Re: how do scientists use org mode?

Re: how do scientists use org mode?

[GMX Christoph 13]

Hi all

Real life took precedence for a while and also I realized that making the step towards org mode would be a rather more substantial leap than I had anticipated. Given how dissatisfied I had become with the more "traditional" solutions to the problem one would expect a shift in paradigms though. 

This is to do more with the underlying emacs rather than org mode itself but sadly one cannot have one without the other. I hope that  I will learn to appreciate one as well as the other but my previous exposure to emacs was limited to one mind-blowingly powerful major emacs mode which I treated strictly as a tool (RALEE by S. Griffiths-Jones), ignoring the emacs specifics for the most part. It seems that now is the time to dive into emacs for real, and org mode is the culprit...

At the moment decades of muscle memory get in the way in accomplishing even simple tasks, but Aquamacs provides some basic familiarity and alleviates at least some of the pain. 

For the moment I will limit myself to one project notebook with embedded todos and go from there. This is BTW the main reason I asked for feedback from fellow scientists (no offense to anyone else). GTD and other task management systems are generally discussed in a way that implies that most tasks simply appear out of nowhere presumably from your superior hence little thought is devoted to WHY or even IF it should be done. The thing about science is that we tend to grow our ideas as well as create the market for them. I have no real experience in the corporate world, maybe there is a difference maybe not, but the context of tasks is very important hence the idea of having it available when needed but hidden when not required is one of the most appealing features of org mode for me now. 

I will probably be around and asking silly questions for a while. Thanks for the friendly welcome and your constructive tips, all of which I studied most attentively but it may take a while. 
May the force be with me :-)

Christoph

how do scientists use org mode?

[GMX Christoph 13]

Hi
this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way. 
Are you putting exclusively your todos in, well, your todo file and perhaps keep project-related things, such as data and progress, notes, ideas etc. somewhere else? Or do you embed your notes and todos within their original context, i.e. is org mode your one-stop solution for data management? Do you maintain a separate file for every major project you are responsible for or involved in or throw everything into one or few humungous  files and differentiate using hierarchies and tags? 
In the past I have hit some road blocks not so much with other softwares but rather concepts such as GTD, which I think is tailored to the needs of people outside science, so I would deeply appreciate your views and experience.

If this list is geared towards the proximate aspects of development and less towards philosophy of usage, I apologize

Christoph

Re: how do scientists use org mode?

[Thomas S. Dye]

Aloha Christoph,

Welcome to Org Mode.

I'm an archaeologist who has found Org mode to be a great help in my
scientific work.  I use it as a laboratory notebook, a project planner,
a platform for carrying out statistical analyses, and a tool for putting
together compendia for reproducible research projects.

I prefer to put everything for one project in a project-specific Org
mode file, with a structure something like this:

* Introduction
* Results
* Conclusions
* Laboratory notebook  :noexport
* Project plan :noexport
* Statistical analysis :noexport

In this hypothetical example, the first three headlines hold the
publication, which will be exported to LaTeX.  The last three headlines
are not exported, but set up spaces to accomplish different kinds of
work.

In one case, I use the publication facility of Org mode to create a web
site that tracks a long running data entry project.  Blocks of R code
summarize the data entry with tables and graphs.  I update this
periodically so that the members of the team can see where we're at and
spot data entry errors.

I don't make anywhere near full use of Org Mode's capabilities, but find
that I am (by my own standards, at least) insanely productive in this
environment.  It is flexible enough that I feel free to add information,
knowing I can reorganize later without difficulty.  It is structured
enough that I don't waste time looking for things.  Even at the early
stages of a project, when the best organization hasn't crystallized yet,
it is easy enough to identify bits and pieces so they can be easily
found later.

hth,
Tom

GMX Christoph 13 <christoph-13@gmx.net> writes:

> Hi
> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way. 
> Are you putting exclusively your todos in, well, your todo file and perhaps keep project-related things, such as data and progress, notes, ideas etc. somewhere else? Or do you embed your notes and todos within their original context, i.e. is org mode your one-stop solution for data management? Do you maintain a separate file for every major project you are responsible for or involved in or throw everything into one or few humungous  files and differentiate using hierarchies and tags? 
> In the past I have hit some road blocks not so much with other softwares but rather concepts such as GTD, which I think is tailored to the needs of people outside science, so I would deeply appreciate your views and experience.
>
> If this list is geared towards the proximate aspects of development and less towards philosophy of usage, I apologize
>
> Christoph
>

-- 
Thomas S. Dye
http://www.tsdye.com

Re: how do scientists use org mode?

