[Biopython] Fwd: Your abstract (11) has been accepted for a short talk at BOSC 2020!

Sat Jun 13 05:10:02 UTC 2020

 For novel functionality (see the first reviewer) you could point to the new pairwise sequence aligner in Biopython. It is as fast as aligners implemented as standalone (C/C++) programs, maybe even faster if you want to align many sequences, but much more flexible. I don't know of any existing programs that offer this speed and flexibility.
Best,-Michiel

    On Sunday, June 7, 2020, 9:16:22 PM GMT+9, Peter Cock <p.j.a.cock at googlemail.com> wrote:  

 Good news: The abstract was accepted for a lightning talk, and we have the opportunity to improve the abstract (see reviews below).
Specifically I think we should add something about the alphabet changes underway on GitHub (which in hindsight I wish we'd drawn more attention to in the NEWS file for Biopython 1.78). Quoting the DEPRECATED file,
"The design of Bio.Aphabet included a number of historic design choices which, with the benefit of hindsight, were regretable. While the details remain to be agreed, we intend to remove or replace Bio.Alphabet in 2020."
GMail has just flagged that regrettable was misspelt. Opps.
The BOSC/BCC 20202 abstract is here:
https://github.com/biopython/talks/tree/master/2020_BOSC/abstract

Peter

---------- Forwarded message ---------
From: BCC2020 Track Chairs <bcc2020 at easychair.org>
Date: Sun, Jun 7, 2020 at 2:22 AM
Subject: Your abstract (11) has been accepted for a short talk at BOSC 2020!
To: Peter Cock <p.j.a.cock at googlemail.com>

Dear Peter Cock,

Congratulations! An abstract on which you are an author (11, Biopython Project Update 2020) has been chosen for a short talk in the BOSC track of the Bioinformatics Community Conference (BCC2020). Short (lightning) talks are 5 minutes. Long talks are 15 minutes. There will be time allocated at the end of each session for live Q&A with presenters from that session.

All talks at BCC2020 (except for keynotes) will be presented via pre-recorded videos prepared by the presenters (that means you!) and submitted to us by July 6. We will send you more information about this process soon.

In order to accept our invitation to present and secure a spot in our packed schedule, please fill out the response form at XXX by June 15. If we don’t hear from you by the end of the day on June 15, we will assume you are declining the invitation to give a talk at BCC2020 and will offer your talk spot to another author. 

All accepted speakers will also be welcome to present their work as a poster/demo. We're still thinking about how posters and demos will work. We will likely hold them as breakout videoconferences where you can share a live or prerecorded short presentation and a PDF and discuss your work with attendees. We’re also open to suggestions on ways to present posters - a giant poster-sized PDF would not be easy to examine on screens! 

If you want to make any changes to the abstract that you submitted, you will have until June 22 to upload a revised abstract at https://easychair.org/conferences/?conf=bcc2020. 

Sincerely,
   Program Committee, BOSC 2020

P.S. The reviewers' feedback on your abstract is at the end of this message. If you have any questions, please contact the BOSC organizing committee <bosc at open-bio.org>.

SUBMISSION: 11
TITLE: Biopython Project Update 2020

----------------------- REVIEW 1 ---------------------
SUBMISSION: 11
TITLE: Biopython Project Update 2020
AUTHORS: Peter Cock

----------- Relevant -----------
SCORE: 1 (yes)
----------- Available -----------
SCORE: 1 (yes)
----------- Open -----------
SCORE: 1 (yes)
----------- Updated -----------
SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates)
----------- Formatted -----------
SCORE: 1 (yes)
----------- Community -----------
SCORE: -1 (no)
----- TEXT:
The project obviously has some impact (with more than 4K followers on twitter), but the abstract does not mention anything specifically. A proxy indicator is the number of code contributors, but its not the same thing.
----------- Novelty -----------
SCORE: -1 (no)
----- TEXT:
Its an update which focuses on black and pep 8 python code formatting guides and unit tests etc - not functionality.
----------- Example -----------
SCORE: -1 (no (and it needs one))
----------- Runnable -----------
SCORE: 1 (yes)
----------- Quality score -----------
SCORE: 1 (ok)
----- TEXT:
Even though this is an update, a sentence or two on that the library actually does and what its good for would have been very helpful. Otherwise it seems like an update on a well-used code base in bioinformatics - although the focus on code formatting, unit tests and CI is not that exciting for users I would think, but maybe for prospective contributors.
----------- Suitability for a long talk -----------
SCORE: 1 (Fine for short talk)

----------------------- REVIEW 2 ---------------------
SUBMISSION: 11
TITLE: Biopython Project Update 2020
AUTHORS: Peter Cock

----------- Relevant -----------
SCORE: 1 (yes)
----------- Available -----------
SCORE: 1 (yes)
----------- Open -----------
SCORE: 1 (yes)
----------- Updated -----------
SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates)
----------- Formatted -----------
SCORE: 1 (yes)
----------- Community -----------
SCORE: 1 (yes)
----------- Novelty -----------
SCORE: 1 (yes)
----------- Example -----------
SCORE: 0 (sort of or not applicable)
----- TEXT:
Not applicable
----------- Runnable -----------
SCORE: 1 (yes)
----------- Quality score -----------
SCORE: 2 (good)
----- TEXT:
Given the importance of Biopython for the community and the continued improvement that the abstract details (3 releases since last year's BOSC), I think an update is valuable.
----------- Suitability for a long talk -----------
SCORE: 2 (Good for short or long talk)

----------------------- REVIEW 3 ---------------------
SUBMISSION: 11
TITLE: Biopython Project Update 2020
AUTHORS: Peter Cock

----------- Relevant -----------
SCORE: 1 (yes)
----------- Available -----------
SCORE: 1 (yes)
----------- Open -----------
SCORE: 1 (yes)
----------- Updated -----------
SCORE: 1 (project was previously presented at BOSC/GCC but abstract describes updates)
----------- Formatted -----------
SCORE: 1 (yes)
----------- Community -----------
SCORE: 1 (yes)
----------- Novelty -----------
SCORE: 1 (yes)
----------- Example -----------
SCORE: 0 (sort of or not applicable)
----------- Runnable -----------
SCORE: 1 (yes)
----------- Quality score -----------
SCORE: 3 (excellent)
----- TEXT:
BioPython is a well-established project and of very general interest to the bioinformatics community. In many ways it is an example to follow for other smaller and/or younger open source projects, so it will be very interesting to hear the news and updates from last year.
----------- Suitability for a long talk -----------
SCORE: 2 (Good for short or long talk)
----- TEXT:
I believe that most of the audience will already know the BioPython project, so a short talk should be enough to explain news and updates, rather than going into all the details of the library.

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