<p>I fear this entire thread is going to veer dangerously close to opinionation. But regardless of how one feels about the Perl language and its various libraries and communities, I think we can objectively say that the era of Perl's dominance in the bioinformatics community has passed. A lot of tools and libraries implemented in Perl are still widely used, and there is a tremendous amount of legacy Perl code around. The ability to read and write Perl remains a valuable skill.</p>

<p>But in 2019, few people (with a choice) are learning Perl or implementing new tools and frameworks in Perl. Python fits snuggly into the niche once occupied by Perl, and its native OO support is (I dare to say) objectively superior to any <em>post hoc</em> OO support Perl 3rd-party libraries provide.</p>

<p>The broader web/tech community moved on from Perl to Python (and Ruby and others) even before the bioinformatics community did, and this broader community's offerings (IPython, Jupyter, scipy, numpy, pytest, etc.) make Python an even more attractive alternative to Perl for bioinformatics work.</p>

<p>In the meantime, the "hadleyverse" ecosystem of R packages for data manipulation make R much more capable of the types of data pre-processing tasks for which an R programmer might have previously used a language like Perl or Python.</p>

<p>In short, Perl is waning in popularity (if not relevance), and I would not expect much enthusiasm from the bioinformatics community for a new framework built around a relatively obscure Perl extension.</p>

CC BY-SA 4.0
2019-05-09T20:08:42.277Z
Dangerously close ;-) but I definitely disagree about R, but lets see.
M__
CC BY-SA 4.0
2019-05-16T08:52:34.877Z
I will revise this question shortly and resubmit it. My perception of Python is that although the syntax is easy, precisely what the program is doing with the code appears poorly described. In Perl most coders know how the code relates to its functionality, e.g. memory allocation, where the variables reside, %INC. For example an "orchish maneuver" is understood by most coders, even if they don't know it by name.
M__
CC BY-SA 4.0
2019-05-09T20:01:13.580Z
2019-05-09T20:01:13.580Z
Daniel Standage
<p>This is a silly post, but hope it makes a point. We have BioPerl (which never impressed me, in fact there isn't even a BioPerl tag), BioPython (which admittedly is impressive), and even now BioRust. </p>

<p>Why not BioMoose? </p>

<p>Moose is Perl5s answer to objects and is really impressive in its simplicity and ease of use. Before Moose Perl5 objects, were/are, how can I say, make evolutionary chaos theory look hip and relevant. Moose changed that completely, but stacking Moose code into BioPerl is never gonna work.</p>

CC BY-SA 4.0
2019-05-10T08:42:56.623Z
I don't understand your question. Do you ask why BioMoose is...? Or do you want to have a tag with BioMoose here on bioinformatics.SE? The reason why there isn't a BioPerl tag is that no one asked a question about it. So if you want to have the BioMoose tag, ask questions about it here.
llrs
CC BY-SA 4.0
2019-05-10T09:38:41.347Z
Hi Llrs, I will provide a clearer explanation as a brief post at the end of the chat. The post is more about the future of Perl in bioinformatics, it isn't meant to be taken at face value. We don't have a tag for BioPerl because BioPerl was never a success, that was my point. If we don't have a tag about BioPython we should do (because it's good).
M__
CC BY-SA 4.0
2019-05-10T10:02:00.553Z
Sorry but I'm missing something. You will provide an explanation at the end of which chat? So, what is your question? What is the problem you are facing?
llrs
CC BY-SA 4.0
2019-05-10T11:00:29.330Z
@DanielStandage summarises the status quo behind the question and is saying 'not impressed'. If you've never tried writing Perl objects (which are terrible) it's difficult emote. BioPerl likely never succeeded because it required writing Perl objects. .Moose overcomes this with aplomb, but skepticism remains.
M__
CC BY-SA 4.0
2019-05-10T12:41:47.353Z
I still don't understand what is your question (and I've briefly used BioPerl). You seem to ask why people do not use BioMoose instead of BioPerl. but that is primarily opinion-based.
llrs
CC BY-SA 4.0
2019-05-10T13:14:14.427Z
Using BioPerl is not a problem, its writing it. Using objects is easy, writing Perl objects is hard and buggy. So the idea of the question is that there is a very easy way of writing Perl objects (Moose), would that enable a new Bio- repository to succeed, or (more realistically) become a Perl "revival" or "greater acceptance" within bioinformatics. I think the question is clear, and the response in one instance is "no". Perl6 might change that response and Perl5 Moose is part the transition. The foundational concepts do affect how you code.
M__
<perl>
How about BioMoose?
# How about BioMoose?

(Asked by: username_0 on 2019-05-09)

This is a silly post, but hope it makes a point. We have BioPerl (which never impressed me, in fact there isn't even a BioPerl tag), BioPython (which admittedly is impressive), and even now BioRust.

Why not BioMoose?

Moose is Perl5s answer to objects and is really impressive in its simplicity and ease of use. Before Moose Perl5 objects, were/are, how can I say, make evolutionary chaos theory look hip and relevant. Moose changed that completely, but stacking Moose code into BioPerl is never gonna work.

**Tags:** perl
> **Comments:**
> **username_1**: I don't understand your question. Do you ask why BioMoose is...? Or do you want to have a tag with BioMoose here on bioinformatics.SE? The reason why there isn't a BioPerl tag is that no one asked a question about it. So if you want to have the BioMoose tag, ask questions about it here.  
> **username_0**: Hi Llrs, I will provide a clearer explanation as a brief post at the end of the chat. The post is more about the future of Perl in bioinformatics, it isn't meant to be taken at face value. We don't have a tag for BioPerl because BioPerl was never a success, that was my point. If we don't have a tag about BioPython we should do (because it's good).  
> **username_1**: Sorry but I'm missing something. You will provide an explanation at the end of which chat? So, what is your question? What is the problem you are facing?  
> **username_0**: @DanielStandage summarises the status quo behind the question and is saying 'not impressed'. If you've never tried writing Perl objects (which are terrible) it's difficult emote. BioPerl likely never succeeded because it required writing Perl objects. .Moose overcomes this with aplomb, but skepticism remains.  
> **username_1**: I still don't understand what is your question (and I've briefly used BioPerl). You seem to ask why people do not use BioMoose instead of BioPerl. but that is primarily opinion-based.  
> **username_0**: Using BioPerl is not a problem, its writing it. Using objects is easy, writing Perl objects is hard and buggy. So the idea of the question is that there is a very easy way of writing Perl objects (Moose), would that enable a new Bio- repository to succeed, or (more realistically) become a Perl "revival" or "greater acceptance" within bioinformatics. I think the question is clear, and the response in one instance is "no". Perl6 might change that response and Perl5 Moose is part the transition. The foundational concepts do affect how you code.  

---

## 1 answers

### Answer by username_2 on 2019-05-09. Score: 2

I fear this entire thread is going to veer dangerously close to opinionation. But regardless of how one feels about the Perl language and its various libraries and communities, I think we can objectively say that the era of Perl's dominance in the bioinformatics community has passed. A lot of tools and libraries implemented in Perl are still widely used, and there is a tremendous amount of legacy Perl code around. The ability to read and write Perl remains a valuable skill.

But in 2019, few people (with a choice) are learning Perl or implementing new tools and frameworks in Perl. Python fits snuggly into the niche once occupied by Perl, and its native OO support is (I dare to say) objectively superior to any *post hoc* OO support Perl 3rd-party libraries provide.

The broader web/tech community moved on from Perl to Python (and Ruby and others) even before the bioinformatics community did, and this broader community's offerings (IPython, Jupyter, scipy, numpy, pytest, etc.) make Python an even more attractive alternative to Perl for bioinformatics work.

In the meantime, the "hadleyverse" ecosystem of R packages for data manipulation make R much more capable of the types of data pre-processing tasks for which an R programmer might have previously used a language like Perl or Python.

In short, Perl is waning in popularity (if not relevance), and I would not expect much enthusiasm from the bioinformatics community for a new framework built around a relatively obscure Perl extension.

> **Comments:**
> **username_0**: Dangerously close ;-) but I definitely disagree about R, but lets see.  
> **username_0**: I will revise this question shortly and resubmit it. My perception of Python is that although the syntax is easy, precisely what the program is doing with the code appears poorly described. In Perl most coders know how the code relates to its functionality, e.g. memory allocation, where the variables reside, %INC. For example an "orchish maneuver" is understood by most coders, even if they don't know it by name.  

---

