An Org centric research lab: Goodbye MS word, excel, and powerpoint

An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

Dear All,

Here is a link to a manuscript my research group produced completely with org
http://medicalimaging.spiedigitallibrary.org/issue.aspx. 

For the last 6 years, I have used org mainly for teaching (beamer),
productivity, outlining ideas, and note taking. Inspired by John
Kitchin's 2013 Scipy talk, I tried to encourage members of my research
group to use Org. Since the gentle approach didn't work, I made it 
mandatory requirement that all junior members must generate
manuscripts in org, and now I am seeing the fruits of this decision--- we are now a org-centric  research group :)

I would like to thank  Carsten and all the other contributors for creating such
an awesome research tool. 

Cheers,
M

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[John Kitchin]

That is great! Congratulations, and thanks for sharing. I have also
converted my group into an org-centric group.  Did you find many
challenges in implementing this in your group?

"Doyley, Marvin M." <mdoyley@ur.rochester.edu> writes:

> Dear All,
>
> Here is a link to a manuscript my research group produced completely with org
> http://medicalimaging.spiedigitallibrary.org/issue.aspx. 
>
> For the last 6 years, I have used org mainly for teaching (beamer),
> productivity, outlining ideas, and note taking. Inspired by John
> Kitchin's 2013 Scipy talk, I tried to encourage members of my research
> group to use Org. Since the gentle approach didn't work, I made it 
> mandatory requirement that all junior members must generate
> manuscripts in org, and now I am seeing the fruits of this decision--- we are now a org-centric  research group :)
>
> I would like to thank  Carsten and all the other contributors for creating such
> an awesome research tool. 
>
> Cheers,
> M
>

-- 
-----------------------------------
John Kitchin
Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Grant Rettke]

Congratulations on your effort.
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson


On Tue, Jul 8, 2014 at 7:24 PM, Doyley, Marvin M.
<mdoyley@ur.rochester.edu> wrote:
> Dear All,
>
> Here is a link to a manuscript my research group produced completely with org
> http://medicalimaging.spiedigitallibrary.org/issue.aspx.
>
> For the last 6 years, I have used org mainly for teaching (beamer),
> productivity, outlining ideas, and note taking. Inspired by John
> Kitchin's 2013 Scipy talk, I tried to encourage members of my research
> group to use Org. Since the gentle approach didn't work, I made it
> mandatory requirement that all junior members must generate
> manuscripts in org, and now I am seeing the fruits of this decision--- we are now a org-centric  research group :)
>
> I would like to thank  Carsten and all the other contributors for creating such
> an awesome research tool.
>
> Cheers,
> M

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

Thanks John,

The biggest challenge has been getting my team to use emacs, and appreciate its power. A few of the students are now comfortable with it, but most are still novices, even the computationally savvy  members of my team. For now I am forcing everybody to use org as a latex replacement no babel or beamer yet. However, In the fall I will mandate that all data analysis (matlab babel) should be included with all manuscripts. I notice that you prefer to use python rather than matlab. Is there a reason  for this ? Matlab is free at my institution so cost  is not an issue.

I welcome any advise or tips you may have 

Best Wishes,

M


On Jul 9, 2014, at 3:08 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> That is great! Congratulations, and thanks for sharing. I have also
> converted my group into an org-centric group.  Did you find many
> challenges in implementing this in your group?
> 
> "Doyley, Marvin M." <mdoyley@ur.rochester.edu> writes:
> 
>> Dear All,
>> 
>> Here is a link to a manuscript my research group produced completely with org
>> https://urldefense.proofpoint.com/v1/url?u=http://medicalimaging.spiedigitallibrary.org/issue.aspx&k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0A&r=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0A&m=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0A&s=f6e37fd82613c5c7a791b1df10042b390be86728522e227f9316ec27d12c08c1. 
>> 
>> For the last 6 years, I have used org mainly for teaching (beamer),
>> productivity, outlining ideas, and note taking. Inspired by John
>> Kitchin's 2013 Scipy talk, I tried to encourage members of my research
>> group to use Org. Since the gentle approach didn't work, I made it 
>> mandatory requirement that all junior members must generate
>> manuscripts in org, and now I am seeing the fruits of this decision--- we are now a org-centric  research group :)
>> 
>> I would like to thank  Carsten and all the other contributors for creating such
>> an awesome research tool. 
>> 
>> Cheers,
>> M
>> 
> 
> -- 
> -----------------------------------
> John Kitchin
> Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> https://urldefense.proofpoint.com/v1/url?u=http://kitchingroup.cheme.cmu.edu/&k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0A&r=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0A&m=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0A&s=c42f68beb01d6c32f1ce25775cb9df73f29f6198e9a3dc71beb1514a293e1533

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Grant Rettke]

On Wed, Jul 9, 2014 at 5:37 PM, Doyley, Marvin M.
<mdoyley@ur.rochester.edu> wrote:
> I notice that you prefer to use python rather than matlab. Is there a reason  for this ? Matlab is free at my
> institution so cost  is not an issue.

