wwood (Ben J Woodcroft)

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Name: Ben J Woodcroft

Email

Company: University of Melbourne, University of Queensland

Location: Melbourne, Brisbane

Member Since: Jun 27, 2008 (about 1 year)

Following 2 githubbers and watching 28 repositories view all →

Public Repositories (14)

- 1
- 3
excelsior

Ruby gem that uses C bindings to read CSV files superfast. I'm totally serial!

Forked from toastyapps/excelsior Sun Dec 13 16:05:58 -0800 2009

Last updated Sun Dec 13 16:18:15 -0800 2009
- 1
- 1
bbbin

A collection of working and non-working bioinformatics scripts

Last updated Fri Nov 27 12:38:18 -0800 2009
- 1
- 1
blast_link

A few scripts for turning a vanilla NCBI wwwblast installation into a link filled paradise.

Last updated Thu Nov 19 15:01:43 -0800 2009
- 3
- 0
rarff

(fork) A Ruby library for handling ARFF files, as popularized by the WEKA machine learning program

Last updated Wed Nov 18 17:12:59 -0800 2009
- 1
- 26
bioruby

bioruby

Forked from bioruby/bioruby Sun Sep 07 18:05:47 -0700 2008

Last updated Mon Nov 16 20:30:22 -0800 2009
- 1
- 34
rip

Ruby's Intelligent Packaging

Forked from defunkt/rip Fri Jun 12 05:28:23 -0700 2009

Last updated Fri Jun 12 05:47:45 -0700 2009
- 1
- 70
jeweler

Simple and opinionated helper for creating Rubygem projects on GitHub

Forked from technicalpickles/jeweler Sat Jan 17 16:51:38 -0800 2009

Last updated Fri Jan 16 21:26:47 -0800 2009
- 1
- 0
scim

(Unofficial) Smart Common Input Method

Last updated Mon Dec 29 17:18:23 -0800 2008
- 1
- 0
wwood.github.com

Personal Pages

Last updated Thu Dec 18 18:08:36 -0800 2008
- 2
- 6
rsruby

(Unofficial) Ruby - R bridge - Please send pull requests to alexgutteridge/rsruby

Forked from alexgutteridge/rsruby Sat Nov 22 00:25:42 -0800 2008

Last updated Sat Nov 22 00:29:19 -0800 2008
- 1
- 0
reach

Extend the Ruby Array class for less loops and blocks

Last updated Thu Nov 06 23:40:33 -0800 2008
- 1
- 0
eupathdb_ubiquity

EuPathDB Ubiquity scripts

Last updated Wed Oct 29 21:55:56 -0700 2008
- 1
- 15
query_trace

Adds query origin tracing to your logs - this fork allows the plugin to be turned on/off in datab...

Forked from jonleighton/query_trace Sun Nov 02 03:54:55 -0800 2008

Last updated Wed Sep 03 08:30:07 -0700 2008
- 1
- 3
kawaii

Kawaii is like a web frontend to script/console for your Rails apps, with nicely formatted output

Forked from eviltrout/kawaii Sun Jul 27 22:10:16 -0700 2008

Last updated Sun Jul 27 22:18:56 -0700 2008

Public Activity

wwood pushed to formats at wwood/excelsior Sun Dec 13 16:18:15 -0800 2009

HEAD is 1d245aef5b05e0e82f5e4f6aeb47b26f12a3c882

Ben J Woodcroft committed 1d245aef:

fixed another typo in test, but formats branch still does not work

wwood pushed to formats at wwood/excelsior Sun Dec 13 16:13:57 -0800 2009

HEAD is 46c0e53b1a42189b42402224aac4b3eebf6bf1b3

Ben J Woodcroft committed 46c0e53b:

fixed bug in test, but formats branch still does not work

wwood pushed to formats at wwood/excelsior Sun Dec 13 16:07:55 -0800 2009

HEAD is 2804be4fee8001f29a9e60f4cefeee7e2a5fb6c5

Ben J Woodcroft committed 2804be4f:

added test for tab-separated values file input

wwood forked toastyapps/excelsior Sun Dec 13 16:06:00 -0800 2009

Forked repository is at wwood/excelsior

wwood opened issue 2 on toastyapps/excelsior Sat Dec 12 15:26:27 -0800 2009

tab separated values

wwood started watching toastyapps/excelsior Sat Dec 12 15:23:18 -0800 2009

excelsior's description:

Ruby gem that uses C bindings to read CSV files superfast. I'm totally serial!

wwood updated gist: 30649 Sun Nov 29 14:15:58 -0800 2009

CmdUtils.CreateCommand({ names: ["orthomcl"], arguments: [{label: "gene_or_group_accession", ...

wwood pushed to master at wwood/bbbin Fri Nov 27 12:38:19 -0800 2009

HEAD is da8a772e85874a1fa05f06453c9497089f8c9eae

12 commits »

