Fields, Christopher J | 9 Feb 19:03 2016
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FW: [Open-bio-l] Let's get started with Google Summer of Code 2016

Kai Blin has graciously accepted heading up this year’s GSoC (with some help from Raoul Bonnal); see
below for the original announcement.  Several ideas are present for BioPerl, including submission of
project ideas for Perl 6.  This could run the gamut from writing up new code for BioPerl to creating useful
library bindings for Perl 6.  

Also, we will need potential mentors for projects to help out.  This could be for Perl-related projects but
also for other projects where you may have expertise.  Discussions will be happening on the OBF/GSoC list
should anyone want to suggest project ideas or help mentor.

http://lists.open-bio.org/mailman/listinfo/gsoc

Thanks,

chris

On 2/9/16, 9:43 AM, "Open-Bio-l on behalf of Kai Blin"
<open-bio-l-bounces+cjfields=illinois.edu <at> mailman.open-bio.org on behalf of
kblin <at> biosustain.dtu.dk> wrote:

>Dear Open Bioinformatics community,
>
>Google is now accepting applications for mentoring organizations for the 2016 installment of the Google
Summer of Code. You can find out a bit about the Google Summer of Code from an OBF perspective on our wiki at
http://www.open-bio.org/wiki/Google_Summer_of_Code. My apologies for the 2015 material still on
there, but I've been fighting with the OpenID account creation on our wiki, and have not won so far. Still,
most of the material still applies for this year.
>
>In order to actually collect a number of interesting project ideas that we could have students work on, we
need your help as a community. Please join us on the OBF/GSoC mailing list
(http://lists.open-bio.org/mailman/listinfo/gsoc) so we can get rolling.
(Continue reading)

Hilmar Lapp | 26 Jan 21:01 2016
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Re: Call for Org Admins for OBF's 2016 Google Summer of Code participation

Dear all,

I’m very pleased to announce that Kai Blin will be OBF’s org admin for our 2016 GSoC program
participation. Please join me in offering Kai our full support. You can reach Kai at
kblin <at> biosustain.dtu.dk, and if you haven’t already you’ll hear from him soon. Raoul Bonnal, who
was leading our GSoC participation in the last two years, will work with Kai as the backup org admin.

On behalf of the Board and the community at large, my thanks and kudos to both Kai and Raoul for stepping up.

 -hilmar

> On Jan 15, 2016, at 5:42 PM, Hilmar Lapp <hlapp <at> drycafe.net> wrote:
> 
> The 2016 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring
organization applications from Feb 8 to 19.
> 
> OBF participated on behalf of our member projects from 2010-2012, and in 2014. Those participations were
both important and successful. Through them, our projects gained new contributors, new features, and
new community members. The mentors involved from our projects learned as much from the experience as the
students, and formed bonds. Starting in 2012 and in particular in 2014, we also committed to “paying it
forward” on the organization level, welcoming a much broadened scope of projects to participate under
our umbrella (see [2] for a summary). Finally, the mentoring organization payments have allowed OBF to
sponsor community events, student travel awards, and infrastructure.
> 
> To participate this year, we have to appoint 2-3 people as primary and backup organization
administrators. This is an important role, and we are looking for people from our community to step
forward to serve. Our org admins from previous years (Eric Talevich and Raoul Bonnal) remain available
for backup and guidance, but are unfortunately not in a position to take the lead org admin role. 
> 
> ## What does an org admin do?
(Continue reading)

Carnë Draug | 20 Jan 21:45 2016
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distzilla pluginbundle: bioperl vs BioPerl

Hi

I was searching for the bioperl distzilla plugin bundle when I found
out that there are currently two distributions with the difference
on the capitalization of bioperl:

    https://metacpan.org/pod/Dist::Zilla::PluginBundle::Bioperl
    https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl

The first one (out of date) is the first autocomplete suggestion on
metacpan when searching for bioperl.  I got confused for a while,
assumed that we had regraded to the previous pluginbundle for some
weird reason and went to look into the actual repository.

It should probably be removed.  Is that possible?

