[O] org in the wild update
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
Re: [O] org in the wild update
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.doy...@rochester.eduwrote: 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
Re: [O] org in the wild update
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 jkitc...@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.doy...@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
[O] org in the wild update
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*, IECR, 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
