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Welcome to the BioPerl users list! Ask your BioPerl questions here, and feel free to post comments and suggestions.

We won't do your bioinformatics homework for you, however.

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Fields, Christopher J

Mar 4

[Bioperl-l] AI contributions

Hi everyone! I just wanted to drop a note that we're having a discussion about Bioperl policies

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[Bioperl-l] AI contributions

Hi everyone! I just wanted to drop a note that we're having a discussion about Bioperl policies

Mar 4

Schlachter, Kai, … Fields, Christopher J13

9/27/24

[Bioperl-l] Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

Sorry, this got delayed a bit but I just pushed out a new Bio::DB::SeqFeature release, v 1.7.5. Let

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[Bioperl-l] Support for MariaDB in Bio::DB:SeqFeature:Store::DBI::

Sorry, this got delayed a bit but I just pushed out a new Bio::DB::SeqFeature release, v 1.7.5. Let

9/27/24

Zakariyya Mughal

11/16/23

[Bioperl-l] Science Track Interest Survey for The Perl and Raku Foundation [closes in 1 week]

Hello all, If you haven't come across it yet, I wanted to bring your attention to the following

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[Bioperl-l] Science Track Interest Survey for The Perl and Raku Foundation [closes in 1 week]

Hello all, If you haven't come across it yet, I wanted to bring your attention to the following

11/16/23

Fields, Christopher J

4/14/23

[Bioperl-l] Submit your abstract to BOSC 2023 by April 20!

Submit your abstract to BOSC 2023 by April 20! 🍐 Highlights Submit your 1-2 page abstract by April 20

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[Bioperl-l] Submit your abstract to BOSC 2023 by April 20!

Submit your abstract to BOSC 2023 by April 20! 🍐 Highlights Submit your 1-2 page abstract by April 20

4/14/23

Zakariyya Mughal

4/13/23

[Bioperl-l] Pull request for GitHub Actions on bioperl-live (and possible further devops work)

Hello, I have sent a pull request to update the CI configuration from Travis CI to GitHub Actions at

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[Bioperl-l] Pull request for GitHub Actions on bioperl-live (and possible further devops work)

Hello, I have sent a pull request to update the CI configuration from Travis CI to GitHub Actions at

4/13/23

3/3/23

[Bioperl-l] DNS changes for Bio*.org domains

Those DNS changes have gone through, and touch wood no side effects. Thank you to the team at

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[Bioperl-l] DNS changes for Bio*.org domains

Those DNS changes have gone through, and touch wood no side effects. Thank you to the team at

3/3/23

Zakariyya Mughal

2/1/23

[Bioperl-l] Gene expression model using TensorFlow, BioPerl, and PDL

Hello all, I just wanted to post this example notebook <https://nbviewer.org/github/EntropyOrg/

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[Bioperl-l] Gene expression model using TensorFlow, BioPerl, and PDL

Hello all, I just wanted to post this example notebook <https://nbviewer.org/github/EntropyOrg/

2/1/23

shige...@docomo.ne.jp

3/30/22

Re: [Bioperl-l] Bioperl-l Digest, Vol 193, Issue 2

_______________________________________________ Bioperl-l mailing list Biop...@bioperl.org https://

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Re: [Bioperl-l] Bioperl-l Digest, Vol 193, Issue 2

_______________________________________________ Bioperl-l mailing list Biop...@bioperl.org https://

3/30/22

Christopher Fields, Fields, Christopher J2

3/29/22

[Bioperl-l] Announcing BOSC 2022, the 23rd Bioinformatics Open Source Conference

BOSC 2022 dates: July 13-14, as part of ISMB 2022 Location: Madison, WI, USA, and virtual Website:

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[Bioperl-l] Announcing BOSC 2022, the 23rd Bioinformatics Open Source Conference

BOSC 2022 dates: July 13-14, as part of ISMB 2022 Location: Madison, WI, USA, and virtual Website:

3/29/22

2/16/22

[Bioperl-l] NSF Funding opportunity for open source ecosystems

Hello PDL, BioPerl, The Quantified Onion, and Perl Foundation folks, The NSF just sent out an

