From d.counsell at hgmp.mrc.ac.uk Thu Sep 19 09:00:57 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Thu, 19 Sep 2002 14:00:57 +0100 Subject: rowf! rowf! [was: Re: Photographs of cynodonts] In-Reply-To: <3D89852A.2010909@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Thu, Sep 19, 2002 at 09:04:58AM +0100 References: <3D1C3EF5.CA3@hgmp.mrc.ac.uk> <3D89852A.2010909@uk.lionbioscience.com> Message-ID: <20020919140057.A20116@dev4.hgmp.mrc.ac.uk> > So, if EMBOSS is a cynodont ... who does this remind you of? > > http://news.bbc.co.uk/1/hi/sci/tech/2266954.stm I'm glad Peter mentioned this because I keep forgetting to tell you lot that my EMBOSS Tux-style* cynodont is under development here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/cynodont.png . Comments welcome before I fix his paws and colour him---or, indeed, her---in. Yes, (s)he does look a bit smug, but wouldn't you if you were about to inherit the Earth from a bunch of over-sized, greedy pea-brains? (*"Tux" is the name of the Linux penguin: http://www.isc.tamu.edu/~lewing/linux/ ) all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From rls at ebi.ac.uk Thu Sep 19 10:47:56 2002 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Thu, 19 Sep 2002 15:47:56 +0100 Subject: rowf! rowf! [was: Re: Photographs of cynodonts] In-Reply-To: <20020919140057.A20116@dev4.hgmp.mrc.ac.uk> Message-ID: Oh! My God! It looks just like you! R:) > -----Original Message----- > From: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk]On Behalf Of Damian Counsell > Sent: 19 September 2002 14:01 > To: Peter Rice > Cc: emboss-dev at embnet.org; emboss-bug at embnet.org; Damian Counsell > Subject: rowf! rowf! [was: Re: Photographs of cynodonts] > > > > So, if EMBOSS is a cynodont ... who does this remind you of? > > > > http://news.bbc.co.uk/1/hi/sci/tech/2266954.stm > > I'm glad Peter mentioned this because I keep forgetting to tell you > lot that my EMBOSS Tux-style* cynodont is under development here: > > http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/cynodont.png > > . Comments welcome before I fix his paws and colour him---or, indeed, > her---in. Yes, (s)he does look a bit smug, but wouldn't you if you > were about to inherit the Earth from a bunch of over-sized, greedy > pea-brains? > > (*"Tux" is the name of the Linux penguin: > > http://www.isc.tamu.edu/~lewing/linux/ > > ) > > > all the best > > Damian > > > -- > Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk > MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 > Cambridge CB10 1SB direct: +44 (0)1223 494585 > http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 > > From gwilliam at hgmp.mrc.ac.uk Fri Sep 27 06:18:14 2002 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Fri, 27 Sep 2002 11:18:14 +0100 (BST) Subject: Some comments on EMBOSS Message-ID: <200209271018.g8RAIEi12003@californium.hgmp.mrc.ac.uk> The HGMP has been gathering data from a questionnaire about its service. These are some of the comments that mention EMBOSS... Gary I have recently had to teach myself how to use EMBOSS as I could no longer justify paying for using the GCG package. I was not disappointed though I found it a bit less intuitive, but that could simply be because I had to read the help pages and try things out. I think the EMBOSS package could be promoted a bit better as I would have stopped using GCG sooner had I known what the EMBOSS program could do; not to mention the cost of using GCG.. I need to use GCG all the time and when it became that I had to pay for it I tried using EMBOSS but it just does not do what I require as easily and well as GCG. This is after consultation with your help desk on EMBOSS. Even a simple programme like finding restriction enzymes is really a poor substitute for GCG. I work with large constructs ~90kb -200kb and we clone by homologous recombination. Not very keen on Jemboss cf W2H I can't actually get it to run on my slightly aged PC. If the W2H author isn't