From wolfgang.rumpf at gmail.com Mon Dec 3 15:46:52 2012 From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf) Date: Mon, 03 Dec 2012 15:46:52 -0500 Subject: [EMBOSS] Emboss-explorer broken in Ubuntu 12.10? Message-ID: I just upgraded one of my boxes to 12.10 and it borked emboss-explorer (menus no longer properly load, applications not available). I did a clean install of 12.10 and Emboss/Emboss-Explorer on a different machine, same result. Everything worked fine on 12.04 ? any ideas? Cheers, Wolfgang ---------------------------------------------------------------------------- --- Dr. Wolfgang Rumpf Senior Director of Product, irisnote Inc Adjunct Faculty, Dept. of Biotechnology, UMUC ---------------------------------------------------------------------------- --- wolfgang.rumpf at irisnote.com wolfgang.rumpf at gmail.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf ---------------------------------------------------------------------------- --- http://culture.no-ip.org/quantumthoughts From david.bauer at bayer.com Tue Dec 4 02:09:57 2012 From: david.bauer at bayer.com (David Bauer) Date: Tue, 4 Dec 2012 07:09:57 +0000 Subject: [EMBOSS] WG: Error in Emboss Explorer after updated EMBOSS to 6.5.7 Message-ID: <801E8305DB9A574FB64B5A2EE8366A610165626F@BY09QA.DE.bayer.cnb> Hi Wolfgang, this issue already appeared some time ago. It seems that the emboss explorer at sourceforge is no longer maintained. I did a quick fix to the modules so that they work again with the latest EMBOSS release. Please try it out and drop me a note if it works for you. Kind regards, David. -----Urspr?ngliche Nachricht----- Von: David Bauer Gesendet: 26 October 2012 10:10 An: 'Jean Mao' Betreff: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 Hi Jean, I found the real reason for this problem and fixed it in the XHTML.pm module. There are also some minor additions for the ontology lookup programs. If your system is running, you can just replace the old modules with the new ones in the attached tar file. On my system those modules are installed in "/usr/local/lib/perl5/site_perl/5.14.2/EMBOSS". Kind regards, David. -----Urspr?ngliche Nachricht----- Von: Jean Mao [mailto:maoj at mail.nih.gov] Gesendet: 24 October 2012 13:46 An: David Bauer Betreff: Re: AW: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 Hi David, Thank you so much for looking into this. I will try it and let you know. Regards, Jean On 10/24/12 07:16, David Bauer wrote: > Hi Jean, > > sorry for coming back to you so late but I had some other things on my schedule with higher priority.... > > The problem is the extractalign program in the group ALIGN. > I do not yet fully understand what is exactly the problem but this is the only program in the top level ALIGN group which itself has several subgroups "ALIGN LOCAL" etc. This structure is new and unique and somehow this situation confuses the parser. > > So there are 2 quick fixes (or better workarounds) possible: > > 1) change the extractalign.acd file > If you just change this from > groups: "Alignment, Data retrieval:Sequence data, Edit" > to > groups: "Data retrieval:Sequence data, Edit" > and the emboss explorer works again as expected :-) > > 2) exclude the ALIGN group from the emboss explorer menu > In Conf.pm there is an @EXCLUDED variable which can be used to exclude individual programs or groups from the interface. > You can simply add "ALIGNMENT" to this. > It will only remove the ALIGNEMENT group from the display. > Because extractalign is also in the groups EDIT and DATA RETRIEVAL SEQUENCE DATA, the program will still be there but just not listed under the ALIGNMENT group. > > > I will try to find a better fix for this problem and also add the new data types for the ontology apps. > > > Kind regards, > David. > > > -----Urspr?ngliche Nachricht----- > Von: Jean Mao [mailto:maoj at mail.nih.gov] > Gesendet: 05 September 2012 13:29 > An: David Bauer > Betreff: Re: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 > > Hi David, > > Thank you very much for getting back to me. I also really appreciate > that you are willing to spend your time to check into