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[Bioperl-l] NSF Funding opportunity for open source ecosystems

Hello PDL, BioPerl, The Quantified Onion, and Perl Foundation folks, The NSF just sent out an

2/16/22

Fields, Christopher J

2/15/22

[Bioperl-l] BioPerl Code of Conduct

(Apologies for the double email, but figured this would best be served with a complete subject line)

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[Bioperl-l] BioPerl Code of Conduct

(Apologies for the double email, but figured this would best be served with a complete subject line)

2/15/22

Fields, Christopher J

2/15/22

[Bioperl-l] BioPerl code of conduct

In January the OBF membership voted to accept an official OBF code of conduct, briefly mentioned here

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[Bioperl-l] BioPerl code of conduct

In January the OBF membership voted to accept an official OBF code of conduct, briefly mentioned here

2/15/22

Roy Chaudhuri, Steven Lembark3

2/5/22

[Bioperl-l] No relation

On Wed, 5 Aug 2020 19:25:23 +0100 Roy Chaudhuri <roy.ch...@gmail.com> wrote: > Not sure

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[Bioperl-l] No relation

On Wed, 5 Aug 2020 19:25:23 +0100 Roy Chaudhuri <roy.ch...@gmail.com> wrote: > Not sure

2/5/22

paolo...@gmail.com

4/11/21

[Bioperl-l] Invito: Bioinformatics Open Source Conference 2021 - gio 29 lug - ven 30 lug 2021 (bioperl-l@lists.open-bio.org)

Sei stato invitato al seguente evento. Bioinformatics Open Source Conference 2021 Quando gio 29 lug –

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[Bioperl-l] Invito: Bioinformatics Open Source Conference 2021 - gio 29 lug - ven 30 lug 2021 (bioperl-l@lists.open-bio.org)

Sei stato invitato al seguente evento. Bioinformatics Open Source Conference 2021 Quando gio 29 lug –

4/11/21

Fields, Christopher J

4/9/21

[Bioperl-l] Bioinformatics Open Source Conference 2021

YqPBM_zh36k9ModxQHuuwuK9x253wf0w3ZHhjG-

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[Bioperl-l] Bioinformatics Open Source Conference 2021

YqPBM_zh36k9ModxQHuuwuK9x253wf0w3ZHhjG-

4/9/21

Warren Gallin, … Fields, Christopher J3

3/16/21

[Bioperl-l] Can't find Bio::ext::Align on CPAN

Correct, quite a few of the tools in that package have not been maintained. We have discussed

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[Bioperl-l] Can't find Bio::ext::Align on CPAN

Correct, quite a few of the tools in that package have not been maintained. We have discussed

3/16/21

Frank Schwach, Fields, Christopher J2

3/31/20

[Bioperl-l] which Primer3 module should we use now?

Hi Frank, it would be best to update Bio::Tools::Primer3Redux: https://github.com/cjfields/Bio-Tools-

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[Bioperl-l] which Primer3 module should we use now?

Hi Frank, it would be best to update Bio::Tools::Primer3Redux: https://github.com/cjfields/Bio-Tools-

3/31/20

Warren Gallin, Fields, Christopher J2

3/10/20

[Bioperl-l] One protein accession number that consistently fails to return history

I've seen errors like this before, it's an issue on NCBI's end but to be honest I don

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[Bioperl-l] One protein accession number that consistently fails to return history

I've seen errors like this before, it's an issue on NCBI's end but to be honest I don

3/10/20

Carnë Draug, … Christopher Fields6

12/2/19

Re: [Bioperl-l] Fate of Bio::Perl newbie module?

Not a problem Michael. I also pushed a new Bio::DB::NCBIHelper, which updated a few missing

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Re: [Bioperl-l] Fate of Bio::Perl newbie module?