Doing all of your reproducible research with free software will
maximize the number of people who may reproduce your research. MATLAB
is a great, great tool, and not many people purchase it other than
universities or professional engineers, minimize the number of people
to reproduce your research.

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Ken Mankoff]

* On 2014-07-10 at 20:45, Grant Rettke wrote:
> On Wed, Jul 9, 2014 at 5:37 PM, Doyley, Marvin M.
> <mdoyley@ur.rochester.edu> wrote:
>> I notice that you prefer to use python rather than matlab. Is there a reason  for this ? Matlab is free at my
>> institution so cost  is not an issue.

It won't be free in the future for the people you are training...

  -k.

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

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Good point.
Thanks
On Jul 10, 2014, at 8:45 PM, Grant Rettke <gcr@wisdomandwonder.com<mailto:gcr@wisdomandwonder.com>> wrote:

Doing all of your reproducible research with free software will
maximize the number of people who may reproduce your research. MATLAB
is a great, great tool, and not many people purchase it other than
universities or professional engineers, minimize the number of people
to reproduce your research.


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Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[John Kitchin]

Matlab is "free" for us too, but it does not work in org-babel on
windows. it works ok on linux, but not as well as python. Plus, we use
python for all our research, and most importantly, I like it better ;)

"Doyley, Marvin M." <mdoyley@ur.rochester.edu> writes:

> Thanks John,
>
> The biggest challenge has been getting my team to use emacs, and
> appreciate its power. A few of the students are now comfortable with
> it, but most are still novices, even the computationally savvy members
> of my team. For now I am forcing everybody to use org as a latex
> replacement no babel or beamer yet. However, In the fall I will
> mandate that all data analysis (matlab babel) should be included with
> all manuscripts. I notice that you prefer to use python rather than
> matlab. Is there a reason for this ? Matlab is free at my institution
> so cost is not an issue.
>
> I welcome any advise or tips you may have 
>
> Best Wishes,
>
> M
>
>
> On Jul 9, 2014, at 3:08 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
>> That is great! Congratulations, and thanks for sharing. I have also
>> converted my group into an org-centric group.  Did you find many
>> challenges in implementing this in your group?
>> 
>> "Doyley, Marvin M." <mdoyley@ur.rochester.edu> writes:
>> 
>>> Dear All,
>>> 
>>> Here is a link to a manuscript my research group produced completely with org
>>> https://urldefense.proofpoint.com/v1/url?u=http://medicalimaging.spiedigitallibrary.org/issue.aspx&k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0A&r=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0A&m=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0A&s=f6e37fd82613c5c7a791b1df10042b390be86728522e227f9316ec27d12c08c1.
>>> 
>>> For the last 6 years, I have used org mainly for teaching (beamer),
>>> productivity, outlining ideas, and note taking. Inspired by John
>>> Kitchin's 2013 Scipy talk, I tried to encourage members of my research
>>> group to use Org. Since the gentle approach didn't work, I made it 
>>> mandatory requirement that all junior members must generate
>>> manuscripts in org, and now I am seeing the fruits of this decision--- we are now a org-centric  research group :)
>>> 
>>> I would like to thank  Carsten and all the other contributors for creating such
>>> an awesome research tool. 
>>> 
>>> Cheers,
>>> M
>>> 
>> 
>> -- 
>> -----------------------------------
>> John Kitchin
>> Professor
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> https://urldefense.proofpoint.com/v1/url?u=http://kitchingroup.cheme.cmu.edu/&k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0A&r=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0A&m=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0A&s=c42f68beb01d6c32f1ce25775cb9df73f29f6198e9a3dc71beb1514a293e1533
>
>
>

-- 
-----------------------------------
John Kitchin
Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Martin Schöön]

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Python is widely used in industry and these days many CAD/CAE tools use
Python for scripting...

-- 
Martin Schöön

http://hem.bredband.net/b262106/index.html

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Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Detlef Steuer]

Am Wed, 9 Jul 2014 22:37:12 +0000
schrieb "Doyley, Marvin M." <mdoyley@ur.rochester.edu>:

>  I notice that you prefer to use python rather than matlab. Is there
> a reason  for this ? Matlab is free at my institution so cost  is not
> an issue.

"Free" here, too. 

But we prefer R for Data Analysis, not at least because it is OS agnostic.

Furthermore, when I was a student myself, I *hated* to be forced into 
the overcrowded, overheated lab for programming. Now everybody can choose to programm at home, in the lab, on the train or on the beach. (Ok, the last one is not too important most of the time over here, but today it would be an alternative.)

Have a nice summer

Detlef

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Ken Mankoff]

Hi Marvin,

* On 2014-07-09 at 18:37, Doyley, Marvin M. wrote:
> I notice that you prefer to use python rather than matlab. Is there a
> reason for this ? Matlab is free at my institution so cost is not an
> issue.

An additional blog post (with good discussion and links to other posts)
on the Python v. MATLAB debate:

http://lorenabarba.com/blog/why-i-push-for-python/

and

http://phillipmfeldman.org/Python/Advantages_of_Python_Over_Matlab.html

  -k.

