[EMBOSS] EMBOSS Funding and New developments

[Giovanni Marco Dall'Olio]

On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice <pmr at ebi.ac.uk> 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 http://emboss.sourceforge.net/interfaces/#web is outdated and google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