Not a problem Michael. I also pushed a new Bio::DB::NCBIHelper, which updated a few missing

12/2/19

11/19/19

[Bioperl-l] Code of Conduct Initiative - Request for comments/feedback

Hi everyone, We (the Open Bioinformatics Foundation) are soliciting feedback from the BioPerl

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[Bioperl-l] Code of Conduct Initiative - Request for comments/feedback

Hi everyone, We (the Open Bioinformatics Foundation) are soliciting feedback from the BioPerl

11/19/19

Carnë Draug, Fields, Christopher J2

8/28/19

[Bioperl-l] PAUSE permission issues

Hi Carne, I'll have a look. I'll see if I can add you under BIOPERLML as well. chris On 8/28

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[Bioperl-l] PAUSE permission issues

Hi Carne, I'll have a look. I'll see if I can add you under BIOPERLML as well. chris On 8/28

8/28/19

Gordon Haverland, Peter Cock2

8/20/19

[Bioperl-l] Companion planting

Hello Gordon, In terms of taxonomies, one widely used but general one is the NCBI's - eg https://

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[Bioperl-l] Companion planting

Hello Gordon, In terms of taxonomies, one widely used but general one is the NCBI's - eg https://

8/20/19

Fields, Christopher J

3/19/19

[Bioperl-l] Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference

BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community of Special Interest (COSI)

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[Bioperl-l] Call for abstracts: BOSC 2019 Bioinformatics Open Source Conference

BOSC 2019: Bioinformatics Open Source Conference An ISMB/ECCB Community of Special Interest (COSI)

3/19/19

shalu sharma, Roy Chaudhuri3

2/27/19

[Bioperl-l] reading gz fastq File

Correction - it's not a bug since the SeqIO documentation for 1.7.1 now states "To read from

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[Bioperl-l] reading gz fastq File

Correction - it's not a bug since the SeqIO documentation for 1.7.1 now states "To read from

2/27/19

Colin, Fields, Christopher J2

2/7/19

[Bioperl-l] New version of Bio::DB::SeqFeature

Hi Colin, Yes that would be quite helpful! I want to check in with Lincoln and Scott but I don't

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[Bioperl-l] New version of Bio::DB::SeqFeature

Hi Colin, Yes that would be quite helpful! I want to check in with Lincoln and Scott but I don't

2/7/19

Carnë Draug, Fields, Christopher J10

2/6/19

[Bioperl-l] new bioperl release please?

On February 6, 2019 at 8:57:25 AM, Carnë Draug (carandr...@gmail.com) wrote: On Tue, 5 Feb 2019

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[Bioperl-l] new bioperl release please?

On February 6, 2019 at 8:57:25 AM, Carnë Draug (carandr...@gmail.com) wrote: On Tue, 5 Feb 2019

2/6/19

shalu sharma, … Fields, Christopher J7

1/27/19

[Bioperl-l] BerkeleyDB

On January 27, 2019 at 2:29:58 PM, Gordon Haverland (ghav...@materialisations.com) wrote: On Sun, 27

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[Bioperl-l] BerkeleyDB

On January 27, 2019 at 2:29:58 PM, Gordon Haverland (ghav...@materialisations.com) wrote: On Sun, 27

1/27/19

Carnë Draug, … Fields, Christopher J17

9/13/18

[Bioperl-l] standardize shebang line in bioperl scripts

... > > The point is don't assume that you know more about how someone else > manages

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[Bioperl-l] standardize shebang line in bioperl scripts

... > > The point is don't assume that you know more about how someone else > manages

9/13/18

7/2/18

[Bioperl-l] test since this is what's listed on the distributions

I wonder if this email still works. Is it being redirected to the other mailing list.

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[Bioperl-l] test since this is what's listed on the distributions

I wonder if this email still works. Is it being redirected to the other mailing list.

7/2/18

Carnë Draug, … Hilmar Lapp5

7/2/18

[Bioperl-l] does bioperl-l@bioperl.org still work

It looks like the MX record for the bioperl.org domain got lost. Not sure how and when. I've

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[Bioperl-l] does bioperl-l@bioperl.org still work

It looks like the MX record for the bioperl.org domain got lost. Not sure how and when. I've

7/2/18

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