working on it more it might be nice to take that over ie a non J[ava] web interface. Better Emboss functionality to equal GCG I am missing the GCG package, and would like to see more improvements on the EMBOSS package so that it can fully replace the GCG. I wish to continue accessing GCG programs, and do not wish to swap to EMBOSS!! I can't seem to access any help for EMBOSS programs. Mostly self evident what they do from title. Multiple sequence editor useful - I would however like to be able to see some worked examples of this despite the help section being useful. From gwilliam at hgmp.mrc.ac.uk Fri Sep 27 08:34:29 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 27 Sep 2002 13:34:29 +0100 Subject: [Fwd: Soaplab - a SOAP-based access to EMBOSS] Message-ID: <3D945055.16788D6B@hgmp.mrc.ac.uk> Another interface to EMBOSS. Gary Martin Senger wrote: > I was developing a package of Web Services accessing all EMBOSS tools > (at the moment still the old version 1.9.1 but it's just a question of > short time to move to the latest emboss version). The service is provided > at EBI in the 'experimental mode' for anybody (but particularly used by > the myGrid project). Please feel free to look at it, to use it, and/or > to ask me for more details. > The URL with documentation and examples (btw, it includes all examples > from the EMBOSS Tutorial) is at http://industry.ebi.ac.uk/soaplab. Also > please feel free to re-distribute this message to other emboss developers > and users. > > Regards, > Martin > > -- > Martin Senger > > EMBL Outstation - Hinxton Senger at EBI.ac.uk > European Bioinformatics Institute Phone: (+44) 1223 494636 > Wellcome Trust Genome Campus (Switchboard: 494444) > Hinxton Fax : (+44) 1223 494468 > Cambridge CB10 1SD > United Kingdom http://industry.ebi.ac.uk/~senger -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From d.counsell at hgmp.mrc.ac.uk Thu Sep 19 13:00:57 2002 From: d.counsell at hgmp.mrc.ac.uk (Damian Counsell) Date: Thu, 19 Sep 2002 14:00:57 +0100 Subject: rowf! rowf! [was: Re: Photographs of cynodonts] In-Reply-To: <3D89852A.2010909@uk.lionbioscience.com>; from peter.rice@uk.lionbioscience.com on Thu, Sep 19, 2002 at 09:04:58AM +0100 References: <3D1C3EF5.CA3@hgmp.mrc.ac.uk> <3D89852A.2010909@uk.lionbioscience.com> Message-ID: <20020919140057.A20116@dev4.hgmp.mrc.ac.uk> > So, if EMBOSS is a cynodont ... who does this remind you of? > > http://news.bbc.co.uk/1/hi/sci/tech/2266954.stm I'm glad Peter mentioned this because I keep forgetting to tell you lot that my EMBOSS Tux-style* cynodont is under development here: http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/cynodont.png . Comments welcome before I fix his paws and colour him---or, indeed, her---in. Yes, (s)he does look a bit smug, but wouldn't you if you were about to inherit the Earth from a bunch of over-sized, greedy pea-brains? (*"Tux" is the name of the Linux penguin: http://www.isc.tamu.edu/~lewing/linux/ ) all the best Damian -- Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 Cambridge CB10 1SB direct: +44 (0)1223 494585 http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 From rls at ebi.ac.uk Thu Sep 19 14:47:56 2002 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Thu, 19 Sep 2002 15:47:56 +0100 Subject: rowf! rowf! [was: Re: Photographs of cynodonts] In-Reply-To: <20020919140057.A20116@dev4.hgmp.mrc.ac.uk> Message-ID: Oh! My God! It looks just like you! R:) > -----Original Message----- > From: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk]On Behalf Of Damian Counsell > Sent: 19 September 2002 14:01 > To: Peter Rice > Cc: emboss-dev at embnet.org; emboss-bug at embnet.org; Damian Counsell > Subject: rowf! rowf! [was: Re: Photographs of cynodonts] > > > > So, if EMBOSS is a cynodont ... who does this remind you of? > > > > http://news.bbc.co.uk/1/hi/sci/tech/2266954.stm > > I'm glad Peter mentioned this because I keep forgetting to tell you > lot that my EMBOSS Tux-style* cynodont