* org in the wild update
@ 2014-02-06 21:45 John Kitchin
0 siblings, 0 replies; 4+ messages in thread
From: John Kitchin @ 2014-02-06 21:45 UTC (permalink / raw)
To: emacs-orgmode@gnu.org
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Hi everyone,
Our fourth scientific paper that was prepared with org-mode has been
accepted! Each of these files has freely available supporting information
files created from org-mode with the org-source embedded in them. At the
end of these files are the directions for how we exported the pdf file out
of them. It has been pretty fun writing these papers, and we are at a point
now where all new papers are written this way in my group. Below are some
of the (org-relevant) features in each paper. Anyway, I want to thank
everyone who contributes to org-mode development. It has fundamentally
changed how we write our papers. Best wishes,
1. This paper has an embedded json file that contains all the data in the
paper and the details of the calculations we did.
Mehta, Prateek; Salvador, Paul; Kitchin, John, *Identifying Potential BO2
Oxide Polymorphs for Epitaxial Growth Candidates*", ACS Applied Materials
and Interfaces, accepted 1/27/2014.
http://pubs.acs.org/doi/full/10.1021/am4059149.
2. In this SI, there are tables in the embedded org-file that were used for
analysis, but not printed in the SI file because they were too long.
Spencer D. Miller, Vladimir V. Pushkarev, Andrew J. Gellman and John R.
Kitchin, *Simulating Temperature Programmed Desorption of Oxygen on Pt(111)
Using DFT Derived Coverage Dependent Desorption Barriers*, Topics In
Catalysis, 57(1), 106-117 (2013).
http://link.springer.com/article/10.1007%2Fs11244-013-0166-3
3. this paper contains the code developed for running these calculations.
Zhongnan Xu and John R Kitchin, *Relating the Electronic Structure and
Reactivity of the 3d Transition Metal Monoxide Surfaces*, Catalysis
Communications, Accepted Oct 2013.
http://dx.doi.org/10.1016/j.catcom.2013.10.028
4. This paper has embedded Excel sheets in the SI, which contain data used
in the paper.
Alex Hallenbeck and John R. Kitchin, *Effects of O2 and SO2 on the Capture
Capacity of a Primary-Amine Based Polymeric CO2 Sorbent*, I&ECR, 52 (31),
10788-10794 (2013). http://dx.doi.org/10.1021/ie400582a.
John
-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu
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* org in the wild update
@ 2014-02-08 12:12 Marvin Doyley
2014-02-08 21:28 ` John Kitchin
0 siblings, 1 reply; 4+ messages in thread
From: Marvin Doyley @ 2014-02-08 12:12 UTC (permalink / raw)
To: jkitchin@andrew.cmu.edu; +Cc: emacs-orgmode@gnu.org
Hi John,
Org have also revolutionized the way I work. I use it for teaching (making slides, creating homework and exams), presentation, and in a couple of weeks we will be submitting our first org generated manuscript. In general, works great for me, but for the students and my assistant that have been another story. I would be interested to learn how you (a) cultivated an org centered culture in your lab, and (b) established an org based research environment (i.e., file sharing, org equivalent of track changes, etc. ).
Best Wishes,
M
Sent from my iPad
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: org in the wild update
2014-02-08 12:12 Marvin Doyley
@ 2014-02-08 21:28 ` John Kitchin
2014-02-08 23:03 ` Marvin Doyley
0 siblings, 1 reply; 4+ messages in thread
From: John Kitchin @ 2014-02-08 21:28 UTC (permalink / raw)
To: Marvin Doyley; +Cc: emacs-orgmode@gnu.org
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This has been an ongoing process for the past 3 years that started with me
learning org-mode to manage my todo list. Most of my students have taken
a class with me, where they already had some familiarity with emacs, and
in which I use org-mode for the assignments. Some of them took to it like
fish in water. A few have not drunk the water, and are thirsty as a result
;) For track changes, I use git, and look at diffs when needed.
I have had to train my students to prepare simple documents, e.g. org
documents, that grow in sophistication over time. I generally provide a
lot of support for this, through my blog (http://kitchingroup.cheme.cmu.edu),
and in meetings. I am certain my students are tired of hearing answers to
their questions that start with "I wrote a blog post that explains..." But
they probably realize they get faster and better feedback when they send me
org docs. I am working towards a set of emacs packages for my group that
will streamline manuscript preparation, and communication.
