Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
Grant Rettke g...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
On Tue, Jul 8, 2014 at 5:24 PM, Doyley, Marvin M. mdoy...@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. :)
Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
jorge.a.alf...@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 g...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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
Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
Am Wed, 9 Jul 2014 22:37:12 + schrieb Doyley, Marvin M. mdoy...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
Octave is an option, too: https://www.gnu.org/software/octave/ Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@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 mank...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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 g...@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 g...@wisdomandwonder.com wrote: Octave is an option, too: https://www.gnu.org/software/octave/ Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@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 mank...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
On Wed, Jul 9, 2014 at 5:37 PM, Doyley, Marvin M. mdoy...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
* On 2014-07-10 at 20:45, Grant Rettke wrote: On Wed, Jul 9, 2014 at 5:37 PM, Doyley, Marvin M. mdoy...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
Good point. Thanks On Jul 10, 2014, at 8:45 PM, Grant Rettke g...@wisdomandwonder.commailto:g...@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.
Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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. mdoy...@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 jkitc...@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. mdoy...@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.aspxk=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=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%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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. mdoy...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
Congratulations on your effort. Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@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. mdoy...@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: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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 jkitc...@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. mdoy...@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.aspxk=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=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%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=c42f68beb01d6c32f1ce25775cb9df73f29f6198e9a3dc71beb1514a293e1533
[O] An Org centric research lab: Goodbye MS word, excel, and powerpoint
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
