Kristian Rother | 1 Jul 15:01 2010
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RNA Alphabet with modified nucleotides


Hi,

I've commited code + tests for representing RNA sequences with modified
nucleotides to a branch on Github. See:

http://github.com/krother/biopython/commits/rna_alphabet

I'm done with my list of 'most wanted' features for this class, including
suggestions from Peter.
What could I do next to help integrating the new code with the rest of
Biopython?

Best Regards,
   Kristian
Peter | 1 Jul 15:26 2010
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Re: RNA Alphabet with modified nucleotides

On Thu, Jul 1, 2010 at 2:01 PM, Kristian Rother <krother <at> rubor.de> wrote:
>
> Hi,
>
> I've commited code + tests for representing RNA sequences with modified
> nucleotides to a branch on Github. See:
>
> http://github.com/krother/biopython/commits/rna_alphabet
>
> I'm done with my list of 'most wanted' features for this class, including
> suggestions from Peter.
> What could I do next to help integrating the new code with the rest of
> Biopython?

Hi Kristian,

I haven't had a play with the code, just a very brief look at it.

You'll need to add licence and copyright statements.

A few embedded doctests in the docstrings would be very nice
to help explain how the new classes are to be used.

What happens if you add some of the new DNA seq objects
to test_Seq_objs.py? Is it all fine?

Are you planning to add a reverse complement method etc? Or
does the current fall back on the Seq implementation work OK?

Peter
(Continue reading)

Peter | 2 Jul 15:42 2010
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Active projects list? (BOSC Biopython Project Update)

Hi all,

BOSC is rapidly approaching, so I have been working on slides for the
Biopython Project Update. One thing I would really like help with is listing
current active projects, as I think the wiki is out of date here:
http://biopython.org/wiki/Active_projects

In addition to the GSoC work, my list currently has the following (in some
cases just from looking at github - for example I don't recall Tamas posting
on the mailing lists):

Brad Chapman – GFF parsing
Andrea Pierleoni - UniProt XML parsing
Kristian Rother – Modified RNA sequences
Chris Lasher, Kyle Ellrott, Tamás Nepusz – Gene Ontology
Kyle Ellrott - HMMER parser
Uri Laserson, Peter Cock - IMGT files (EMBL like)

I know Michiel has mentioned some ideas for updating our BLAST parsers,
and I have several smaller things on the side (e.g. an on disk index for
Bio.SeqIO.index, enhancements to SeqFeature and FeatureLocation).

What are we missing that should be there?

Thanks,

Peter
Eric Talevich | 2 Jul 16:47 2010
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Re: Active projects list? (BOSC Biopython Project Update)

On Fri, Jul 2, 2010 at 9:42 AM, Peter <biopython <at> maubp.freeserve.co.uk>wrote:

> Hi all,
>
> BOSC is rapidly approaching, so I have been working on slides for the
> Biopython Project Update. One thing I would really like help with is
> listing
> current active projects, as I think the wiki is out of date here:
> http://biopython.org/wiki/Active_projects
> [...]
> What are we missing that should be there?
>

Biopython's network on GitHub is a good resource for tracking active
projects:
http://github.com/biopython/biopython/network

Should we add a link to that in the preamble? Not every project has its own
public branch, but for those that do, GitHub will always be up to date.

-Eric
Peter | 2 Jul 16:52 2010
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Switching to GitHub Organization

Hi all,

Following Chris' lead with BioPerl (see below), I've also switched Biopython's
github account to an organization. There should be no differences for fetching
code or committing for those of you with access.

Peter

---------- Forwarded message ----------
From: Chris Fields <cjfields <at> illinois.edu>
Date: Fri, Jul 2, 2010 at 2:48 PM
Subject: [Bioperl-l] BioPerl Switching to GitHub Organization
To: BioPerl List <bioperl-l <at> lists.open-bio.org>

GitHub (as expected) just released their setup for organizations,
including open-source projects.  The announcement is here:

http://github.com/blog/674-introducing-organizations

I have already moved bioperl over to an organization account and have
added a few co-owners of the github repository.  The move is
transparent, no one should notice any difference in checking out code.
 I'm working on reassigning teams to projects at this time, so please
post here if there are any problems.

chris
_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
(Continue reading)

Kyle | 2 Jul 16:53 2010
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Re: Active projects list? (BOSC Biopython Project Update)

I also have a fork for adding zxjdbc (the Jython's java database
system) support to BioSQL. And one for parsing MetaGeneAnnotator files
( http://metagene.cb.k.u-tokyo.ac.jp/ )

Kye

On Fri, Jul 2, 2010 at 7:47 AM, Eric Talevich <eric.talevich <at> gmail.com> wrote:
> On Fri, Jul 2, 2010 at 9:42 AM, Peter <biopython <at> maubp.freeserve.co.uk>wrote:
>
>> Hi all,
>>
>> BOSC is rapidly approaching, so I have been working on slides for the
>> Biopython Project Update. One thing I would really like help with is
>> listing
>> current active projects, as I think the wiki is out of date here:
>> http://biopython.org/wiki/Active_projects
>> [...]
>> What are we missing that should be there?
>>
>
> Biopython's network on GitHub is a good resource for tracking active
> projects:
> http://github.com/biopython/biopython/network
>
> Should we add a link to that in the preamble? Not every project has its own
> public branch, but for those that do, GitHub will always be up to date.
>
> -Eric
> _______________________________________________
> Biopython-dev mailing list
(Continue reading)