[Eric S Fraga]

GMX Christoph 13 <christoph-13@gmx.net> writes:

> Hi
> this is my first post here and although I am evaluating org mode with
> great interest, I am also asking myself in which way other scientists
> are making use of org mode. It will take a while to get my head around
> how to accomplish certain things in org mode but for the moment I am
> intrigued by *why* one would want to approach the problem of
> organizing one's research with org mode and in which way.
> Are you putting exclusively your todos in, well, your todo file and
> perhaps keep project-related things, such as data and progress, notes,
> ideas etc. somewhere else? Or do you embed your notes and todos within
> their original context, i.e. is org mode your one-stop solution for
> data management? Do you maintain a separate file for every major
> project you are responsible for or involved in or throw everything
> into one or few humungous files and differentiate using hierarchies
> and tags?

I have *everything* in org these days except for my email (gnus for that
so at least I don't have to leave emacs ;-).

I have GTD stuff in a set of org files in a specific directory.  For
research projects, I do pretty much as Tom as already described.

> In the past I have hit some road blocks not so much with other
> softwares but rather concepts such as GTD, which I think is tailored
> to the needs of people outside science, so I would deeply appreciate
> your views and experience.

I am not sure why you believe that GTD is for people outside
science: it's about task management and that is pretty much universal,
IMO.  Whether you follow any particular GTD approach religiously is
another story, of course.  The trick is to pick and choose the bits that
work for you.  For me, being able to have project specific tasks within
a research org file is very helpful.

> If this list is geared towards the proximate aspects of development
> and less towards philosophy of usage, I apologize

Not at all -- they feed on each other so both are just as important.

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.92.1
: using Org-mode version 7.8.03 (release_7.8.03.243.g0e7f)

Re: how do scientists use org mode?

[John Hendy]

On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph 13 <christoph-13@gmx.net> wrote:
> Hi
> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way.

[...]

> If this list is geared towards the proximate aspects of development and less towards philosophy of usage, I apologize
>
> Christoph

Perfect question for this list. I've asked some like it myself :) I
use org-mode in an engineering consumer product company environment.
If that doesn't qualify me as a "scientist," bummer... you'll have my
input anyway. I originally got into org simply for tracking todos. I
had looked into many, many other todo and note taking applications.
Intellectual Property documentation is a big deal in my organization,
so I was originally looking for a way to capture ideas and have a way
to print them out in a nice format for insertion into an IP notebook
for witnessing.

In my quest, I looked at Evernote, variants of wiki, TaskPaper, Google
Notebook, and some others. I actually settled on TeamTasks (a
TiddlyWiki variant) with many other plugins and custom scripts for
quite a while.[1] It was really neat and allowed me to do quite a lot
of things. Easily searchable (just like a wiki), and nice format.

I also hunted for todo applications: iGTD, Task Coach, todo.txt (Gina
Trapani's script), Tracks, and others.

What I liked about TeamTasks was the todo integration. Many people I
know rave about Evernote. It is pretty cool, but what I didn't like
was having outlines and notes in one place and todos in another. Todos
often come up *in the same context* as your notes. Somewhere in here I
stumbled across org-mode, and it's recognition of this fact is what
really appealed to me. I also really liked the export functions. I
seemed to have something that could do it all -- great notes that I
could search and export *as well as* a very todo-task-tracking focus
and the right "mechanics" to handle those things in a non-kludgy way.

I think this would appeal to me regardless of my job type.

Specifically for sciency stuff, however, I have come to love org-mode
for the ability to output my research into beautiful reports via
LaTeX. I also often use my notes to generate beamer presentations for
team meetings. I am leading my first product development team and will
be using taskjuggler -- I may be able to build exports of timelines
and deliverables into into my orgmode notes. I can run gnuplot or R
right from my files or beamer org files to generate the necessary
graphs or results for me. I can use TikZ to illustrate process flows.
I have access to great looking tables that can live where all my other
notes live rather than having to generate then in excel (or calc) or
something else and then try to insert them as pictures.

Essentially, *everything* can live in one place -- data, code,
outputted results/graphics, todos, project updates, links to other
files or websites that I can retrieve later...