Carnë

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Hilmar Lapp | 15 Jan 23:47 2016
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Call for Org Admins for OBF's 2016 Google Summer of Code participation

(apologies to those receiving duplicates - we are trying to reach our community at large)

The 2016 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring
organization applications from Feb 8 to 19.

OBF participated on behalf of our member projects from 2010-2012, and in 2014. Those participations were
both important and successful. Through them, our projects gained new contributors, new features, and
new community members. The mentors involved from our projects learned as much from the experience as the
students, and formed bonds. Starting in 2012 and in particular in 2014, we also committed to “paying it
forward” on the organization level, welcoming a much broadened scope of projects to participate under
our umbrella (see [2] for a summary). Finally, the mentoring organization payments have allowed OBF to
sponsor community events, student travel awards, and infrastructure.

To participate this year, we have to appoint 2-3 people as primary and backup organization
administrators. This is an important role, and we are looking for people from our community to step
forward to serve. Our org admins from previous years (Eric Talevich and Raoul Bonnal) remain available
for backup and guidance, but are unfortunately not in a position to take the lead org admin role. 

## What does an org admin do?

An org admin’s role is in many ways that of a cat herder with a vision. The whole team of mentors and admins is
what creates the experience for the students, but it falls on the org admin to “keep it together.”
Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions)
of its mentors or community, and it falls on the org admin to carry that accountability through to the
org’s mentors. The org admin’s responsibilities include:

	• Shaping and setting the overall vision (including scope) for our program participation.
	• Serving as the primary contact for our participation to Google, to mentors, and to students.
	• Shepherding our mentoring organization application, and submitting it.
	• Determining processes and rules for mentors as well as students that promote transparency,
(Continue reading)

Brian Osborne | 8 Jan 05:56 2016
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New Jekyll theme at bioperl.github.io

All,

I’ve switched from one of the default themes - dull - to a custom theme I derived from an existing site. Much
better, but there are some issues:

- spacing between text blocks is a bit odd, in various places
- posts (news) do not yet work
- Perl code appears in blocks but without highlights

The last one is mysterious, it may be due to recent Jekyll versions and how they work or don’t work with the
redcarpet MD -> HTML converter.

Check it out.

Brian O.
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asma.rabe | 11 Nov 17:58 2015
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Get strand from pos


Hi all,

I have variant list and I would like to get the sequence and strand for each position. I could get sequence
using Bio::DB::Fasta 
But I am not sure how to get strand information using position only ??

Any help is appreciated
Fields, Christopher J | 8 Oct 16:03 2015
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Re: Important! Redmine issue migration

All tickets have been moved over!  I moved the other project issues right into the project tracker instead of creating a separate repo, e.g. bioperl-db:

https://github.com/bioperl/bioperl-db/issues

We could merge the redmine issues into bioperl-live if needed, though it has way more than the others and was more problematic due to github REST API limits. I have also closed the relevant Redmine project trackers, which makes them read-only.  A number of user names didn’t map, though I don’t think that’s too much of a problem.

chris

On Oct 7, 2015, at 6:17 PM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:

…and the bioperl-live tickets are essentially done.  


We can move over the others, and then I can archive the projects on the OBF instance so they are read-only.

chris

On Oct 7, 2015, at 2:57 PM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:

Just an update: I’m working on the final migration now.  I’ve enabled user name mapping to github IDs for the original bug reports (but not the comments, which should cut down on noise).  Once this is finished I’ll reassign the redmine issues repo over to the bioperl organization. I’ll also check the bioperl-run and other bioperl-* repos on redmine to see how many tickets are left.

chris

On Sep 28, 2015, at 9:25 PM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:

The move will have to be iterative; I seem to have hit a submission limit which forbids sending more than a few hundred queries/updates.  Not sure why, as it’s done via OAuth key.  Not a big problem, just will be in 2-3 batches.

I may do a quick test run to see whether the submitter alone is mapped to the Github ID or if it’s also commenter IDs.  If someone is being pinged for every mention of their name in comments it might get loud :)

chris
...
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Fields, Christopher J | 25 Sep 05:39 2015
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Important! Redmine issue migration

I (finally!) have a set of tools working to migrate Bioperl issues from the old bug report system (https://redmine.open-bio.org) to Github Issues.  You can see a test run of this here:


Note this points back to the original Redmine repo.  We’ll keep that operational since it has attachments present for some tickets, but for any future work the link will become read-only (and may go away in the future as we phase out the Redmine repo).

