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Fwd: Hackathon tomorrow (I think)
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Re: Fwd: Hackathon tomorrow (I think)
by Chris Fields-5
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1) Any help towards bugzilla fixes would be most welcome.
2) Better GFF3 integration 3) Typed but lightweight seqfeatures 4) Bio::Moose? I can dedicate more time to the latter two in about a month, but I'll be tied up until then. Let me know if anyone needs collab on biomoose on github; Mark Jensen's already added. chris On Jun 24, 2009, at 11:13 AM, Bruno Vecchi wrote: > Jay asked me to forward this to the list, since he sometimes has > problems > getting his mails delivered. > Feel free to suggest topics for the bioperl hackathon to take place > tomorrow > and on friday! > > Bruno. > > > From: Jay Hannah <jay@...> > Date: June 24, 2009 11:55:42 AM EDT > To: Bioperl <bioperl-l@...> > Subject: Hackathon tomorrow (I think) > > Hola, > > So a few of us here at YAPC might try to be productive tomorrow (and > Friday?). > > I don't know if we have any commit bits attending. > > Feel free to suggest things: > > http://yapc10.org/yn2009/wiki?node=BioPerl > > Or point me to list(s) of things. Perhaps we'll try to help out in > Bugzilla. > > Come yell at me (us?) in IRC: > > http://www.bioperl.org/wiki/Irc > > Thanks, > > Jay Hannah > http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Jay Hannah
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On Jun 24, 2009, at 12:26 PM, Chris Fields wrote:
> Let me know if anyone needs collab on biomoose on github; Mark > Jensen's already added. Anything on github should be trivial, even with no perms -- we can just fork and then send you (whoever) pull requests. github++ :) > 1) Any help towards bugzilla fixes would be most welcome. I don't know how to make any progress in bugzilla if no one has a commit bit...? > 2) Better GFF3 integration > 3) Typed but lightweight seqfeatures Are there bugzilla tickets (or somewhere) describing those? I wonder if anyone can help me get out of sporadic MailMan purgatory... Thanks, j _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Chris Fields-5
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On Jun 24, 2009, at 11:44 AM, Jay Hannah wrote: > On Jun 24, 2009, at 12:26 PM, Chris Fields wrote: >> Let me know if anyone needs collab on biomoose on github; Mark >> Jensen's already added. > > Anything on github should be trivial, even with no perms -- we can > just fork and then send you (whoever) pull requests. github++ :) > >> 1) Any help towards bugzilla fixes would be most welcome. > > I don't know how to make any progress in bugzilla if no one has a > commit bit...? For some reason I thought you had a commit bit; we can add you in if needed. Anyway, patches are most definitely welcome ;> >> 2) Better GFF3 integration >> 3) Typed but lightweight seqfeatures > > Are there bugzilla tickets (or somewhere) describing those? No as the issues are more complex than one single bug, but we do have something to help track for the time being: http://www.bioperl.org/wiki/GFF_Refactor http://www.bioperl.org/wiki/Align_Refactor I'll probably file TODOs during the process for those refactors. The easiest to tackle would be probably be Align/LocatableSeq refactors. > I wonder if anyone can help me get out of sporadic MailMan > purgatory... > > Thanks, > > j -c PS - Don't feel constrained by the above. There are many many areas to contribute to. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Kevin Clancy
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is there an intention to have a hackathon at ISMB this weekend - I know there is a 2 day BOSC kevin > From: cjfields@... > To: jay@... > Date: Wed, 24 Jun 2009 16:10:34 -0500 > CC: vecchi.b@...; bioperl-l@... > Subject: Re: [Bioperl-l] Fwd: Hackathon tomorrow (I think) > > > On Jun 24, 2009, at 11:44 AM, Jay Hannah wrote: > > > On Jun 24, 2009, at 12:26 PM, Chris Fields wrote: > >> Let me know if anyone needs collab on biomoose on github; Mark > >> Jensen's already added. > > > > Anything on github should be trivial, even with no perms -- we can > > just fork and then send you (whoever) pull requests. github++ :) > > > >> 1) Any help towards bugzilla fixes would be most welcome. > > > > I don't know how to make any progress in bugzilla if no one has a > > commit bit...? > > For some reason I thought you had a commit bit; we can add you in if > needed. Anyway, patches are most definitely welcome ;> > > >> 2) Better GFF3 integration > >> 3) Typed but lightweight seqfeatures > > > > Are there bugzilla tickets (or somewhere) describing those? > > No as the issues are more complex than one single bug, but we do have > something to help track for the time being: > > http://www.bioperl.org/wiki/GFF_Refactor > http://www.bioperl.org/wiki/Align_Refactor > > I'll probably file TODOs during the process for those refactors. The > easiest to tackle would be probably be Align/LocatableSeq refactors. > > > I wonder if anyone can help me get out of sporadic MailMan > > purgatory... > > > > Thanks, > > > > j > > -c > > PS - Don't feel constrained by the above. There are many many areas > to contribute to. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Chris Fields-5
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I have no idea; I don't think there are many bioperl devs attending
this year unfortunately. Any meetings in the next year where we could set up a bioperl hackathon? I will likely be available to attend if it's stateside... chris On Jun 24, 2009, at 9:31 PM, Kevin Clancy wrote: > > is there an intention to have a hackathon at ISMB this weekend - I > know there is a 2 day BOSC > kevin > >> From: cjfields@... >> To: jay@... >> Date: Wed, 24 Jun 2009 16:10:34 -0500 >> CC: vecchi.b@...; bioperl-l@... >> Subject: Re: [Bioperl-l] Fwd: Hackathon tomorrow (I think) >> >> >> On Jun 24, 2009, at 11:44 AM, Jay Hannah wrote: >> >>> On Jun 24, 2009, at 12:26 PM, Chris Fields wrote: >>>> Let me know if anyone needs collab on biomoose on github; Mark >>>> Jensen's already added. >>> >>> Anything on github should be trivial, even with no perms -- we can >>> just fork and then send you (whoever) pull requests. github++ :) >>> >>>> 1) Any help towards bugzilla fixes would be most welcome. >>> >>> I don't know how to make any progress in bugzilla if no one has a >>> commit bit...? >> >> For some reason I thought you had a commit bit; we can add you in if >> needed. Anyway, patches are most definitely welcome ;> >> >>>> 2) Better GFF3 integration >>>> 3) Typed but lightweight seqfeatures >>> >>> Are there bugzilla tickets (or somewhere) describing those? >> >> No as the issues are more complex than one single bug, but we do have >> something to help track for the time being: >> >> http://www.bioperl.org/wiki/GFF_Refactor >> http://www.bioperl.org/wiki/Align_Refactor >> >> I'll probably file TODOs during the process for those refactors. The >> easiest to tackle would be probably be Align/LocatableSeq refactors. >> >>> I wonder if anyone can help me get out of sporadic MailMan >>> purgatory... >>> >>> Thanks, >>> >>> j >> >> -c >> >> PS - Don't feel constrained by the above. There are many many areas >> to contribute to. >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@... >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Luis Miguel Rodríguez
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Dear all,
Is there a way to run muscle silently via Bio::Tools::Run::Alignment::Muscle? Cheers, -- Luis M. Rodriguez-R [http://bioinf.uniandes.edu.co/~miguel/] --------------------------------- Unidad de Bioinformática del Laboratorio de Micología y Fitopatología Universidad de Los Andes, Colombia [http://bioinf.uniandes.edu.co] + 57 1 3394949 ext 2619 lmrodriguezr@... me@... _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Fwd: Hackathon tomorrow (I think)
by Kevin Clancy
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I think ismb will be in Boston in 2010 (feels odd just typing that...) maybe that is enough of a running start to set something up. kevin > CC: jay@...; vecchi.b@...; bioperl-l@... > From: cjfields@... > To: kpclancy@... > Subject: Re: [Bioperl-l] Fwd: Hackathon tomorrow (I think) > Date: Wed, 24 Jun 2009 22:54:28 -0500 > > I have no idea; I don't think there are many bioperl devs attending > this year unfortunately. Any meetings in the next year where we could > set up a bioperl hackathon? I will likely be available to attend if > it's stateside... > > chris > > On Jun 24, 2009, at 9:31 PM, Kevin Clancy wrote: > > > > > is there an intention to have a hackathon at ISMB this weekend - I > > know there is a 2 day BOSC > > kevin > > > >> From: cjfields@... > >> To: jay@... > >> Date: Wed, 24 Jun 2009 16:10:34 -0500 > >> CC: vecchi.b@...; bioperl-l@... > >> Subject: Re: [Bioperl-l] Fwd: Hackathon tomorrow (I think) > >> > >> > >> On Jun 24, 2009, at 11:44 AM, Jay Hannah wrote: > >> > >>> On Jun 24, 2009, at 12:26 PM, Chris Fields wrote: > >>>> Let me know if anyone needs collab on biomoose on github; Mark > >>>> Jensen's already added. > >>> > >>> Anything on github should be trivial, even with no perms -- we can > >>> just fork and then send you (whoever) pull requests. github++ :) > >>> > >>>> 1) Any help towards bugzilla fixes would be most welcome. > >>> > >>> I don't know how to make any progress in bugzilla if no one has a > >>> commit bit...? > >> > >> For some reason I thought you had a commit bit; we can add you in if > >> needed. Anyway, patches are most definitely welcome ;> > >> > >>>> 2) Better GFF3 integration > >>>> 3) Typed but lightweight seqfeatures > >>> > >>> Are there bugzilla tickets (or somewhere) describing those? > >> > >> No as the issues are more complex than one single bug, but we do have > >> something to help track for the time being: > >> > >> http://www.bioperl.org/wiki/GFF_Refactor > >> http://www.bioperl.org/wiki/Align_Refactor > >> > >> I'll probably file TODOs during the process for those refactors. The > >> easiest to tackle would be probably be Align/LocatableSeq refactors. > >> > >>> I wonder if anyone can help me get out of sporadic MailMan > >>> purgatory... > >>> > >>> Thanks, > >>> > >>> j > >> > >> -c > >> > >> PS - Don't feel constrained by the above. There are many many areas > >> to contribute to. > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l@... > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@... > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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