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Interwiki link to BLAST at wikiomics: wikiomics:BLAST


Contents

Template examples

Created Template:PM to simplify Module linking.

By typing {{PM|Bio::SeqIO}} you automatically get a link that looks like this:

Bio::SeqIO

It's a one parameter macro to save duplicate typing of the module name.

--Tseemann 19:19, 27 December 2005 (EST)

Testing new CPAN macro: Digest::MD5

Underscore issues...

Problem with underscores?

Or is it the Doclink macro?



Pdoc documentation: Bio::Graph::IO::psi_xml CPAN documentation: Bio::Graph::IO::psi_xml


Here's my version:

BEFORE

  • _1_ = Bio::Graph::IO::psi xml
  • mod = Bio::Graph::IO::psi_xml
  • dir = bioperl-live
  • url = Bio/Graph/IO/psi_xml.html



AFTER

  • _1_ = Bio::Graph::IO::psi xml
  • mod = Bio::Graph::IO::psi_xml
  • dir = bioperl-live
  • url = Bio/Graph/IO/psi_xml.html


The problem still occurs on this page Bio::Graph::IO::psi_xml - I guess the underscore means space in Wiki article names, but not in a macro paramter?

--Tseemann 18:56, 31 December 2005 (EST)

So this looks to be resolved now. In the future {{PAGENAMEE}} apparently gives you back the pagename with underscores. See PAGENAME and PAGENAMEE and Spaces vs underscores

--jason stajich 12:38, 3 January 2006 (EST)

HOWTO

Testing new HOWTO macro: SearchIO HOWTO (should link to HOWTO:SearchIO ...)

--Tseemann 16:06, 29 December 2005 (EST)

Bio::Tools::Run::PiseApplication


RSS Feed testing

Short on:

full is not working

Travis-CI for Testing
BioRuby, Biopython and BioPerl are now using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated. Continue reading

BioPerl-DB, BioPerl-Run, BioPerl-Network 1.6.9 released
The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network Please report any bugs to our Redmine server. Enjoy! chris
BioPerl 1.6.9 released
OBF and Google Summer of Code 2011
Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code! Continue reading
Introduction of OpenID logins for OBF wikis
Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading
OBF Redmine server now available
BioPerl has moved to GitHub
O|B|F Google Summer of Code Accepted Students
I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment … Continue reading
O|B|F in Google Summer of Code
O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010. Continue reading

BioPerl at GMOD Meeting 2010

--jason stajich 19:59, 23 April 2006 (EDT)


Dumb test

References

I like the wikipedia linking to articles within an article, but the Biblio plugin is so much cooler for not having to type in a whole reference . <biblio>

  1. honeybee2006 pmid=17073008

</biblio>

Transcribing/editing template tests

Your emanuensis trying out some typing-savers...

[[User:{{{2}}}|Fred]] Banjovi

Parm1 is Wittgenstein. On the other hand, Parm2 is, in fact, Sartre. Funny how these things work out.


How's your mom, --[[User:Majensen|]] ?

Marxism: "Time flies like an arrow, but fruitflies like a banana." --Groucho

(thread)

( thread)

(for a good time, click thread)


TreeAndMenu

Let's test the TreeAndMenu

  • Root1
    • Sub-item
    • Another sub-item
  • Root2
    • Sub-item
    • Another sub-item


Widgets

Create a Winter add-in that works like the gravatar add-in:


# ERROR (20): operator maj not defined in (|maj|Tiny). </span>


No biscuit:

# ERROR (20): operator maj?ruin=true not defined in (|maj?ruin=true|Tiny).

No biscuit either:

# ERROR (20): operator maj not defined in (|maj|Furshlugginer).



account_Tiny.gif

NO

Yes

Yes

Yes

NO


can we render the external stuff as-is?? sometimes... set

$wgAllowExternalImagesFrom = array( 'http://www.ohloh.net/' );

then this should work

https://www.ohloh.net/accounts/40601?ref=Tiny

but it doesn't, because this does point directly to a file with an img extension, probably.

or maybe

[1]

No. Hmm.

Firebug to the rescue!! Try....

account_detailed.gif

https://www.ohloh.net/accounts/maj/widgets/account_detailed.gif

YES! Now to create the php widget, so that Ohloh is duly linked back to.


try the custom ohloh gadget

UNIQ74abff854729cc12-widget-00000005-QINU

Ok, a wiki render timing issue. The placement of the widget-generated text comes after point at which figure urls are parsed and rendered. What happens if we template it?

{{Cruft:Ohloh|maj|Tiny}}

Forget about the WikiWidget; just template it:

{{Cruft:OhlohWidget|maj|Tiny}}

OOOOH! That works!


bad widget, no biscuit:

UNIQ74abff854729cc12-widget-00000008-QINU

bad widget, down boy!:

UNIQ74abff854729cc12-widget-00000009-QINU



try:

UNIQ74abff854729cc12-widget-0000000A-QINU

... Yes we can -- but how safe??? try the ohloh gadget:

UNIQ74abff854729cc12-widget-0000000B-QINU

works but Google cruft everywhere.

Gravatars

should see one here:

a95faf027ae8ac4d34e3e94847b374fa.jpg

Sweet. Now...what about the new Winter function?...

# ERROR (3): Syntax error in (var|gravatar|maj@fortinbras.us).

Again, a timing problem.


# ERROR (3): Syntax error in (var|gravatar|maj -at- fortinbras -dot- us). </span>


# ERROR (3): Syntax error in (var|gravatar|maj-at-fortinbras-dot-us). # ERROR (3): Syntax error in (var|gravatar|maj at fortinbras dot us).


# ERROR (3): Syntax error in (var|gravatar|maj -at- fortinbras -dot- us).


Templating just won't get the url to the page on time. Have to resort to Winter itself.

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