this. > > Regards, > > Jean > > On 09/05/12 02:46, David Bauer wrote: >> Hi Jean, >> >> I've been using the emboss explorer in the past, when I was responsible for providing this package to our users. >> Since my focus has shifted, I use emboss just for my own work, where I don't need the web interface. >> >> The emboss explorer interface is created dynamically from the acd files and there have been several fundamental changes in the last few emboss versions to those. >> >> I will take a look at this to see, if I can get the emboss explorer working again with the latest emboss version. >> >> >> Kind regards, >> David. >> >> -----Urspr?ngliche Nachricht----- >> Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Jean Mao >> Gesendet: 04 September 2012 17:31 >> An: emboss at lists.open-bio.org >> Betreff: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 >> >> Hi, >> >> I know this list is for EMBOSS, not emboss explorer. However, I am not >> sure where to look for help with emboss explorer anymore so I am trying >> my luck here. Really appreciate if someone can point me to the right >> direction. >> >> Recently I updated emboss to 6.5.7 from 6.3.1. Emboss Explorer was >> functional before I switched the link. Once the link is switched to >> point to 6.5.7, the main manu panel on the left of the webpage is >> comletely messed up. In stead of showing categories and apps under each >> category, now there is only categories showing and no apps that one can >> click and load. The most current emboss explorer I can find is 2.2.0 and >> was out since 2006. >> >> Regards, >> >> Jean >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_expl_fix.tar.gz Type: application/x-gzip Size: 18126 bytes Desc: emboss_expl_fix.tar.gz URL: From Geetha.Vasudevan at bms.com Fri Dec 21 11:26:19 2012 From: Geetha.Vasudevan at bms.com (Vasudevan, Geetha) Date: Fri, 21 Dec 2012 11:26:19 -0500 Subject: [EMBOSS] EMBOSS - IEP/PEPSTATS Message-ID: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> >Hi, >> >>I have been trying to figure out the origin for the difference in computed pI >>value between EMBOSS-IEP (or EMBOSS-PEPSTATS) and Vector NTI (which uses >Expasy Compute pI/MW). > > >>I get 7.07 with EMBOSS and 6.65 with Expasy. I also tried the web site of >Expasy and I get the same as VectorNTI. >> >>Do you know the origin of the variation? >> >>Any input is highly appreciated. >> >> >>Thanks, >>-Geetha >> > This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. From ricepeterm at yahoo.co.uk Sun Dec 23 04:04:14 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Sun, 23 Dec 2012 09:04:14 +0000 Subject: [EMBOSS] EMBOSS - IEP/PEPSTATS In-Reply-To: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> References: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> Message-ID: <50D6C90E.7000801@yahoo.co.uk> On 21/12/2012 16:26, Vasudevan, Geetha wrote: >>> I have been trying to figure out the origin for the difference in computed pI >>> value between EMBOSS-IEP (or EMBOSS-PEPSTATS) and Vector NTI (which uses >> Expasy Compute pI/MW). >> >>> I get 7.07 with EMBOSS and 6.65 with Expasy. I also tried the web site of >> Expasy and I get the same as VectorNTI. >>> >>> Do you know the origin of the variation? We use amino acid data values calculated for native amino acids. Expasy uses values calculated from protein isoelectric focussing (e.g. for 2D gels) under specific conditions, with a note that for highly basic proteins these values may not approximate experimentally determined values. There are multiple possible data values that can be used for isoelectric point calculations, for example Wikipedia gives a third set without attribution. You can choose your own pKa values for each amino acid by using a local copy of file Epk.dat. For the next release we will add further documentation on the origin of the default values used by EMBOSS, and may add a choice of pKa data sets depending on the reason for the pI calculation and make the Epk.dat file name specifiable by a new command line qualifier. Hope this helps, Peter Rice EMBOSS Team From wolfgang.rumpf at gmail.com Mon Dec 3 20:46:52 2012 