[BioRuby] The third BioRuby IRC conference on Dec 30th
Toshiaki Katayama
ktym at hgc.jp
Fri Dec 31 04:44:31 UTC 2010
Hi,
Last night, we discussed about the "blessed" plugins,
which will be a set of recommended plugins.
You can read the IRC log at the following page as always:
http://bioruby.org/irc/?date=2010-12
We agreed to maintain two "meta" packages of plugins
* "bio-full" --> not reviewd but includes all plugins
* "bio-core" --> reviewed/selected/recommended plugins
and Raoul provided the first example of the "bio-full"
meta package at https://github.com/helios/bioruby-full
Although, the name of these meta packages and the system
to maintain those in detail are still under discussion.
Additionally, I created a toy plugin "bio-hello" for fun
(and hopefully a working example of the BioRuby plugin).
% gem install bio-hello
% biohello.rb -x -c "A happy new year!"
gcataacatgcacctccttattaaaatgaatggtaatatgaagcaaga
gc
c--g
a---t
t----a
a----t
a---t
c--g
at
at
c--g
g---c
t----a
g----c
g---c
a--t
gc
cg
t--a
t---a
a----t
t----a
t---a
a--t
at
ta
t--a
a---t
c----g
t----a
t---a
a--t
cg
gc
t--a
a---t
a----t
t----a
a---t
t--a
gc
ta
t--a
c---g
g----c
t----a
t---a
c--g
ta
% ruby -rubygems -r bio -e 'p Bio::Sequence::NA.new("gcataacatgcacctccttattaaaatgaatggtaatatgaagcaaga").translate'
==> "A*HAPPY*NEW*YEAR"
Please see https://github.com/ktym/bioruby-hello/blob/master/lib/bio-hello.rb and try
% biohello.rb --help
for more details. I hope you enjoy!
Toshiaki
On 2010/12/24, at 9:21, Toshiaki Katayama wrote:
> Hi,
>
> Last night, conversation was not so active but we talked about
>
> * The actual usage of the BioGem, newly created BioRuby's plugin development system
> * NGS support including samtools
>
> The log is available at
>
> http://bioruby.org/irc/?date=2010-12
>
> and I also wrote a step-by-step documentation on the use of BioGem at
>
> http://bioruby.open-bio.org/wiki/BiogemDevelopment
>
> Enjoy.
>
> Toshiaki
>
>
> On 2010/12/23, at 21:09, Toshiaki Katayama wrote:
>
>> Hi all,
>>
>> The 2nd IRC conf will be started in less than 2 hours from now.
>>
>> Toshiaki
>>
>> On 2010/12/20, at 3:49, Toshiaki Katayama wrote:
>>
>>> Hi all,
>>>
>>> Today, we had >10 participants and discussed about
>>>
>>> * Current and future of BioRuby plugin system
>>> * BioRuby with JVM for high performance computing
>>> * Regularly continue the IRC meeting?
>>>
>>> etc. Details will be reported from Pjotr.
>>>
>>> We agreed to continue this IRC meeting on every Thursday as a "core time",
>>> and we may also keep the #bioruby channel open for everyone
>>> as much as possible, I just setup an IRC bot to log discussions.
>>>
>>> From now on, the log of this channel will be made public at
>>>
>>> http://bioruby.org/irc/
>>>
>>> so please join us (and please pay attention to privacy
>>> as a netiquette as well ;-).
>>>
>>> Toshiaki
>>>
>>>
>>> On 2010/12/19, at 21:53, Pjotr Prins wrote:
>>>
>>>> Today is the day!!
>>>>
>>>> I use the bitchx client, with logging.
>>>>
>>>> Pj.
>>>>
>>>> On Tue, Dec 07, 2010 at 08:51:32PM +0900, Toshiaki Katayama wrote:
>>>>> Dear BioRuby developers,
>>>>>
>>>>> Here we announce the first BioRuby world wide IRC conference!
>>>>>
>>>>> The topic is: "Current and future BioRuby development"
>>>>>
>>>>> The meeting is Sunday, Dec. 19, 2010, at 23pm JST (Japanese Standard Time),
>>>>> which is 15pm CET (Central European Time) and 9am EST (New York) and
>>>>> 6am PST (California time).
>>>>>
>>>>> You are kindly invited to join!
>>>>>
>>>>> Server: irc.freenode.org
>>>>> Channel: #bioruby
>>>>>
>>>>> Toshiaki Katayama on behalf of the BioRuby staff.
>>>>> _______________________________________________
>>>>> BioRuby Project - http://www.bioruby.org/
>>>>> BioRuby mailing list
>>>>> BioRuby at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>
>>
>
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