I used to have a file per project, but migrated to having a structure like this:

-----
* Tracking
Misc todos go in here
* Project 1
* Project 2
* Project 3
* Misc Journals
Updates that don't fit into a project
* References
Stuff I just want to put somewhere and refer back to later
-----

I also have a file called devel.org that tracks any internal
technology classes I take and corresponding notes. I have a recurring
todo setup where I take notes on highlights of my progress each month
so that my end of the year review form is easier to fill out.

So, there's a snapshot into how I use it. I just used org-mode +
R-babel to create a beamer presentation on analytical test results for
a team progress update.

Hope that was at least somewhat helpful.


Best regards,
John

[1] http://getteamtasks.com/

Re: how do scientists use org mode?

[Tomas Grigera]

Hi Cristoph

On Fri, Jan 27, 2012 at 15:27, John Hendy <jw.hendy@gmail.com> wrote:
> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph 13 <christoph-13@gmx.net> wrote:
>> Hi
>> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way.
>
> [...]

Thomas, Eric and John gave very useful answers, I just want to add my
$0.02 as a physicist who recently (about a year ago) started using Org
mode.  I started mainly looking for a workflow organization system,
but slowly discovered it has many other possibilities. For research, I
find org-babel is a great tool. It allows you to have a document
collecting together thoughts and discussion along with data, data
analysis, scripts for data manipulations and plots (Org tables are
actually more like a spreadsheet since Org supports quite complex
formulas and even plotting directly from the table).  The many export
possibilities mean that you can share your notes with colleagues not
using Org (or even Emacs).

I have also discovered it is a great tool for drafting presentations
and then actually producing your slides via Latex- Beamer export.

HTH,

Tomas

Re: how do scientists use org mode?

[Christopher W. Ryan]

I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
started to dabble in Org mode in the past couple of weeks. Just as
Christoph is, I'm trying to decide whether/how Org-mode might be useful
in organizing and carrying out research projects, presentations, etc. So
this thread has been very useful and timely.

I'm trying to envision what a small research project, managed via a
single Org file, might look like. There would be notes from meetings,
thoughts from brainstorming sessions, scheduled appointments, data, R
code, R output, and manuscript/presentation prose. Some of this might be
destined for a manuscript, some for a beamer presentation, and some only
for "internal consumption." How are all these pieces differentiated in
the Org file, so that Org knows what to put in the
presentation/manuscript, and what not to? Could anyone share or point to
a short, perhaps fictional, example?

Thanks very much.

--Chris
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu

"Observation is a more powerful force than you could possibly reckon.
The invisible, the overlooked, and the unobserved are the most in danger
of reaching the end of the spectrum. They lose the last of their light.
From there, anything can happen . . ."  [God, in "Joan of Arcadia,"
episode entitled, "The Uncertainty Principle."]

Tomas Grigera wrote:
> Hi Cristoph
> 
> On Fri, Jan 27, 2012 at 15:27, John Hendy <jw.hendy@gmail.com> wrote:
>> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph 13 <christoph-13@gmx.net> wrote:
>>> Hi
>>> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way.
>>
>> [...]
> 
> Thomas, Eric and John gave very useful answers, I just want to add my
> $0.02 as a physicist who recently (about a year ago) started using Org
> mode.  I started mainly looking for a workflow organization system,
> but slowly discovered it has many other possibilities. For research, I
> find org-babel is a great tool. It allows you to have a document
> collecting together thoughts and discussion along with data, data
> analysis, scripts for data manipulations and plots (Org tables are
> actually more like a spreadsheet since Org supports quite complex
> formulas and even plotting directly from the table).  The many export
> possibilities mean that you can share your notes with colleagues not
> using Org (or even Emacs).
> 
> I have also discovered it is a great tool for drafting presentations
> and then actually producing your slides via Latex- Beamer export.
> 
> HTH,
> 
> Tomas
> 

Re: how do scientists use org mode?

[cberry]

"Christopher W. Ryan" <cryan@binghamton.edu> writes:

> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
> started to dabble in Org mode in the past couple of weeks. Just as
> Christoph is, I'm trying to decide whether/how Org-mode might be useful
> in organizing and carrying out research projects, presentations, etc. So
> this thread has been very useful and timely.
>
> I'm trying to envision what a small research project, managed via a
> single Org file, might look like. There would be notes from meetings,
> thoughts from brainstorming sessions, scheduled appointments, data, R
> code, R output, and manuscript/presentation prose. Some of this might be
> destined for a manuscript, some for a beamer presentation, and some only
> for "internal consumption." How are all these pieces differentiated in
> the Org file, so that Org knows what to put in the
> presentation/manuscript, and what not to? Could anyone share or point to
> a short, perhaps fictional, example?

