[HELICONIUS] heliconius.org & butterflybase

Fri Mar 10 19:04:39 GMT 2006

Hello all,

Chris is more or less correct.  I have not been working on Butterflybase,
per se, but on extending the Chado Schema, the schema that underlies
flybase, to include genotypic and phenotypic information.  The advantage is
that it will both allow us to organize our data and use established (and
quite powerful) tools.  For example, check out Comparative Map Viewer (CMap)
in the Gramene database (http://www.gramene.org/).  This is going well and
next week, I hope to begin importing data and testing how well we have done.

I am also thinking about designing some new tools that utilize the new data
elements that we have added. Some time ago, I wrote everybody asking for
suggestions about some to the types of queries that we might wish to make in
the future.  I haven't gotten much feedback, so if anybody gets a lighting
bolt of an idea, please send it this way.

Owen 

On 3/10/06 12:49 PM, "Chris Jiggins" <chris.jiggins at ed.ac.uk> wrote:

> Dear all,
> 
> I basically agree with Alexie that heliconius.org should be turned into
> a mouthpiece for the 'Heliconius consortium' with information on all
> the labs and people involved.  I have been meaning to do this for a
> while - the format of the pages will change once I get round to it.
> However I would very much welcome any suggestions for layout (Owen
> already suggested that we model it on the Daphnia genome pages, which
> are very nicely organised http://daphnia.cgb.indiana.edu/).  Once the
> pages are set up we will want a small piece of text about each lab (or
> would people rather stick with a link to their own web pages?).  I
> would also be keen to take up Jim's offer to put together an overview
> page with links to pertinent literature in different subject areas - I
> think this would be very useful.
> 
>   For the moment the site will stay at heliconius.cap.ed.ac.uk and I
> will leave it here in Edinburgh until I have figured out how we can
> best host it - either in Cambridge or on Jim's site.
> 
> As for ButterflyBase development, Owen is supposed to have some people
> working on it in Duke.  Please send your suggestions and we can discuss
> what are the priorities for added features and improvements.
> 
> chris
> 
> 
> 
> On 9 Mar 2006, at 17:20, Jim Mallet wrote:
> 
>> Dear Alexie and others,
>> 
>> At 17:28 08/03/2006, you wrote:
>>> Hello hello... Am I the one to devirginise this email list? I hope I'm
>>> worth it.
>> 
>> As the parent of the virginal HELICONIUS list, I like to protect my
>> child, and I believe that she dealt effectively with your advances!
>> Anyway, I think you will find that there were some incestuous messages
>> in her cavities before yours.
>> 
>>> I'm taking requests on feature development for ButterflyBase. Also we
>>> can start a discussion of whether we want to set up a dedicated
>>> www.heliconius.org website server with all the helic info as well as
>>> lab
>>> pages. One person from each lab will responsible for updating one bit
>>> of
>>> the Heliconius wunderworld. It's good for funding applications... eh i
>>> mean public image.
>> 
>> General information pages.
>> I am not sure that we should be doing much in the way of public
>> relations or school-level science-type work -- I don't think we need
>> popular pieces available on Heliconius butterflies or anything like
>> that.  But perhaps that wasn't what you meant.
>> 
>> What we do need, perhaps, is pointers to the literature on any
>> particular topic, such as to review articles on evolution, colour
>> pattern genetics, host plant ecology, etc.  We should also attempt to
>> digitise theses and other unpublished grey literature, old literature
>> no longer available, especially in Latin American libraries or
>> information that still is not online anywhere (such as some of the
>> Zoologica, NY articles) etc., unpublished data not available in online
>> appendices (and some that is), e.g. alignments etc.  I would be happy
>> to oversee efforts in some topics like this.  There is already a
>> certain amount of Heliconius information already on the
>> www.ucl.ac.uk/taxome/jim/ website, and it seems to me that this kind
>> of provision of information could be improved, for example a more
