Re: works-with-format for bioinformatics
Le Mon, Nov 17, 2008 at 10:02:08AM -0800, Shaun Jackman a écrit : 2008/11/17 Enrico Zini [EMAIL PROTECTED]: Also, since we have biology::format:fasta, why are you suggesting works-with-format::fasta and works-with-format::fastq instead of just biology::format:fastq? I noticed biology::format:fasta only after I suggested works-with-format::fasta. I'm now asking what the difference between the two would be. The two categories biology::format and works-with-format seem redundant. Hi Shaun, the biology:: facet was the product of a disucussion during which I had some misunderstandings about debtags. I wouldn't mind to see it removed. Here is the lastest wishlist I made to the Debtags team: http://lists.alioth.debian.org/pipermail/debtags-devel/2008-September/001841.html I would of course welcome the creation of a works-with-format:: tags for the bioinformatics programs we package. Have a nice day, -- Charles Plessy Debian Med packaging team, Tsurumi, Kanagawa, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Missing packages in the per-maintainer list ?
Dear Debtags team, I am trying to polish Debian Med's Debtags for Lenny. To do so, I click on our PTS page, and follow the Debtags link: http://qa.debian.org/[EMAIL PROTECTED]ubuntu=1 http://debtags.alioth.debian.org/todo.html?maint=debian-med-packaging%40lists.alioth.debian.org Strangely, some packages that show up in the PTS do not appear in the Debtags page. Any hint ? Have a nice day, -- Charles Plessy Debian Med packaging team, Tsurumi, Kanagawa, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
different (although one does often the first before the second), and comparison is very broad. A researcher will never search just for a comparison tool when looking for alignment software or phylogenetic analysis software. Of course, looking at all the pacakges tagged field::biology which have alignment in their description can also do the job in most cases, so the need for these tags depend on wether you feel like that tag searchs should be useable independantly or complementarly to other tools. Pay attention that, in the case of software having many functions such as EMBOSS, the keyword may be absent from the description. A few words of the proposals you made in another mail: * ::bioinformatics, ::molecular-biology, ::structural-biology I would rather see field::biology:molecular than field::biology:molecular-biology, but it is a matter of taste. biology::molecular-biology:structural instead of biology::structural(-biology) may horrify some of our colleagues, though. * ::emboss I strongly advocate suite::emboss we will get the critical mass for it. In conclusion, about the possiblity to manage ourselves our sets of tags. In the everyday work, one has a very narrow point of view of his tools. I use a PCR machine to make a PCR, I use a Pipetmanⓡ to pipette,... this could be expressed by biology::PCR, and biology::pipetting. But if we think harder, we can have a higher point of view. Instead of biology::PCR it would be use::amplification, or use::diagnostic, for instance, because the PCR machine produces DNA, but sometimes we want to keep it as a reagent, and some other times we just want to see its size and then we throw it away. So the questions I am wondering about are : - What is the most powerful approach ? - What is the expectations of our users ? - How can we interest our users in an unexpeced and powerful usage of the DebTags ? Biological research is very conservative in the tools it uses, and some software have an enormous advantage on others just because of the oral tradition. Standard usage of DebTags will help us to show alternative software to our userbase - just look at how much clustalw, non-free, is still more popular than programs which are either faster, more precise, or both: http://people.debian.org/~igloo/popcon-graphs/index.php?packages=hmmer+boxshade+clustalw+clustalx+seaview+muscle+t-coffee+sim4+sibsim4+arb+dialign+kalign+probcons+wise+amap-align+poashow_installed=onwant_legend=onfrom_date=to_date=hlght_date=date_fmt=beenhere=1 I think that an advanced usage of Debtags is the only way to bring attention of users and ourselves to programs which we do not expect to be relevant to their fields. This is why I am pushing a bit for more fine-grained tags in mutliple official facets, rather than a private biology:: facet in which we will reproduce the idiosyncrasies of our disciplines... Many thanks for your patience with our long mails :) -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
Le Thu, Sep 06, 2007 at 10:21:57PM +0200, Benjamin Mesing a écrit : There are two more things to consider: 1. the users who do searching based on tags and 2. the people doing the tagging. With each tag, the complexity of the vocabulary will be increased and only a small percentage of the people mentioned above is interested in the level of detail provided by the med-specific tags. Hello, nobody wants to be lost in a space with too many dimentions which are almost empty. This is why I would prefer to express the properties of the package with already existing tags rather than with private biology:: tags. But I will of course not oppose anybody using this approach, and will do my best so that the packages in our radar are using them appropriately if they exist. So unless there is a new idea popping out, my recommendation is to commit the tags for which we all aggreed on, and re-open the discussion in a few monthes where: - we in Debian-Med have extended our software coverage, - you have got diverse feedback from other Debian teams. Have a nice day, PS: biology::molecular-biology:structural instead of biology::structural(-biology) may horrify some of our colleagues, though. I think you have misread my proposal here. Or I am misunderstand you. What would horrify your colleagues? That structural biology is a whole discipline of its own, and not a mere offspring of molecular biology ;) -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
New tags for biology and medicine.