Have you looked at 

     http://orgmode.org/worg/org-contrib/babel/uses.html
??

There are almost too many possibilities --- it is a bit overwhelming. 

Here are three things I find useful:

1) The ability to export a subtree allows you to have many documents
within the *.org file. Setting EXPORT_* properties for the subtree gives
you a lot of flexibility. And it is easy to do with TAB completion to
prompt you to fill in the needed pieces.

2) Internal hyperlinks are really useful in staying on course in a big,
complicated document.

3) Noweb syntax allows you to mix and match different parts of the
document. Below is a minimal example. The latex chunks can be used
anywhere I need them. Navigating to '* mini report' and typing 

         'C-c @ C-c C-e l'

produces mini.tex.


,----
| * COMMENT latex chunks
| 
| #+name: chunk1
| #+begin_src latex
|   \begin{displaymath}
|     y = r\sin\theta
|   \end{displaymath}
| #+end_src
| 
| #+name: chunk2
| #+begin_src latex
|   \begin{displaymath}
|     x = s\cos\theta
|   \end{displaymath}
| #+end_src
| 
| 
| * mini report
|   :PROPERTIES:
|   :EXPORT_FILE_NAME: mini.tex
|   :EXPORT_TITLE: Minimal Report
|   :EXPORT_AUTHOR: Mister CCB
|   :END:
| 
| #+begin_src latex :noweb yes
| <<chunk1>>
| <<chunk2>>
| #+end_src
`----

HTH,

Chuck

>
> Thanks very much.
>
> --Chris

[snip]

-- 
Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at ucsd edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901

Re: how do scientists use org mode?

[Christopher W Ryan]

Ah, now I'm beginning to understand: I can export a *part* of an
org-mode file; I'm not limited to exporting the whole thing. Cool!

I also use bibtex/biblatex a lot. I've started to read that these
tools work with Org-mode also. Can anyone speak to that from
experience?

Thanks.

--Chris

On Mon, Jan 30, 2012 at 2:51 PM,  <cberry@tajo.ucsd.edu> wrote:
> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>
>> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
>> started to dabble in Org mode in the past couple of weeks. Just as
>> Christoph is, I'm trying to decide whether/how Org-mode might be useful
>> in organizing and carrying out research projects, presentations, etc. So
>> this thread has been very useful and timely.
>>
>> I'm trying to envision what a small research project, managed via a
>> single Org file, might look like. There would be notes from meetings,
>> thoughts from brainstorming sessions, scheduled appointments, data, R
>> code, R output, and manuscript/presentation prose. Some of this might be
>> destined for a manuscript, some for a beamer presentation, and some only
>> for "internal consumption." How are all these pieces differentiated in
>> the Org file, so that Org knows what to put in the
>> presentation/manuscript, and what not to? Could anyone share or point to
>> a short, perhaps fictional, example?
>
> Have you looked at
>
>     http://orgmode.org/worg/org-contrib/babel/uses.html
> ??
>
> There are almost too many possibilities --- it is a bit overwhelming.
>
> Here are three things I find useful:
>
> 1) The ability to export a subtree allows you to have many documents
> within the *.org file. Setting EXPORT_* properties for the subtree gives
> you a lot of flexibility. And it is easy to do with TAB completion to
> prompt you to fill in the needed pieces.
>
> 2) Internal hyperlinks are really useful in staying on course in a big,
> complicated document.
>
> 3) Noweb syntax allows you to mix and match different parts of the
> document. Below is a minimal example. The latex chunks can be used
> anywhere I need them. Navigating to '* mini report' and typing
>
>         'C-c @ C-c C-e l'
>
> produces mini.tex.
>
>
> ,----
> | * COMMENT latex chunks
> |
> | #+name: chunk1
> | #+begin_src latex
> |   \begin{displaymath}
> |     y = r\sin\theta
> |   \end{displaymath}
> | #+end_src
> |
> | #+name: chunk2
> | #+begin_src latex
> |   \begin{displaymath}
> |     x = s\cos\theta
> |   \end{displaymath}
> | #+end_src
> |
> |
> | * mini report
> |   :PROPERTIES:
> |   :EXPORT_FILE_NAME: mini.tex
> |   :EXPORT_TITLE: Minimal Report
> |   :EXPORT_AUTHOR: Mister CCB
> |   :END:
> |
> | #+begin_src latex :noweb yes
> | <<chunk1>>
> | <<chunk2>>
> | #+end_src
> `----
>
> HTH,
>
> Chuck
>
>>
>> Thanks very much.
>>
>> --Chris
>
> [snip]
>
> --
> Charles C. Berry                            Dept of Family/Preventive Medicine
> cberry at ucsd edu                          UC San Diego
> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>
>