Peter | 2 Jul 17:09 2010
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Re: Active projects list? (BOSC Biopython Project Update)

On Fri, Jul 2, 2010 at 3:53 PM, Kyle <kellrott <at> gmail.com> wrote:
> I also have a fork for adding zxjdbc (the Jython's java database
> system) support to BioSQL. And one for parsing MetaGeneAnnotator files
> ( http://metagene.cb.k.u-tokyo.ac.jp/ )

Maybe this will be two slides then - or small font ;)

> On Fri, Jul 2, 2010 at 7:47 AM, Eric Talevich <eric.talevich <at> gmail.com> wrote:
>>
>> Biopython's network on GitHub is a good resource for tracking active
>> projects:
>> http://github.com/biopython/biopython/network
>>
>> Should we add a link to that in the preamble? Not every project has its own
>> public branch, but for those that do, GitHub will always be up to date.
>>
>> -Eric

Good idea (I'd been trawling it to make the original list).

Peter
Andrea Pierleoni | 3 Jul 08:52 2010
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Re: Active projects list? (BOSC Biopython Project Update)

> Hi all,
>
> BOSC is rapidly approaching, so I have been working on slides for the
> Biopython Project Update. One thing I would really like help with is
> listing
> current active projects, as I think the wiki is out of date here:
> http://biopython.org/wiki/Active_projects
>
> In addition to the GSoC work, my list currently has the following (in some
> cases just from looking at github - for example I don't recall Tamas
> posting
> on the mailing lists):
>
> Brad Chapman – GFF parsing
> Andrea Pierleoni - UniProt XML parsing
> Kristian Rother – Modified RNA sequences
> Chris Lasher, Kyle Ellrott, Tamás Nepusz – Gene Ontology
> Kyle Ellrott - HMMER parser
> Uri Laserson, Peter Cock - IMGT files (EMBL like)
>
> I know Michiel has mentioned some ideas for updating our BLAST parsers,
> and I have several smaller things on the side (e.g. an on disk index for
> Bio.SeqIO.index, enhancements to SeqFeature and FeatureLocation).
>
> What are we missing that should be there?
>
> Thanks,
>
> Peter
>
(Continue reading)

Tiago Antão | 3 Jul 12:01 2010
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Re: Active projects list? (BOSC Biopython Project Update)

On Fri, Jul 2, 2010 at 2:42 PM, Peter <biopython <at> maubp.freeserve.co.uk> wrote:
> What are we missing that should be there?

The Population genetics code is still alive, though I have to update
the documentation a bit. I want to support the dfdist application
soon. Most unexpectedly the fdist code is being used quite a bit (via
an application), currently 33 citations on scholar. And people
constantly ask me for dfdist support. A close second is support for
large genepop files supporting thousands of markers.

By the way, I suppose python 2 to 3 is the elephant in the room? I bet
all of us have run 2to3 on biopython ;) ... The results are not that
bad...
Peter | 3 Jul 12:12 2010
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Re: Active projects list? (BOSC Biopython Project Update)

On Sat, Jul 3, 2010 at 7:52 AM, Andrea Pierleoni
<andrea <at> biocomp.unibo.it> wrote:
> Dear Peter,
> I'm actually working on two more projects than the XML parsing, that could
> be useful in biopython.
>
> 1) together with Mauro Amico, we hare developing a graphical library very
> similar to the Bio::Graphics module pf BioPerl. The project is at good
> point, and will come with documentation and tutorial as a standalone
> package we call BioGraPy. I know that in biopython one can already use
> GenomeDiagram to draw, for example, seqrecord features, but this could
> extend biopython plotting capability significantly. You can use BioGraPy
> to plot a blast output (with its HTML map), to plot hydrophobicity plot
> along the sequence (read as per letter annotations), mRNA and CDS with
> their splicing sites, and so on... BioGrapy relies on matplotlib, so this
> will be an additional external dependence, but worthwhile in my opinion.

That does sound interesting. I'm not saying it couldn't be rolled into
Biopython, but perhaps shipping it a separate package building on
Biopython and matplotlib is a good plan. There are advantages either
way.

> 2) Since I'm working with the web2py web framework, and I work with biosql
> databases, I spent some time adapting the current BioSQL code to be used
> with the web2py DAL (Database Abstraction Layer). DAL is much more simpler
> (and sometimes faster) than SQLAlchemy, and its syntax and use are very
> similar to SQL queries, so it was very easy to adapt the current code to
> use the DAL. Main advantages of using the web2py DAL are that it can be
> used on almost any DB engine. listing from the web2py site: SQLite,
> PostgreSQL, MySQL, MSSQL, FireBird, Oracle, IBM DB2, Informix, Ingres, and
(Continue reading)


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