From: wolfgang.rumpf at gmail.com (Wolfgang Rumpf) Date: Mon, 03 Dec 2012 15:46:52 -0500 Subject: [EMBOSS] Emboss-explorer broken in Ubuntu 12.10? Message-ID: I just upgraded one of my boxes to 12.10 and it borked emboss-explorer (menus no longer properly load, applications not available). I did a clean install of 12.10 and Emboss/Emboss-Explorer on a different machine, same result. Everything worked fine on 12.04 ? any ideas? Cheers, Wolfgang ---------------------------------------------------------------------------- --- Dr. Wolfgang Rumpf Senior Director of Product, irisnote Inc Adjunct Faculty, Dept. of Biotechnology, UMUC ---------------------------------------------------------------------------- --- wolfgang.rumpf at irisnote.com wolfgang.rumpf at gmail.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf ---------------------------------------------------------------------------- --- http://culture.no-ip.org/quantumthoughts From david.bauer at bayer.com Tue Dec 4 07:09:57 2012 From: david.bauer at bayer.com (David Bauer) Date: Tue, 4 Dec 2012 07:09:57 +0000 Subject: [EMBOSS] WG: Error in Emboss Explorer after updated EMBOSS to 6.5.7 Message-ID: <801E8305DB9A574FB64B5A2EE8366A610165626F@BY09QA.DE.bayer.cnb> Hi Wolfgang, this issue already appeared some time ago. It seems that the emboss explorer at sourceforge is no longer maintained. I did a quick fix to the modules so that they work again with the latest EMBOSS release. Please try it out and drop me a note if it works for you. Kind regards, David. -----Urspr?ngliche Nachricht----- Von: David Bauer Gesendet: 26 October 2012 10:10 An: 'Jean Mao' Betreff: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 Hi Jean, I found the real reason for this problem and fixed it in the XHTML.pm module. There are also some minor additions for the ontology lookup programs. If your system is running, you can just replace the old modules with the new ones in the attached tar file. On my system those modules are installed in "/usr/local/lib/perl5/site_perl/5.14.2/EMBOSS". Kind regards, David. -----Urspr?ngliche Nachricht----- Von: Jean Mao [mailto:maoj at mail.nih.gov] Gesendet: 24 October 2012 13:46 An: David Bauer Betreff: Re: AW: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 Hi David, Thank you so much for looking into this. I will try it and let you know. Regards, Jean On 10/24/12 07:16, David Bauer wrote: > Hi Jean, > > sorry for coming back to you so late but I had some other things on my schedule with higher priority.... > > The problem is the extractalign program in the group ALIGN. > I do not yet fully understand what is exactly the problem but this is the only program in the top level ALIGN group which itself has several subgroups "ALIGN LOCAL" etc. This structure is new and unique and somehow this situation confuses the parser. > > So there are 2 quick fixes (or better workarounds) possible: > > 1) change the extractalign.acd file > If you just change this from > groups: "Alignment, Data retrieval:Sequence data, Edit" > to > groups: "Data retrieval:Sequence data, Edit" > and the emboss explorer works again as expected :-) > > 2) exclude the ALIGN group from the emboss explorer menu > In Conf.pm there is an @EXCLUDED variable which can be used to exclude individual programs or groups from the interface. > You can simply add "ALIGNMENT" to this. > It will only remove the ALIGNEMENT group from the display. > Because extractalign is also in the groups EDIT and DATA RETRIEVAL SEQUENCE DATA, the program will still be there but just not listed under the ALIGNMENT group. > > > I will try to find a better fix for this problem and also add the new data types for the ontology apps. > > > Kind regards, > David. > > > -----Urspr?ngliche Nachricht----- > Von: Jean Mao [mailto:maoj at mail.nih.gov] > Gesendet: 05 September 2012 13:29 > An: David Bauer > Betreff: Re: AW: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 > > Hi David, > > Thank you very much for getting back to me. I also really appreciate > that you are willing to spend your time to check into this. > > Regards, > > Jean > > On 09/05/12 02:46, David Bauer