>> snazzy and informative http://www.ucl.ac.uk/taxome/jim/helicinf.htm
>> page, or a series of such pages could itemize different kinds of
>> information.
>> 
>> The location of Heliconius information.
>> Whether or not the actual pages are online on www.heliconius.org 's
>> own server should not matter from the point of view of the heliconius
>> community.  A central heliconius.org page will have pointers to
>> information occurring on any the servers of the partcular labs hosting
>> the data.  We can also think about mirroring information later for
>> safe keeping.
>> 
>> Who will now host the Heliconius.org pages?
>> Incidentally, with Chris Jiggins' impending move to Cambridge,
>> heliconius.org will presumably want move server as well.  I could
>> offer you space on www.ucl.ac.uk/taxome. A subdirectory like
>> www.ucl.ac.uk/taxome/heliconius/ makes a certain amount of sense
>> anyway in my overall grandiose ambitions for the Taxome Project.  UCL
>> lets me have reasonably large amounts of space on their central
>> servers, and if it isn't TOO, too large, I think they will give me
>> more whenever I need it. (Whole genome sequence information, perhaps
>> will start to become getting too large for them, without scoring
>> proper income to fund the server space, I don't know!)  So if
>> Cambridge are more sniffy about this sort of thing, you should realize
>> you are free to use /taxome as a home (it has its own separate
>> account). (Many universities, and especially museums like the NHM are
>> extremely sniffy, and have lots of annoying restrictions on web page
>> formats and content)
>> 
>> The advantages of managed university servers.
>> When we're really rich, and can afford paid IS experts to run a server
>> properly and securely, then we'll undoubtedly need our own servers.
>> But while we are still a cottage industry, it makes sense to use the
>> free security and management services of a well-set up university IS
>> department like UCL's.
>> 
>> Jim
>> 
>> 
>> 
>>> Here are some section suggestions
>>> -Plain speak of our research (incl. any school level science facts
>>> someone might have already generated).
>>> -Ecological data (habitats, distribution, phylogenies).
>>> -Morphological data of species, races, hybrids.
>>> -Genomic data (i.e. Butterflybase).
>>> -Genetic Data (inc. primer database, crossing results people have
>>> accumulated (specimendb?) etc).
>>> -others
>>> 
>>> I think the first point should be tackled as soon as possible. my
>>> humble
>>> opionion is that it will be good for a genome application
>>> 
>>> As Owen has suggested elsewhere, it will be good idea to utilise WiKi
>>> technology on this. we will see...
>>> 
>>> enjoy the snow/sand/jungle
>>> 
>>> Alexie Papanicolaou
>>> http://www.halcyoni.org
>>> 'Scientists' from the Evangelical Center For Faith-Based Reasoning are
>>> now asserting that the long-held 'theory of gravity' is flawed, and
>>> they
>>> have responded to it with a new theory of Intelligent Falling.
>>> "What the gravity-agenda scientists need to realize is that 'gravity
>>> waves' and 'gravitons' are just secular words for 'God can do whatever
>>> He wants.'"
>>> -theonion.com
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> HELICONIUS mailing list
>>> HELICONIUS at ucl.ac.uk
>>> http://www.mailinglists.ucl.ac.uk/mailman/listinfo/heliconius
>> 
>> James Mallet
>> http://www.ucl.ac.uk/taxome/jim/
>> 
>> 
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>> 
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> Chris Jiggins
> Institute of Evolutionary Biology
> School of Biology
> University of Edinburgh
> Edinburgh EH9 3JT
> Scotland  UK
> Tel: (+44)(0)131 650 8624
> Fax: (+44)(0)131 650 6564
> Home: 0131 228 6389
> http://www.heliconius.org/
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> 
> 
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> 

***************************************
W. Owen McMillan
Associate Professor
Department of Biology
University of Puerto Rico- Rio Piedras
P.O. Box 23360
San Juan, PR  00931-3360
wmcmilla at rrpac.upr.clu.edu
http://zephyr.hpcf.upr.edu/~mcmi-lab/

Contact details during Sabbatical:
National Evolutionary Synthesis Center
2024 West Main Street, Suite A200
Durham, North Carolina  27705
919-668-4598 (voice)
919-668-9192 (fax)
omcmillan at nescent.org