As for the migrated issues, we’ll likely keep this as a separate (empty) repository for the time being (I will change the ownership to 'bioperl' once it looks fine).  This is primarily to ensure we don’t clutter or munge up the main bioperl-live repo Issues already in place, since we can’t delete Github issues once they are created.  I will be adding a placeholder ticket pointing to them within the bioperl-live ticket system for the time being.  

The important part: once the test run is finished, we could implement the user map; however, old bioperl users/contributors may see a flood of Github emails if you submitted or replied to any ticket in the past.  We do not have to implement this functionality, in fact I’m reluctant to spam past contributors unless we see an overwhelming need to do so (particularly since we can simply add their Github user ID to a comment if needed).  So my official position is that we won’t map Github users to tickets, except manually via comments and only when necessary.  Welcome to any dissenting opinions.

Thanks!

chris


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Cacau Centurion | 23 Sep 06:57 2015
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Downloading genbank (full) format

Hi,

I would like to download sequences in genbank (full) format in batch. What should the format be (see the codes)?

I tried 'gb' but got sequences in genbank format. Sometimes the full genome sequences might not be downloaded.


#code
$seqin = Bio::SeqIO->new(-file   => $out,
                                -format => $format,
                                );  


Yours,
Cacau
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Fields, Christopher J | 17 Sep 06:07 2015
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Bio::Root back in master

All,

Just a note that we decided the split out of Bio::Root was causing too many headaches, so decided to merge the
code back into the master branch as of today (in commit c5b1cf8a).  

Major thanks to Brian Osborne for doing the work on merging the code back in on a branch (including changes
made in the now-defunct Bio-Root repo)!

chris
Cook, Malcolm | 12 Sep 07:16 2015

using Bio::SeqIO to convert from table to genbank format ..... attribute_map example

Fellow long-time BioPerlers,

I am using Bio::SeqIO with success to convert between table (c.f. 
http://search.cpan.org/~cjfields/BioPerl/Bio/SeqIO/table.pm) and genbank flatfile format.

I have Bio::SeqIO sequence format conversion wrapped in a command-line script.  The script exposes to the
command line the parameters to ->new for both input and output objects through judicious use of
GetOptions.  I have used this script in many conversion tasks between many different formats.

... except now ...

I am having trouble with reading the flatfile format.

Happily, at first, I see that -display_id and -accession_number are both parameters to
Bio::SeqIO::table->new.  So they are naturally exposed to the command line as `in format=table header=1
display_id=1 seq=3"

Alas however -description is not a parameter to ->new.

The only way I can see to configure table.pm to take the sequence description (aka desc) from the 2nd column
of my .tab file is as follows:

	$in->attribute_map({-description => 2});

... however my trace shows me that even though this does work to set the desc attribute of the wrapped
Bio::Primary_seq to the value from column 2, unfortunately using the attribute_map also removes the
individual values passed in for -display_id and -accession_number

Ideally (I think) Bio::SeqIO::table->new  would take a -description=2 instead of having to call
attribute_map.  

Or, Bio::SeqIO::table->new  would take  -attribute_map and even accept it as a string which gets evaluated
to a hash reference, just as I see -colnames can be passed as a string evaling to an array (which I see in the
unit test: http://cpansearch.perl.org/src/CJFIELDS/BioPerl-1.6.924/t/SeqIO/table.t).  This
would allow the hash to be supplied at the command line.

Or, am I missing something?

FWIW: I am trying to help a lab convert a few years of plasmids from DNAPlasmid to Genbank (for load into
Vector NTI) and I am passing through Bio::SeqiO::table in-so-diong.....

Cheers, and Thanks for help and suggestions....

Malcolm Cook
Stowers Institute for Medical Research
1000 E 50th Street
Kanas City, MO 64110
(816) 926-4449
mec <at> stowers.org

Gmane