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Grant Rettke]

Octave is an option, too: https://www.gnu.org/software/octave/
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson


On Fri, Jul 11, 2014 at 7:31 PM, Ken Mankoff <mankoff@gmail.com> wrote:
> Hi Marvin,
>
> * On 2014-07-09 at 18:37, Doyley, Marvin M. wrote:
>> I notice that you prefer to use python rather than matlab. Is there a
>> reason for this ? Matlab is free at my institution so cost is not an
>> issue.
>
> An additional blog post (with good discussion and links to other posts)
> on the Python v. MATLAB debate:
>
> http://lorenabarba.com/blog/why-i-push-for-python/
>
> and
>
> http://phillipmfeldman.org/Python/Advantages_of_Python_Over_Matlab.html
>
>   -k.
>

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Grant Rettke]

Now that I wrote that... MATLAB is totally worth the money.

A nice option for reproducible research is also to develop on MATLAB
and just make sure that OCTAVE can run it, too. Nice when you don't
want to worry about N licenses for deploying on a HPC cluster.
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson


On Fri, Jul 11, 2014 at 9:03 PM, Grant Rettke <gcr@wisdomandwonder.com> wrote:
> Octave is an option, too: https://www.gnu.org/software/octave/
> Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
> gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
> “Wisdom begins in wonder.” --Socrates
> ((λ (x) (x x)) (λ (x) (x x)))
> “Life has become immeasurably better since I have been forced to stop
> taking it seriously.” --Thompson
>
>
> On Fri, Jul 11, 2014 at 7:31 PM, Ken Mankoff <mankoff@gmail.com> wrote:
>> Hi Marvin,
>>
>> * On 2014-07-09 at 18:37, Doyley, Marvin M. wrote:
>>> I notice that you prefer to use python rather than matlab. Is there a
>>> reason for this ? Matlab is free at my institution so cost is not an
>>> issue.
>>
>> An additional blog post (with good discussion and links to other posts)
>> on the Python v. MATLAB debate:
>>
>> http://lorenabarba.com/blog/why-i-push-for-python/
>>
>> and
>>
>> http://phillipmfeldman.org/Python/Advantages_of_Python_Over_Matlab.html
>>
>>   -k.
>>

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Jorge A. Alfaro-Murillo]

Grant Rettke <gcr@wisdomandwonder.com> writes:

> Octave is an option, too: https://www.gnu.org/software/octave/

Since people are championing python, and R and Octave have been
mentioned, let me throw this one into the discussion:
http://www.sagemath.org/

"Sage is a free open-source mathematics software system licensed under
the GPL. It builds on top of many existing open-source packages: NumPy,
SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more"

"Many more" includes Octave as well. If you know python, then you can
use only python in Sage, no need for learning anything new.

Actually you do not need to install anything to use it:
https://cloud.sagemath.com/

At Sage Math Cloud (SMC) besides Sage, you can access a terminal there
and it has emacs already installed. Also you can ssh to their servers,
and tramp with emacs locally works well connecting to it. That is what I
use for research.

Come to think about it, there is no ob-sage.el yet. I write my papers
directly to LaTeX (and my collaborators write at SMC since they are not
emacs users and it provides direct compilation and shows already the
results) so I never thought about exporting to sage. Does someone have
any plans for this?

Jorge.

Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[TP]

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On Tue, Jul 8, 2014 at 5:24 PM, Doyley, Marvin M. <mdoyley@ur.rochester.edu>
wrote:

> Since the gentle approach didn't work, I made it
> mandatory requirement that all junior members must generate
> manuscripts in org,
>

"It's good to be the king." :)

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Re: An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin]

jorge.a.alfaro@gmail.com (Jorge A. Alfaro-Murillo) writes:

Thanks everybody for highlighting the benefits of python. I am exploring
python with a few undergraduates. I am impressed how well python plays
with Fortran, f2py is awesome. The syntax is very similar to MATLAB so
migration should be easy, if I decided to move in that direction.

Best Wishes,
M

 
> Grant Rettke <gcr@wisdomandwonder.com> writes:
>
>> Octave is an option, too: https://www.gnu.org/software/octave/
>
> Since people are championing python, and R and Octave have been
> mentioned, let me throw this one into the discussion:
> http://www.sagemath.org/
>
> "Sage is a free open-source mathematics software system licensed under
> the GPL. It builds on top of many existing open-source packages: NumPy,
> SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more"
>
> "Many more" includes Octave as well. If you know python, then you can
> use only python in Sage, no need for learning anything new.
>
> Actually you do not need to install anything to use it:
> https://cloud.sagemath.com/
>
> At Sage Math Cloud (SMC) besides Sage, you can access a terminal there
> and it has emacs already installed. Also you can ssh to their servers,
> and tramp with emacs locally works well connecting to it. That is what I
> use for research.
>
> Come to think about it, there is no ob-sage.el yet. I write my papers
> directly to LaTeX (and my collaborators write at SMC since they are not
> emacs users and it provides direct compilation and shows already the
> results) so I never thought about exporting to sage. Does someone have
> any plans for this?
>
> Jorge.
>
>
>

--