> Send EMBOSS mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/emboss > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of EMBOSS digest..." > > > Today's Topics: > > 1. Re: [emboss-dev] EMBOSS Funding and New developments (Peter Rice) > 2. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 3. Re: EMBOSS Funding and New developments (Peter Rice) > 4. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 5. Re: EMBOSS Funding and New developments (Guy Bottu) > 6. Packaging EMBOSS for Fedora (Julian Sikorski) > 7. Re: Packaging EMBOSS for Fedora (Mahmut Uludag) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 09 Jun 2009 16:11:58 +0100 > From: Peter Rice <[email protected]> > Subject: Re: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments > To: George Magklaras <[email protected]> > Cc: emboss <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > George Magklaras wrote: >> That's very good news Peter. >> >> I would add to the list the production of documentation for the EMBOSS >> admins. In terms of improving the indexing, may node managers (including >> myself) have created scripts to automate the formatting of large >> databases. Maybe it might be an idea to include them in some sort of >> add-on section, so that people can have error-free formatted dbs with >> the click of a button or a script call. > > Documentation is on the way in the form of an Administrators Guide ... > long promised but we are now adding the final touches to the text. > > The book will be open source and the text will also appear on the EMBOSS > website. > > As to the scripts ... yes, and excellent suggestion. We could make a > directory adminscripts in the distribution for these. > > Please contribute useful scripts for use to include. We would like to > include some documentation on what the script is intended to do and how > to modify it. As the target users are administrators, we can expect them > to be able to make their own modifications. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 2 > Date: Tue, 9 Jun 2009 17:44:54 +0200 > From: "Giovanni Marco Dall'Olio" <[email protected]> > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice <[email protected]> > Cc: [email protected], > [email protected], emboss <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice <[email protected]> wrote: > >> Dear EMBOSS Users and Developers >> > > >> Suggestions for new applications are very welcome. >> > > I think EMBOSS is highly effective when combined with Makefiles or tools > to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. > > Another need that people have asked me several times (I am administrator > of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google > doesn't > return clear results. > > > > >> >> >> We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of >> this month, We will arrange a lunchtime "Birds of a Feather" session >> at ISMB to discuss the needs of users over the next 3 years. >> >> regards, >> >> Peter Rice >> _______________________________________________ >> EMBOSS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 3 > Date: Tue, 09 Jun 2009 16:59:45 +0100 > From: Peter Rice <[email protected]> > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: [email protected] > Cc: [email protected], emboss > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > Giovanni Marco Dall'Olio wrote: >> I think EMBOSS is highly effective when combined with Makefiles or tools >> to >> describe pipelines. >> Maybe in the future you could add some recipe or example in the >> documentation, it would be useful. In any case, it would be good to add >> to >> the tutorials some references on methods to describe pipelines. > > What pipelines so users prefer? > > We have experience with Taverna and with SoapLab web services. We have > also worked with Accelrys/Scitegic's Pipeline Pilot. These all include > EMBOSS examples in their documentation. > >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > We have long hoped that one interface would become the standard. Our > usual recommendation for web-based users is the wEMBOSS interface but > when ever we ask which interfaces users prefer we get many different > replies. > > So, please let us know which interfaces you like best and we will try to > work with the developers to make sure it keeps up with changes to EMBOSS > ... and we can try to help them by adding new features or by > automatically building their interface to a new EMBOSS release. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 4 > Date: Tue, 9 Jun 2009 19:11:11 +0200 > From: "Giovanni Marco Dall'Olio" <[email protected]> > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice <[email protected]> > Cc: [email protected], emboss > <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice <[email protected]> wrote: > >> Giovanni Marco Dall'Olio wrote: >> > I think EMBOSS is highly effective when combined with Makefiles or >> tools >> to >> > describe pipelines. >> > Maybe in the future you could add some recipe or example in the >> > documentation, it would be useful. In any case, it would be good to >> add >> to >> > the tutorials some references on methods to describe pipelines. >> >> What pipelines so users prefer? >> >> We have experience with Taverna and with SoapLab web services. We have >> also worked with Accelrys/Scitegic's Pipeline Pilot. These all include >> EMBOSS examples in their documentation. > > > Yes, taverna and soaplab services are very good but they are more oriented > to write applications that connect to Internet and execute tools which are > also web services. > > Sometimes you need much simpler tools, e.g. organize a workflow of command > line tools to be run in local on an unix shell, and this is something for > which emboss is very good, since it resembles many unix tools like grep > and > similar. > > My favorite introduction to Makefiles is the one on the Software Carpentry > manual: > - http://swc.scipy.org/lec/build.html > > I could write some example for you if you want, but actually I haven't > been > using emboss for a while, so.. let me re-read the documentation first :-) > > > > > Another need that people have asked me several times (I am > administrator >> of >> > a web forum on bioinformatics) is to have a standard and official web >> > interface to the emboss tools, since the list at >> > http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> > return clear results. >> >> We have long hoped that one interface would become the standard. Our >> usual recommendation for web-based users is the wEMBOSS interface but >> when ever we ask which interfaces users prefer we get many different >> replies. >> >> So, please let us know which interfaces you like best and we will try to >> work with the developers to make sure it keeps up with changes to EMBOSS >> ... and we can try to help them by adding new features or by >> automatically building their interface to a new EMBOSS release. >> > > the web forum is this one (in Italian): > - http://www.molecularlab.it/forum/default.asp > usually, people ask questions like 'how to I translate a sequence to > protein?', 'how to create a dotplot', etc.. - there is not always a good > answer to these questions, but in the past I have suggested the emboss > tools > because they seemed a kind of standard. > (by the way, it would be good to know which tests have being applied to > verify emboss code. I don't like telling people to use a command line > tool, > if there is no way to tell that it has been proved to work fine). > > I used to like very much this interface: > - http://embossgui.sourceforge.net/demo/ > which is very clear and has a list of all the tools, but is still running > the 3.0 version. > > I also like the ebi interface, because it is hosted on an well-known > server > (people don't like using servers they don't know) but it supports very few > tools; > > galaxy has also a nice web interface to emboss, but sometimes you just > need > to link a paste&submit interface to execute simple tasks like translating > a > sequence, and I haven't found anything like that yet. > > > >> regards, >> >> Peter Rice >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 5 > Date: Thu, 11 Jun 2009 16:41:10 +0200 > From: Guy Bottu <[email protected]> > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice <[email protected]> > Cc: [email protected], emboss > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Giovanni Marco Dall'Olio wrote: >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > Now that we are at it, could the hyperlink not be changed ? It is > http://wemboss.sourceforge.net and not anymore http://www.wemboss.org > > Guy Bottu > > > > > ------------------------------ > > Message: 6 > Date: Fri, 12 Jun 2009 22:40:08 +0200 > From: Julian Sikorski <[email protected]> > Subject: [EMBOSS] Packaging EMBOSS for Fedora > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > a while ago I made an attempt to create an EMBOSS package for Fedora > [1]. The progress was stalled for a while due to my MSc having higher > priority, but I have recently picked up the work again. > I have one crucial question: is it worth to package jemboss? It seems it > didn't see development since 2005, and I have experienced some important > issues when trying to use it (mainly not working with files with spaces > in filenames). What do you think? > > Kind regards, > Julian > > [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133 > > > > ------------------------------ > > Message: 7 > Date: Sat, 13 Jun 2009 00:49:16 +0100 > From: Mahmut Uludag <[email protected]> > Subject: Re: [EMBOSS] Packaging EMBOSS for Fedora > To: Julian Sikorski <[email protected]> > Cc: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain > > Hi Julian, > >> I have one crucial question: is it worth to package jemboss? It seems it >> didn't see development since 2005, and I have experienced some important >> issues when trying to use it (mainly not working with files with spaces >> in filenames). What do you think? > > I had a quick look into the files with spaces in filenames problem, we > can include a fix in the coming release (6.1) for this problem. Previous > release of EMBOSS (6.0) included some fixes of similar nature, as well > as some small gui improvements. We recently have updated EMBOSS/Jemboss > make/install machinery to make standalone Jemboss come out of box when > users install EMBOSS, i think we were successful and this will be a new > feature in EMBOSS 6.1. > > Regards, > Mahmut > > > > > ------------------------------ > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > > > End of EMBOSS Digest, Vol 48, Issue 2 > ************************************* >
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