[Biopython-dev] Biopython update talk at BOSC 2014

[Peter Cock]

Hi all,

Thanks for handling this Bow, and I'm sorry I didn't see the emails
while I was away - thank you to Eric, Tiago and anyone else who
had commented directly.

Regarding (1), authorship: Bow is presenting, so I think he should
be first author and corresponding author. But Tiago has raised
an important point:

Past BOSC talk authorship has been largely unplanned - often
just named presenter and anyone directly contributing to the
talk slides. Last year I'd just put Peter Cock et al. which was not
very explicit. We could and perhaps should use something
like "W. Arindrarato, ... and the Biopython Consortium" or
"Team" or "Contributors"?

(The phrase "Biopython Consortium" is what it says on our
PyPy page, but it sounds very formal to me.)

Regarding (2), yes - assuming the reviewers don't reject the
abstract completely (which would be a shock!), we will have
a chance to revise the abstract. This is usually to address
reviewers' comments, but for the project update talks it helps
ensure that the abstract is as up to date as possible.

Regards,

Peter

On Mon, Apr 7, 2014 at 12:00 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi Tiago,
>
> 1. I have no objections to that. Could we change it post submission?
> If you noticed, I listed the authors initially alphabetically based on
> last name. After talking with Eric, I updated the order with the last
> one submitted. But in general, I'm ok with any ordering so long as we
> all agree.
>
> 2. I didn't have chance to add this prior to submission, unfortunately
> :/. But adding this would be nice. Is it possible to do this during
> abstract review?
>
> 3. Noted, thanks :).
>
> Best,
> Bow
>
> On Mon, Apr 7, 2014 at 12:41 PM, Tiago Antao <tra at popgen.net> wrote:
>> Hi,
>>
>> 1. Shouldn't Peter be the first author on the list?
>>
>> 2. We have 2 containers:
>>    1. a container with all (almost) the dependencies, which can be used
>>    to deploy biopython on the fly (for normal usage):
>> https://github.com/tiagoantao/my-containers/blob/master/biopython/Biopython
>>    2. A buildbot test container (that is in used for builbot testing):
>> https://github.com/tiagoantao/my-containers/blob/master/biopython/Biopython-Test
>>
>> 3. My address: Vector Biology Department, Liverpool School of Tropical
>> Medicine, Pembroke Place, Liverpool, United Kingdom
>>
>> On Wed, 2 Apr 2014 11:52:07 +0200
>> Wibowo Arindrarto <w.arindrarto at gmail.com> wrote:
>>
>>> Hello everyone,
>>>
>>> I've finished the first draft of our update (attached). Please let me
>>> know if there are additions / deletions you would like me to make
>>> before I submit the abstract.
>>>
>>> Also, some things I would like to note:
>>>
>>> * I am missing the formal affiliations of everybody in the authors
>>> list except for me and Peter. Could you please send me your most
>>> recent affiliation?
>>>
>>> * I'm not sure about whether to include Tiago's recent Biopython
>>> docker container (I think it would be nice). Tiago, do we have the
>>> container up and running for our tests?
>>>
>>> Cheers,
>>> Bow
>>>
>>> On Tue, Apr 1, 2014 at 11:37 PM, Peter Cock
>>> <p.j.a.cock at googlemail.com> wrote:
>>> > On Mon, Mar 31, 2014 at 10:08 PM, Wibowo Arindrarto
>>> > <w.arindrarto at gmail.com> wrote:
>>> >> Hi Peter, everyone,
>>> >>
>>> >> A LaTeX template would be great :). I'm still preparing the
>>> >> abstract, should be ready for everyone to check soon.
>>> >>
>>> >> Cheers,
>>> >> Bow
>>> >
>>> > LaTeX template sent.
>>> >
>>> > I will be travelling the next few days and may be largely out of
>>> > email contact - so if you don't hear from me, don't worry and
>>> > submit the abstract anyway. I'm confident the others will have
>>> > good advice and suggestions (and I'm not the only one who
>>> > does email list moderation - but it might be simpler to send
>>> > round plain text and a link to the PDF if you want to show it
>>> > and not worry about the attachment triggering moderation).
>>> >
>>> > As usual this will get reviewed by the BOSC panel, and you'll
>>> > have a chance to revise the abstract at that point - for the
>>> > project updates is it OK if the initial text has a couple of details
>>> > "to be confirmed", like a summary of the forthcoming release
>>> > Biopython 1.64 (time for another thread, maybe we can aim
>>> > for the end of this month?).
>>> >
>>> > Thanks Bow,
>>> >
>>> > Peter
>>