[BioRuby] The third BioRuby IRC conference on Dec 30th

[Toshiaki Katayama]

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
>>> 
>> 
>