Re: how do scientists use org mode?

[Thomas S. Dye]

Aloha Chris,

There is a tutorial of sorts on LaTeX export.  It includes information
on how to use bibtex with Org mode.

http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17

Eric Schulte has written some elisp helpers for managing bibliographies
in Org mode.  I believe this is in the contrib directory of the Org mode
distribution. 

All the best,
Tom

Christopher W Ryan <cryan@binghamton.edu> writes:

> Ah, now I'm beginning to understand: I can export a *part* of an
> org-mode file; I'm not limited to exporting the whole thing. Cool!
>
> I also use bibtex/biblatex a lot. I've started to read that these
> tools work with Org-mode also. Can anyone speak to that from
> experience?
>
> Thanks.
>
> --Chris
>
> On Mon, Jan 30, 2012 at 2:51 PM,  <cberry@tajo.ucsd.edu> wrote:
>> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>>
>>> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
>>> started to dabble in Org mode in the past couple of weeks. Just as
>>> Christoph is, I'm trying to decide whether/how Org-mode might be useful
>>> in organizing and carrying out research projects, presentations, etc. So
>>> this thread has been very useful and timely.
>>>
>>> I'm trying to envision what a small research project, managed via a
>>> single Org file, might look like. There would be notes from meetings,
>>> thoughts from brainstorming sessions, scheduled appointments, data, R
>>> code, R output, and manuscript/presentation prose. Some of this might be
>>> destined for a manuscript, some for a beamer presentation, and some only
>>> for "internal consumption." How are all these pieces differentiated in
>>> the Org file, so that Org knows what to put in the
>>> presentation/manuscript, and what not to? Could anyone share or point to
>>> a short, perhaps fictional, example?
>>
>> Have you looked at
>>
>>     http://orgmode.org/worg/org-contrib/babel/uses.html
>> ??
>>
>> There are almost too many possibilities --- it is a bit overwhelming.
>>
>> Here are three things I find useful:
>>
>> 1) The ability to export a subtree allows you to have many documents
>> within the *.org file. Setting EXPORT_* properties for the subtree gives
>> you a lot of flexibility. And it is easy to do with TAB completion to
>> prompt you to fill in the needed pieces.
>>
>> 2) Internal hyperlinks are really useful in staying on course in a big,
>> complicated document.
>>
>> 3) Noweb syntax allows you to mix and match different parts of the
>> document. Below is a minimal example. The latex chunks can be used
>> anywhere I need them. Navigating to '* mini report' and typing
>>
>>         'C-c @ C-c C-e l'
>>
>> produces mini.tex.
>>
>>
>> ,----
>> | * COMMENT latex chunks
>> |
>> | #+name: chunk1
>> | #+begin_src latex
>> |   \begin{displaymath}
>> |     y = r\sin\theta
>> |   \end{displaymath}
>> | #+end_src
>> |
>> | #+name: chunk2
>> | #+begin_src latex
>> |   \begin{displaymath}
>> |     x = s\cos\theta
>> |   \end{displaymath}
>> | #+end_src
>> |
>> |
>> | * mini report
>> |   :PROPERTIES:
>> |   :EXPORT_FILE_NAME: mini.tex
>> |   :EXPORT_TITLE: Minimal Report
>> |   :EXPORT_AUTHOR: Mister CCB
>> |   :END:
>> |
>> | #+begin_src latex :noweb yes
>> | <<chunk1>>
>> | <<chunk2>>
>> | #+end_src
>> `----
>>
>> HTH,
>>
>> Chuck
>>
>>>
>>> Thanks very much.
>>>
>>> --Chris
>>
>> [snip]
>>
>> --
>> