

#171: url security ---------------------+------------------------------------------------------ Reporter: liste | Owner: liste Type: defect | Status: new Priority: major | Milestone: BOGAS_v4 Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ need to look into 'security' issues concerning 'genome' replacements in URL => sometimes possible to get to another (non-registrated) genome. eg with the newlocus function. =>possible to check 'login' on every URL?? -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/171> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] EBI HELP: InterProScan WS end-point changes
by User Support 13 Jan '11

13 Jan '11

Dear User A new InterProScan service is now available providing REST and document/literal SOAP interfaces. These have been tested extensively and are now ready for production. The present versions of this interface are scheduled for retirement mid February 2011. Please provide feedback on any issues encountered and any suggestions for additional features using http://www.ebi.ac.uk/support/. For details see the documentation: InterProScan (REST) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest InterProScan (SOAP) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap All the best, Support@Ebi

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[Beg-bogas] EBI HELP: Services downtime Jan 7th-10th 2011
by User Support 06 Jan '11

06 Jan '11

Dear User, As announced on our web site, services from EMBL-EBI will not be available from Friday January 7th 2011 16:30 GMT and until Monday January 10th 2011 12:00 GMT (if not earlier). This is due to urgent maintenance on the campus data centre. However, some services will remain operational (or semi-operational) as these are not running from the data centre in Hinxton: http://www.ebi.ac.uk/Tools/sss http://www.ebi.ac.uk/Tools/msa http://www.ebi.ac.uk/Tools/pfa http://www.ebi.ac.uk/QuickGo http://www.ebi.ac.uk/citexplore The corresponding SOAP/REST Web Services interfaces for the above will also remain operational. EMBL-EBI apologises for the inconvenience this may cause. Support@Ebi

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[Beg-bogas] EBI HELP: Services downtime Jan 7th-10th 2011
by User Support 06 Jan '11

06 Jan '11

Dear User, As announced on our web site, services from EMBL-EBI will not be available from Friday January 7th 2011 16:30 GMT and until Monday January 10th 2011 12:00 GMT (if not earlier). This is due to urgent maintenance on the campus data centre. However, some services will remain operational (or semi-operational) as these are not running from the data centre in Hinxton: http://www.ebi.ac.uk/Tools/sss http://www.ebi.ac.uk/Tools/msa http://www.ebi.ac.uk/Tools/pfa http://www.ebi.ac.uk/QuickGo http://www.ebi.ac.uk/citexplore The corresponding SOAP/REST Web Services interfaces for the above will also remain operational. EMBL-EBI apologises for the inconvenience this may cause. Support@Ebi

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[Beg-bogas] EBI HELP: Services downtime Jan 7th-10th 2011
by User Support 06 Jan '11

06 Jan '11

Dear User, As announced on our web site, services from EMBL-EBI will not be available from Friday January 7th 2011 16:30 GMT and until Monday January 10th 2011 12:00 GMT (if not earlier). This is due to urgent maintenance on the campus data centre. However, some services will remain operational (or semi-operational) as these are not running from the data centre in Hinxton: http://www.ebi.ac.uk/Tools/sss http://www.ebi.ac.uk/Tools/msa http://www.ebi.ac.uk/Tools/pfa http://www.ebi.ac.uk/QuickGo http://www.ebi.ac.uk/citexplore The corresponding SOAP/REST Web Services interfaces for the above will also remain operational. EMBL-EBI apologises for the inconvenience this may cause. Support@Ebi

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[Beg-bogas] FW: Ectocarpus siliculosus
by Meijer, Harold 20 Dec '10

20 Dec '10

Since I could not contact Mr. Farnham, I contact you with the observation/question below. Cheers, Harold ______________________________________________ From: Meijer, Harold Sent: Monday 20 December 2010 16:19 To: 'GAFA(a)MBA.ac.uk' Subject: Ectocarpus siliculosus Dear Mr. Farnham, During a blast I encountered a PLC annotated by you. However, I have doubts on the genemodel. Currently, it is denoted as http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/current/… However, I have a strong feeling that the http://bioinformatics.psb.ugent.be/webtools/bogas/annotation/Ectsi/current/… should be connected via a small region between the gene models. Maybe you could have a look again and mail me your findings on this. Yours sincerely, Harold Meijer Dr. ing. Harold J. G. Meijer Wageningen University and Research Centre Plant Sciences Group Laboratory of Phytopathology Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands Tel (room): +31 317 483138 fax : +31 317 483412 Email: Harold.meijer(a)wur.nl

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[Beg-bogas] account
by ACE 16 Dec '10

16 Dec '10

Dear: I need an account. Thanks. best wishes!

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[Beg-bogas] EBI HELP: INTERPROSCAN - New SOAP/REST Web Service
by User Support 10 Dec '10

10 Dec '10

Hi folks, A new InterProScan service is now available providing REST and document/literal SOAP interfaces. These have been tested extensively and are now ready for production. The present versions of this interface are scheduled for retirement mid February 2011. Please provide feedback on any issues encountered and any suggestions for additional features using http://www.ebi.ac.uk/support/. For details see the documentation: InterProScan (REST) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest InterProScan (SOAP) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap All the best, Support@Ebi

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[Beg-bogas] EBI HELP: INTERPROSCAN - New SOAP/REST Web Service
by User Support 10 Dec '10

10 Dec '10

Hi folks, A new InterProScan service is now available providing REST and document/literal SOAP interfaces. These have been tested extensively and are now ready for production. The present versions of this interface are scheduled for retirement mid February 2011. Please provide feedback on any issues encountered and any suggestions for additional features using http://www.ebi.ac.uk/support/. For details see the documentation: InterProScan (REST) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest InterProScan (SOAP) http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap All the best, Support@Ebi

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[Beg-bogas] novice annotator has problem
by David Nelson 05 Dec '10

05 Dec '10

Dear help, I have annotated the pseudogene Solyc04g079620.1.1 I merged it with its two neighbors (one on each side). I saved it and it looks the way I intended in ANNOJ and Genome View, but the BOGAS page is empty. Can you tell me why? What did I do wrong? When I saved the three merged models in Genome View I chose to delete the obsolete structures. Did this eliminate the BOGAS models? -- David R. Nelson Associate Professor Dept. of Microbiology, Immunology and Biochemistry 858 Madison Ave. Suite G01 University of Tennessee Memphis TN 38163 (901) 448-8303 phone (901) 448-7360 fax dnelson(a)uthsc.edu

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