>> When implementing this workflow in a portal, what would you like as
>> available options for species and chromosome?

How much time do you have??? At least human, mouse, pufferfish, zebrafish, dros, c.elegans,aradadopsis, yeast, ciona, chick, rat, chimp, xenopus, new world monkey(?) (cat, dog, pig, cow - perhaps)

And do these examples

>> only make sense in pairs? (what I mean is, given a particular
>> species had been entered, do only certain chromosome numbers apply -
>> I vaguely remember from doing GCSE Biology that plants and humans
>> have different numbers of chromosomes, but to humans and cows for
>> example have different numbers of chromosomes?)

unfortunalty yes - different chromosome numbers for different species.

But the workflow will work if you don't enter a species or chromosome (although you need to give it a space instead) - ie you don't want to filter the results Or if you only give it a species and no chromosome (again use a space) but NOT if only enter a chromosome number.

Do you need the exact details now?? It'll take me a little while to get that list and chromosome numbers together, but I'll mail them on as soon as I've got them.

Hope that helps Hannah

>>
>>
>>
>> h.j.tipney@stud.man.ac.uk wrote:
>>
>
>>> >Hi Steffen
>>> >Sorry - I probably didn't elaborate enough and just gave you a
>>> >bunch on files!
>>> >
>>> >Right, you are correct about the inputs
>>> >INPUT_BareSeq.txt -> bare_seq_in
>>> >INPUT_oldBlastResults.txt -> old_result
>>> >use 'Homo sapiens' (with out quotes) as species input (or any other
>>> >species you fancy! Mus musculus etc) and '7' (again without quotes)
>>> >for chromosome - or any other digit.
>>> >
>>> >
>>> >
>>
>>>> >>1> what do you do if you don't have any old results, so want to
>>>> >>run the workflow with no input on 'old_result'? I remember you
>>>> >>saying something about using an input of just one space?
>>>> >>
>>>> >>
>>
>>> >This is what happens the very first time the workflow is ran - and
>>> >yes, because of the way soaplab works you need to give it an entry
>>> >or is breaks, so use a space (' ') -again no quotes
>>> >
>>> >
>>> >
>>
>>>> >>3> after running the workflow once with no input on 'old_results',
>>>> >>which output of the workflow should be passed to 'old_results'
>>>> >>next time I run the workflow?
>>>> >>
>>>> >>
>>
>>> >You'll notice that the output from the simplifier service is put
>>> >into
>>> > comparer and also as a stand alone output 'simple'.This is the
>>> > file
>>> >you need. Comparer takes the 'new' blast output and compares it to
>>> >the 'new' one - any new hits are then fed into retrieve.
>>> >
>>> >I wanted to check all of this to makes sure everything works fine
>>> >but
>>> > I can't access taverna at the mo - so if you put everything in
>>> > like
>>> >I said and there is still any problems let me know - it might be
>>> >some
>>> > of the newer services being picky! Oh the joys of myGrid!
>>> >
>>> >Good luck!
>>> >Hannah
>>> >
>>> >------------------------------------------
>>> >Hannah Tipney
>>> >Manchester University,
>>> >Academic Unit of Medical Genetics,
>>> >St Mary's Hospital,
>>> >Hathersage Road,
>>> >Manchester. M13 0JH.
>>> >UK
>>> >
>>> >tel: +44 (0)161 276 6602
>>> >fax: +44 (0)161 276 6606
>>> >
>>> >
>
>>
>>
>>
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