is under development here: > > http://www.hgmp.mrc.ac.uk/~dcounsel/EDP/cynodont.png > > . Comments welcome before I fix his paws and colour him---or, indeed, > her---in. Yes, (s)he does look a bit smug, but wouldn't you if you > were about to inherit the Earth from a bunch of over-sized, greedy > pea-brains? > > (*"Tux" is the name of the Linux penguin: > > http://www.isc.tamu.edu/~lewing/linux/ > > ) > > > all the best > > Damian > > > -- > Damian COUNSELL email: d.counsell at hgmp.mrc.ac.uk > MRC Human Genome Mapping Project RC phone: +44 (0)1223 494500 > Cambridge CB10 1SB direct: +44 (0)1223 494585 > http://www.hgmp.mrc.ac.uk/~dcounsel/ fax: +44 (0)1223 494512 > > From gwilliam at hgmp.mrc.ac.uk Fri Sep 27 10:18:14 2002 From: gwilliam at hgmp.mrc.ac.uk (gwilliam at hgmp.mrc.ac.uk) Date: Fri, 27 Sep 2002 11:18:14 +0100 (BST) Subject: Some comments on EMBOSS Message-ID: <200209271018.g8RAIEi12003@californium.hgmp.mrc.ac.uk> The HGMP has been gathering data from a questionnaire about its service. These are some of the comments that mention EMBOSS... Gary I have recently had to teach myself how to use EMBOSS as I could no longer justify paying for using the GCG package. I was not disappointed though I found it a bit less intuitive, but that could simply be because I had to read the help pages and try things out. I think the EMBOSS package could be promoted a bit better as I would have stopped using GCG sooner had I known what the EMBOSS program could do; not to mention the cost of using GCG.. I need to use GCG all the time and when it became that I had to pay for it I tried using EMBOSS but it just does not do what I require as easily and well as GCG. This is after consultation with your help desk on EMBOSS. Even a simple programme like finding restriction enzymes is really a poor substitute for GCG. I work with large constructs ~90kb -200kb and we clone by homologous recombination. Not very keen on Jemboss cf W2H I can't actually get it to run on my slightly aged PC. If the W2H author isn't working on it more it might be nice to take that over ie a non J[ava] web interface. Better Emboss functionality to equal GCG I am missing the GCG package, and would like to see more improvements on the EMBOSS package so that it can fully replace the GCG. I wish to continue accessing GCG programs, and do not wish to swap to EMBOSS!! I can't seem to access any help for EMBOSS programs. Mostly self evident what they do from title. Multiple sequence editor useful - I would however like to be able to see some worked examples of this despite the help section being useful. From gwilliam at hgmp.mrc.ac.uk Fri Sep 27 12:34:29 2002 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Fri, 27 Sep 2002 13:34:29 +0100 Subject: [Fwd: Soaplab - a SOAP-based access to EMBOSS] Message-ID: <3D945055.16788D6B@hgmp.mrc.ac.uk> Another interface to EMBOSS. Gary Martin Senger wrote: > I was developing a package of Web Services accessing all EMBOSS tools > (at the moment still the old version 1.9.1 but it's just a question of > short time to move to the latest emboss version). The service is provided > at EBI in the 'experimental mode' for anybody (but particularly used by > the myGrid project). Please feel free to look at it, to use it, and/or > to ask me for more details. > The URL with documentation and examples (btw, it includes all examples > from the EMBOSS Tutorial) is at http://industry.ebi.ac.uk/soaplab. Also > please feel free to re-distribute this message to other emboss developers > and users. > > Regards, > Martin > > -- > Martin Senger > > EMBL Outstation - Hinxton Senger at EBI.ac.uk > European Bioinformatics Institute Phone: (+44) 1223 494636 > Wellcome Trust Genome Campus (Switchboard: 494444) > Hinxton Fax : (+44) 1223 494468 > Cambridge CB10 1SD > United Kingdom http://industry.ebi.ac.uk/~senger -- Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512 mailto:G.Williams at hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK