http://bioinformatics.oxfordjournals.org/content/early/2015/02/18/bioinformatics.btv098.full.pdf+html

and a feature
http://google-opensource.blogspot.nl/2015/03/gsoc-project-sambamba-published-in.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+GoogleOpenSourceBlog+(Google+Open+Source+Blog)


D may hold a sweet spot in bioinformatics where you often require quick turnaround (productivity) , raw speed and agility.

On Monday, 30 March 2015 at 06:50:19 UTC, george wrote:
>
> http://bioinformatics.oxfordjournals.org/content/early/2015/02/18/bioinformatics.btv098.full.pdf+html
>
> and a feature
> http://google-opensource.blogspot.nl/2015/03/gsoc-project-sambamba-published-in.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+GoogleOpenSourceBlog+(Google+Open+Source+Blog)
>
>
> D may hold a sweet spot in bioinformatics where you often require quick turnaround (productivity) , raw speed and agility.

Thanks.  Added to Python wiki section here: http://wiki.dlang.org/Coming_From/Python

But we should also create anchors for guides by different use domains for D: finance, bioinformatics, etc.  Enterprise users often like to know they are not the first.

On Monday, 30 March 2015 at 06:50:19 UTC, george wrote:
>
> http://bioinformatics.oxfordjournals.org/content/early/2015/02/18/bioinformatics.btv098.full.pdf+html
>
> and a feature
> http://google-opensource.blogspot.nl/2015/03/gsoc-project-sambamba-published-in.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+GoogleOpenSourceBlog+(Google+Open+Source+Blog)
>
>
> D may hold a sweet spot in bioinformatics where you often require quick turnaround (productivity) , raw speed and agility.

.NET actually already has a foothold in bioinformatics, specially in user facing software and steering of reading equipments and robots.

So D's needs a story over C# and F# (alongside WPF for data visualization) use cases.

--
Paulo

> .NET actually already has a foothold in bioinformatics, specially in user facing software and steering of reading equipments and robots.
>
> So D's needs a story over C# and F# (alongside WPF for data visualization) use cases.
>
> --
> Paulo

Though when it comes to open source bioinformatics projects, Perl and Python have a large foothold
among most most bioinformaticians. Most utilities that require speed are often written in C and C++ (BLAST, HMMER, SAMTOOLS etc).

I think D stands a good chance as a language of choice for bioinformatics projects.

George

On 3/29/15 11:50 PM, george wrote:
>
> http://bioinformatics.oxfordjournals.org/content/early/2015/02/18/bioinformatics.btv098.full.pdf+html
>
>
> and a feature
> http://google-opensource.blogspot.nl/2015/03/gsoc-project-sambamba-published-in.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+GoogleOpenSourceBlog+(Google+Open+Source+Blog)
>
>
>
> D may hold a sweet spot in bioinformatics where you often require quick
> turnaround (productivity) , raw speed and agility.

Nice! Went to post it on reddit, was already there: http://www.reddit.com/r/programming/comments/30tvlf/d_in_bioinformatics_gsoc_project_sambamba/

More:

https://news.ycombinator.com/newest

https://twitter.com/D_Programming/status/582603844355424257

https://www.facebook.com/dlang.org/posts/1041963349150679


Andrei

On Mon, 2015-03-30 at 18:04 +0000, george via Digitalmars-d wrote:
> > .NET actually already has a foothold in bioinformatics, specially in user facing software and steering of reading equipments and robots.
> > 
> > So D's needs a story over C# and F# (alongside WPF for data visualization) use cases.
> > 
> > --
> > Paulo

Paulo,

Can you send me some pointers to this stuff?

> 
> Though when it comes to open source bioinformatics projects, Perl
> and Python have a large foothold
> among most most bioinformaticians. Most utilities that require
> speed are often written in C and C++ (BLAST, HMMER, SAMTOOLS etc).
> 
> I think D stands a good chance as a language of choice for bioinformatics projects.
> 
> George

My "prejudice", based on training people in Python and C++ over the last few years, is that Python and C++ have a very strong position in the bioinformatics community, with the use of IPython (now becoming Jupyter) increasing and solidifying the Python position.

D's position is quite weak here because one of the important things is visualising data, something SciPy/Matplotlib are very good at. D has no real play in this arena and so there is no way (currently) of creating a foothold. Sad, but…

-- 
Russel. ============================================================================= Dr Russel Winder      t: +44 20 7585 2200   voip: sip:russel.winder@ekiga.net 41 Buckmaster Road    m: +44 7770 465 077   xmpp: russel@winder.org.uk London SW11 1EN, UK   w: www.russel.org.uk  skype: russel_winder

On 3/30/15 11:23 AM, Russel Winder via Digitalmars-d wrote:
> On Mon, 2015-03-30 at 18:04 +0000, george via Digitalmars-d wrote:
>>> .NET actually already has a foothold in bioinformatics,
>>> specially in user facing software and steering of reading
>>> equipments and robots.
>>>
>>> So D's needs a story over C# and F# (alongside WPF for data
>>> visualization) use cases.
>>>
>>> --
>>> Paulo
>
> Paulo,
>
> Can you send me some pointers to this stuff?
>
>>
>> Though when it comes to open source bioinformatics projects, Perl
>> and Python have a large foothold
>> among most most bioinformaticians. Most utilities that require
>> speed are often written in C and C++ (BLAST, HMMER, SAMTOOLS etc).
>>
>> I think D stands a good chance as a language of choice for
>> bioinformatics projects.
>>
>> George
>
> My "prejudice", based on training people in Python and C++ over the
> last few years, is that Python and C++ have a very strong position in
> the bioinformatics community, with the use of IPython (now becoming
> Jupyter) increasing and solidifying the Python position.
>
> D's position is quite weak here because one of the important things is
> visualising data, something SciPy/Matplotlib are very good at. D has
> no real play in this arena and so there is no way (currently) of
> creating a foothold. Sad, but…

... incongruent with the recently-published bioinformatics paper. -- Andrei

> My "prejudice", based on training people in Python and C++ over the last few years, is that Python and C++ have a very strong position in the bioinformatics community, with the use of IPython (now becoming Jupyter) increasing and solidifying the Python position.

It's just possible there is a selection effect ;)  Plus the future may not be like the past.

> D's position is quite weak here because one of the important things is visualising data, something SciPy/Matplotlib are very good at. D has no real play in this arena and so there is no way (currently) of
> creating a foothold. Sad, but…

You're right about the lack of visualization being a shame. I have been thinking about porting Bokeh bindings to D.  There isn't much too it on the server side - all you need to do is build up the object model and translate it to JSON - but I have not time right now to do it all myself.

https://github.com/bokeh/bokeh

I did port MathGL C API to D, although I haven't tested yet beyond the simplest example.  The C++ bindings aren't so much work to add, although even the C API is not so ugly.

http://mathgl.sourceforge.net/doc_en/Main.html

On Monday, 30 March 2015 at 18:23:31 UTC, Russel Winder wrote:
> On Mon, 2015-03-30 at 18:04 +0000, george via Digitalmars-d wrote:
>> > .NET actually already has a foothold in bioinformatics, specially in user facing software and steering of reading equipments and robots.
>> > 
>> > So D's needs a story over C# and F# (alongside WPF for data visualization) use cases.
>> > 
>> > --
>> > Paulo
>
> Paulo,
>
> Can you send me some pointers to this stuff?
>

Sure, just sent to your email.

--
Paulo

On Monday, 30 March 2015 at 20:09:35 UTC, Laeeth Isharc wrote:
>
clip
>
> You're right about the lack of visualization being a shame. I have been thinking about porting Bokeh bindings to D.  There isn't much too it on the server side - all you need to do is build up the object model and translate it to JSON - but I have not time right now to do it all myself.
>
clip

A comment on the visualization thing. Is this really a big issue?  Data processing (D's strong point) and visualization are different tasks, and presumably as long as outputs are to standard file types (ie. NetCDF, HDF5 or other domain specific formats) then existing visualization tools should be usable.

I did some image processing work with D and didn't find the lack of specific D tools for visualization a big issue.

There is some advantage to being able to perform visualization tasks in the same lanaguage as you do the data processing work, but I wouldn't this this would be a major obstacle.