For file sharing there are two main approaches we use. 1) Part of my group
is computational and we all have accounts on a shared cluster. We share
some documents there. 2) PArt of my group does experimental research. We
use Dropbox too. I have a folder for each student that is shared with them.
Each student has an org-file that outlines their current research projects
and priorities. We use this document to guide our meetings. These documents
are on my agenda list so I know what should be done and by when. And the
students know it too. This is also how we coordinate manuscripts.
Manuscripts are a primary learning experience. Our supporting information
files are routinely 20-100 pages long now because I make my students put
comprehensive detail about what they did in them. Partly so I can be sure
of what they did, and partly for others to learn from.
So, it is still ongoing. The only alternative I am offering my group to
org-mode is LaTeX. They usually make a wise choice ;)
John
-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu
On Sat, Feb 8, 2014 at 7:12 AM, Marvin Doyley <m.doyley@rochester.edu>wrote:
> Hi John,
>
> Org have also revolutionized the way I work. I use it for teaching
> (making slides, creating homework and exams), presentation, and in a
> couple of weeks we will be submitting our first org generated manuscript.
> In general, works great for me, but for the students and my assistant
> that have been another story. I would be interested to learn how you (a)
> cultivated an org centered culture in your lab, and (b) established an org
> based research environment (i.e., file sharing, org equivalent of track
> changes, etc. ).
>
> Best Wishes,
> M
>
>
> Sent from my iPad
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^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: org in the wild update
2014-02-08 21:28 ` John Kitchin
@ 2014-02-08 23:03 ` Marvin Doyley
0 siblings, 0 replies; 4+ messages in thread
From: Marvin Doyley @ 2014-02-08 23:03 UTC (permalink / raw)
To: John Kitchin; +Cc: emacs-orgmode@gnu.org
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Hi John,
I really appreciate your input. I think my first challenge will be to encourage them to learn emacs. I switch from Vi to emacs five years ago after watching Carsten google talk online.
Best Wishes,
M
Sent from my iPad
> On Feb 8, 2014, at 4:28 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>
> This has been an ongoing process for the past 3 years that started with me learning org-mode to manage my todo list. Most of my students have taken a class with me, where they already had some familiarity with emacs, and in which I use org-mode for the assignments. Some of them took to it like fish in water. A few have not drunk the water, and are thirsty as a result ;) For track changes, I use git, and look at diffs when needed.
>
> I have had to train my students to prepare simple documents, e.g. org documents, that grow in sophistication over time. I generally provide a lot of support for this, through my blog (http://kitchingroup.cheme.cmu.edu[kitchingroup.cheme.cmu.edu]), and in meetings. I am certain my students are tired of hearing answers to their questions that start with "I wrote a blog post that explains..." But they probably realize they get faster and better feedback when they send me org docs. I am working towards a set of emacs packages for my group that will streamline manuscript preparation, and communication.
>
> For file sharing there are two main approaches we use. 1) Part of my group is computational and we all have accounts on a shared cluster. We share some documents there. 2) PArt of my group does experimental research. We use Dropbox too. I have a folder for each student that is shared with them. Each student has an org-file that outlines their current research projects and priorities. We use this document to guide our meetings. These documents are on my agenda list so I know what should be done and by when. And the students know it too. This is also how we coordinate manuscripts.
>
> Manuscripts are a primary learning experience. Our supporting information files are routinely 20-100 pages long now because I make my students put comprehensive detail about what they did in them. Partly so I can be sure of what they did, and partly for others to learn from.
>
> So, it is still ongoing. The only alternative I am offering my group to org-mode is LaTeX. They usually make a wise choice ;)
>
>
>
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu[kitchingroup.cheme.cmu.edu]
>
>
>
>> On Sat, Feb 8, 2014 at 7:12 AM, Marvin Doyley <m.doyley@rochester.edu> wrote:
>> Hi John,
>>
>> Org have also revolutionized the way I work. I use it for teaching (making slides, creating homework and exams), presentation, and in a couple of weeks we will be submitting our first org generated manuscript. In general, works great for me, but for the students and my assistant that have been another story. I would be interested to learn how you (a) cultivated an org centered culture in your lab, and (b) established an org based research environment (i.e., file sharing, org equivalent of track changes, etc. ).
>>
>> Best Wishes,
>> M
>>
>>
>> Sent from my iPad
>
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