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From BioPerl

Interwiki link to BLAST at wikiomics: wikiomics:BLAST

Contents 1 Template examples 1.1 Underscore issues... 1.2 HOWTO 2 RSS Feed testing 3 Dumb test 4 References 5 Transcribing/editing template tests 6 TreeAndMenu 7 Widgets 8 Gravatars

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?

• CGI_Lite
• Bio::Graph::IO::psi_xml
• Bio::Graph::IO::psi%5Fxml

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

---

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

---

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:

O|B|F News BioPerl has moved to GitHub O|B|F Google Summer of Code Accepted Students O|B|F in Google Summer of Code BioPerl at GMOD Meeting 2010 Sanger FASTQ format and the Solexa/Illumina variants BioPerl interview in latest FLOSS Weekly BioPerl core 1.6.1 PPM available First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network BioPerl 1.6.1 released Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network

full is not working

O|B|F News BioPerl has moved to GitHub BioPerl has migrated to git and 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 Algorithms Jianjiong Gao (PM Peter Rose) – BioJava Packages for Identification, Classification, and Visualization of [...] 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. BioPerl at GMOD Meeting 2010 BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just Sanger FASTQ format and the Solexa/Illumina variants I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby), Michael L. [...] BioPerl interview in latest FLOSS Weekly Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. BioPerl core 1.6.1 PPM available BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated. First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is the first run where we’ve switched to a regular Module::Build installation, so expect some initial [...] BioPerl 1.6.1 released We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes [...] Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network All, I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000). FIXED: 1) Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names 2) Bio::Tools::Run::Vista tests now pass [...]

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

Dumb test

• Bio::SearchIO
• Yes

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 .

1. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006 Oct 26; 443(7114) 931-49. pmid:17073008. PubMed HubMed [honeybee2006]

Transcribing/editing template tests

Your emanuensis trying out some typing-savers...

• Template:Discuss:Pers

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

• Template:Cruft:Boog : getting parameters...

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

• Template:Discuss:Ed

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

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

• Template:Discuss:Thread : fooling about...

(thread)

( thread)

(for a good time, click thread)

• Template:Discuss:Thread
• Template:Discuss:Ed
• Template:Discuss:Quips
• Template:Discuss:Opines
• Template:Discuss:HoldsForth
• Template:Discuss:EdQuips
• Template:Discuss:EdOpines
• Template:Discuss:Date

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:

No biscuit:

# ERROR: Account maj?ruin=true not valid (arg 1)

No biscuit either:

# ERROR: Valid widget types are 'Detailed', 'Rank', and 'Tiny' (arg 2)

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....

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

http://www.ohloh.net/accounts/maj/widgets/account_tiny.gif http://www.ohloh.net/accounts/maj/widgets/account_tiny.gif

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:

Sorry, account/widget spec is invalid : got /../narb and Tiny

bad widget, down boy!:

Sorry, account/widget spec is invalid : got 40601 and EraseAll

try:

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

works but Google cruft everywhere.

Gravatars

should see one here:

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

http://www.gravatar.com/avatar/a95faf027ae8ac4d34e3e94847b374fa.jpg

Again, a timing problem.

http://www.gravatar.com/avatar/a95faf027ae8ac4d34e3e94847b374fa.jpg # ERROR: Email maj at fortinbras dot us not valid

http://www.gravatar.com/avatar/a95faf027ae8ac4d34e3e94847b374fa.jpg

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