wrote: >> Hi Jean, >> >> I've been using the emboss explorer in the past, when I was responsible for providing this package to our users. >> Since my focus has shifted, I use emboss just for my own work, where I don't need the web interface. >> >> The emboss explorer interface is created dynamically from the acd files and there have been several fundamental changes in the last few emboss versions to those. >> >> I will take a look at this to see, if I can get the emboss explorer working again with the latest emboss version. >> >> >> Kind regards, >> David. >> >> -----Urspr?ngliche Nachricht----- >> Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Jean Mao >> Gesendet: 04 September 2012 17:31 >> An: emboss at lists.open-bio.org >> Betreff: [EMBOSS] Error in Emboss Explorer after updated EMBOSS to 6.5.7 >> >> Hi, >> >> I know this list is for EMBOSS, not emboss explorer. However, I am not >> sure where to look for help with emboss explorer anymore so I am trying >> my luck here. Really appreciate if someone can point me to the right >> direction. >> >> Recently I updated emboss to 6.5.7 from 6.3.1. Emboss Explorer was >> functional before I switched the link. Once the link is switched to >> point to 6.5.7, the main manu panel on the left of the webpage is >> comletely messed up. In stead of showing categories and apps under each >> category, now there is only categories showing and no apps that one can >> click and load. The most current emboss explorer I can find is 2.2.0 and >> was out since 2006. >> >> Regards, >> >> Jean >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss -------------- next part -------------- A non-text attachment was scrubbed... Name: emboss_expl_fix.tar.gz Type: application/x-gzip Size: 18126 bytes Desc: emboss_expl_fix.tar.gz URL: From Geetha.Vasudevan at bms.com Fri Dec 21 16:26:19 2012 From: Geetha.Vasudevan at bms.com (Vasudevan, Geetha) Date: Fri, 21 Dec 2012 11:26:19 -0500 Subject: [EMBOSS] EMBOSS - IEP/PEPSTATS Message-ID: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> >Hi, >> >>I have been trying to figure out the origin for the difference in computed pI >>value between EMBOSS-IEP (or EMBOSS-PEPSTATS) and Vector NTI (which uses >Expasy Compute pI/MW). > > >>I get 7.07 with EMBOSS and 6.65 with Expasy. I also tried the web site of >Expasy and I get the same as VectorNTI. >> >>Do you know the origin of the variation? >> >>Any input is highly appreciated. >> >> >>Thanks, >>-Geetha >> > This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. From ricepeterm at yahoo.co.uk Sun Dec 23 09:04:14 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Sun, 23 Dec 2012 09:04:14 +0000 Subject: [EMBOSS] EMBOSS - IEP/PEPSTATS In-Reply-To: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> References: <4F3EC1CE7A305245A71338EEC51D821FCD25276497@USHPWBMSCMP002.one.ads.bms.com> Message-ID: <50D6C90E.7000801@yahoo.co.uk> On 21/12/2012 16:26, Vasudevan, Geetha wrote: >>> I have been trying to figure out the origin for the difference in computed pI >>> value between EMBOSS-IEP (or EMBOSS-PEPSTATS) and Vector NTI (which uses >> Expasy Compute pI/MW). >> >>> I get 7.07 with EMBOSS and 6.65 with Expasy. I also tried the web site of >> Expasy and I get the same as VectorNTI. >>> >>> Do you know the origin of the variation? We use amino acid data values calculated for native amino acids. Expasy uses values calculated from protein isoelectric focussing (e.g. for 2D gels) under specific conditions, with a note that for highly basic proteins these values may not approximate experimentally determined values. There are multiple possible data values that can be used for isoelectric point calculations, for example Wikipedia gives a third set without attribution. You can choose your own pKa values for each amino acid by using a local copy of file Epk.dat. For the next release we will add further documentation on the origin of the default values used by EMBOSS, and may add a choice of pKa data sets depending on the reason for the pI calculation and make the Epk.dat file name specifiable by a new command line qualifier. Hope this helps, Peter Rice EMBOSS Team