Hi Debtags team ! This is the monthly reminder that the Debian-Med team proposed new tags in May, http://lists.alioth.debian.org/pipermail/debtags-devel/2007-May/001630.html http://lists.alioth.debian.org/pipermail/debtags-devel/2007-July/001658.html Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: Tags for biology and medecine (was : Debian Menu transition)
Le Mon, Jul 23, 2007 at 06:53:38AM +0200, Luca Brivio a écrit : Alle ven 20 luglio 2007, Charles Plessy ha scritto: actually, the Debian-Med project discussed about this in the past, and for the moment we are just happy to use field::biology and request the addition of field::medecine. I guess field::medicine. :-) BTW: Would any debtags translation be useful [soon]? Ciao Luca, From the debian-med point of view, I would say that it is not particulary prioritary, especially that the vocabulary of the Debtags is rather simple. I think that the translation of the package descriptions is more challenging, but more useful. If you want an easier start, we have some .desktop files for which you could provide Italian translations: ./treeviewx/trunk/debian/treeviewx.desktop ./perlprimer/trunk/debian/perlprimer.desktop ./seaview/trunk/debian/seaview.desktop ./clustalw/trunk/debian/clustalx.desktop ./melting/trunk/debian/melting-gui.desktop They are in our SVN repository : http://svn.debian.org/wsvn/debian-med/trunk/packages/?rev=0sc=0 Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Tags for biology and medecine (was : Debian Menu transition)
-- Science/Medicine (CDDs are already using a suite::debian-med) Dear Debtags developpers, actually, the Debian-Med project discussed about this in the past, and for the moment we are just happy to use field::biology and request the addition of field::medecine. A diff file was posted in May, but was overlooked : http://lists.alioth.debian.org/pipermail/debtags-devel/2007-May/001630.html Have a nice day, -- Charles Plessy Debian-Med packaging team Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: Which DebTag for Debian-Med ?
Le Mon, Jan 08, 2007 at 02:25:59PM +0100, Steffen Moeller a écrit : On Monday 08 January 2007 10:41, Thijs Kinkhorst wrote: I do not think that suite is the right choice, tagging with field is much more useful; as you can see, under field are such fields as astronomy, biology and chemistry already available. Adding field::medicine would be useful to me, and to put subclasses of medicine below it: Hi all, Thijs has a point: with the suite:: tags I just would like to transfer existing information in the debtags system. In the future, the information could flow in the opposite direction, but this is up to the people developing the CDD framework. (the metapackages of debian-med are Custom Debian Distribution metapackages). fields::biology::sequence fields::biology::sequence::dna fields::biology::sequence::rna fields::biology::sequence::protein fields::biology::structure fields::biology::interaction fields::biology::genomics fields::biology::proteomics fields::biology::metabolomics If we are affraid of not having enough packages to populate all the subfields, we could group all the omics with interaction, and call this systems-biology, or biology::systems. If necessary, we could revive the distinction in another facet, such as use for instance, like: field::biology::systems use::experimental::genomics::microarrays works-with-format::xml::miame or, in an example similar to Steffen's: field::biology::sequence use::analysis::comparison works-with-format::plaintext::aln If the debtags list agrees on the main lines, we could finalise the discussion on the debian-med list. By the way, does anybody knows an ontology of the scientific fields? This could save some time... Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