Ben J Woodcroft committed da8a772e:

made ncbi not default
Ben J Woodcroft committed 0e7a8ce0:

added topbash for tilda integration
Ben J Woodcroft committed 338de762:

b
Ben J Woodcroft committed 678ec0f1:

added doc and indented blast_to_blastclust.rb
Ben J Woodcroft committed 15583dac:

merging easily
Ben J Woodcroft committed 87c6f94e:

a more fleshed out apicomplexan database creator and server starter
Ben J Woodcroft committed 9d54877e:

added cryptoDB 4.2 to database_create
Ben J Woodcroft committed 44330e9f:

working database_create
Ben J Woodcroft committed 34fb08a5:

updated apicomplexan_database_create.sh to plasmodb 6.1
Ben J Woodcroft committed 97dcdb2b:

apicomplexan_database_create now has eupath_db version numbers as constants
Ben J Woodcroft committed 9d7f1c49:

fixed a small bug in trees_distance
Ben J Woodcroft committed 0e9f3524:

fixed trees_parsimony problems that were introduced by allowing bootstrap=1 (and bad coding)

wwood created branch master at wwood/blast_link Thu Nov 19 15:01:44 -0800 2009

New branch is at wwood/blast_link/tree/master

wwood created repository blast_link Thu Nov 19 15:01:00 -0800 2009

New repository is at wwood/blast_link

wwood pushed to master at wwood/rarff Wed Nov 18 17:12:59 -0800 2009

HEAD is ebbb933a322adc7a8fc45cca16ad6dcd6ae0ae6a

9 commits »

Ben J Woodcroft committed ebbb933a:

moved from hoe to jeweler, gem now up on gemcutter
Ben J Woodcroft committed d2f72dbc:

Version bump to 0.2.4
Ben J Woodcroft committed c9785a03:

Version bump to 0.2.3
Ben J Woodcroft committed 7926c55c:

Version bump to 0.2.2
Ben J Woodcroft committed b1f72708:

Version bump to 0.2.1
Ben J Woodcroft committed 1650c017:

Version bump to 0.2.0
Ben J Woodcroft committed 4629c68f:

Version bump to 0.1.0
Ben J Woodcroft committed 8a5c2e82:

Version bump to 0.0.0
Ben J Woodcroft committed 14eb2875:

added more tests, and set_string_attributes_as_nominal can now handle a subset of attributes to set as nominal

wwood pushed to url at wwood/bioruby Mon Nov 16 20:30:25 -0800 2009

HEAD is 5a61d88c00163340300053c5916838f2f99e94ca

208 commits »

Naohisa Goto committed 9def7df5:

install.rb is replaced by new setup.rb
Naohisa Goto committed 637f97de:

Improvement of Bio::NCBI::REST by Toshiaki Katayama
Naohisa Goto committed 02de70cb:

Bug fix: Bio::Sequence::Common#randomize severely biased
Ra committed 99421059:

Test
Ra committed 67fbbb93:

Fix: typing error
Naohisa Goto committed c699253d:

Merging patches by Raoul in commit 496561a70784d3a1a82bf3117b2d267c7625afac which are ignored when rebasing, probably because of manually editing during merge
Ra committed f701e9a7:

Fix: check on nil objects (to_biosql)
Ra committed f6e1530f:

BugFix: ex. /focus="true" in output was /focus="t", qualifie.value.to_s fix the bug
Ra committed fb740093:

BugFix: seqfeature_qualifier_value returned ordered only by rank
Ra committed 25a249d8:

BugFix: seqfeatures returned ordered by rank
Ra committed 198a1e89:

WarnFix: Bio::Features is obsoleted.
Ra committed c037ec56:

Removed alias comment
Ra committed bd3b24ea:

Implemented Entry's comments and reference's comments
Ra committed 14bcf903:

Cleaned, deleted pk and seq reference
Ra committed 54976693:

Cleaned
Ra committed 5394ecea:

Added comments, comment adapter
Ra committed efb61d7c:

test
Ra committed 29211059:

Added support for reference. ToDo: handling comments
Ra committed eba61ba6:

Fix: compisite primary keys :bioentry_id, :reference_id, :rank
Ra committed e149f944:

removed explicit pk and seq

And 188 more commits...

wwood pushed to master at wwood/bioruby Mon Nov 16 20:30:25 -0800 2009

HEAD is 90329532b0f1907d0a215def66eda1781839a598

143 commits »

Naohisa Goto committed 4e1cd3bf:

Automatically gemerated bioruby.gemspec from bioruby.gemsepc.erb
Naohisa Goto committed 099217f1:

Added rdoc task; changed to get the tar.gz version number from bio.rb, etc.
Naohisa Goto committed f0146850:

ChangeLog is included to RDoc, etc.
Naohisa Goto committed 92ac06c8:

Added recent changes and fixed typo for recent changes.
Naohisa Goto committed be2254dd:

Added ChangeLog and doc/Changes-1.3.rdoc for recent changes
Naohisa Goto committed 4c54597e:

Added bioruby.gemspec created from bioruby.gemspec.erb
Naohisa Goto committed 44ed958a:

Bug fix: parsing of exit code failed when ignoring fatal errors
Naohisa Goto committed 7b081c17:

Added package tasks and changed to use ERB instead of eruby
Naohisa Goto committed 5d5cb24f:

Use git-ls-files command to obtain list of files when available
Naohisa Goto committed d5161d16:

Simple Rakefile for dynamic generation of bioruby.gemspec
Naohisa Goto committed bef31166:

bioruby.gemspec is renamed to bioruby.gemspec.erb with modification
Naohisa Goto committed eda9fd0a:

Added details about newly added classes etc
Naohisa Goto committed 1aef5996:

Changes-1.3.rd is renamed to Changes-1.3.rdoc with format conversion, and fixed typo
Naohisa Goto committed 1f63d3d5:

Changed version to 1.2.9001, set has_rdoc = true and rdoc options
jandot committed f0d91e07:

Edited gemspec because github returned an error while building gem
Naohisa Goto committed 561ae16d:

Renamed gemspec.rb to bioruby.gemspec because so github builds the gem automatically
Naohisa Goto committed ff63658b:

Updated descriptions about RubyGems, and added Ruby 1.9 partial support
Naohisa Goto committed acd9e6d6:

Clarified copyright of README.rdoc and BioRuby
Naohisa Goto committed cb8781d7:

Changed format from RD to RDoc with some additional URLs
Naohisa Goto committed 5df2a9dc:

Ruby 1.9.1 support: using alternatives if no Test::Unit::AutoRunner

And 123 more commits...

wwood updated gist: 226784 Mon Nov 09 17:50:51 -0800 2009

CmdUtils.CreateCommand({ names: ["genbank blast"], arguments: [{role: 'object', nountype: nou...

wwood updated gist: 226784 Fri Nov 06 20:45:33 -0800 2009

CmdUtils.CreateCommand({ names: ["genbank blast"], arguments: [{role: 'object', nountype: nou...

wwood updated gist: 226784 Wed Nov 04 21:07:15 -0800 2009

CmdUtils.CreateCommand({ names: ["genbank blast"], arguments: [{role: 'object', nountype: nou...

wwood created gist: 226784 Wed Nov 04 21:05:39 -0800 2009

CmdUtils.CreateCommand({ names: ["genbank blast"], arguments: [{role: 'object', nountype: nou...

wwood updated gist: 73638 Mon Nov 02 15:24:06 -0800 2009

CmdUtils.CreateCommand({ names: ["genbank-blast-local"], arguments: [{role: 'object', nountyp...

wwood updated gist: 30649 Sat Oct 17 20:47:35 -0700 2009

CmdUtils.CreateCommand({ names: ["orthomcl"], arguments: [{label: "gene_or_group_accession", ...

wwood updated gist: 30649 Sat Oct 17 20:14:14 -0700 2009

CmdUtils.CreateCommand({ names: ["orthomcl"], arguments: [{label: "gene_or_group_accession", ...

wwood updated gist: 30649 Sat Oct 17 20:12:14 -0700 2009

CmdUtils.CreateCommand({ names: ["orthomcl"], arguments: [{label: "gene_or_group_accession", ...

wwood updated gist: 73638 Tue Oct 13 19:50:39 -0700 2009

CmdUtils.CreateCommand({ names: ["genbank-blast-local"], arguments: [{role: 'object', nountyp...

wwood updated gist: 131652 Sat Oct 10 21:22:21 -0700 2009

CmdUtils.CreateCommand({ names: ["entrez-nucleotide"], arguments: [{role: 'object', nountype:...

wwood pushed to master at wwood/bbbin Sat Oct 10 19:40:08 -0700 2009

HEAD is 674decf76c7624da482e2141f1d658245d67a16d

Ben J Woodcroft committed 674decf7:

small stuff

wwood updated gist: 201838 Sun Oct 04 20:30:43 -0700 2009

CmdUtils.CreateCommand({ names: ["scholar"],

wwood created gist: 201838 Sun Oct 04 20:22:10 -0700 2009

CmdUtils.CreateCommand({ names: ["scholar"], icon: "http://www.google.com/favicon.ico",

wwood updated gist: 199664 Sat Oct 03 00:42:14 -0700 2009

var ezp = 'http://ezp.lib.unimelb.edu.au/login?url='; var link = FireGestures.getLinkURL();

wwood created gist: 199664 Fri Oct 02 04:06:07 -0700 2009

var ezp = 'http://ezp.lib.unimelb.edu.au/login?url='; var link = FireGestures.getLinkURL();

wwood updated gist: 168938 Wed Sep 30 16:41:22 -0700 2009

CmdUtils.CreateCommand({ names: ["amigo", "go"], arguments: [{label:"GO term query", nountype...

wwood updated gist: 168938 Wed Sep 30 16:39:24 -0700 2009

CmdUtils.CreateCommand({ names: ["amigo", "go"], arguments: [{label:"GO term query", nountype...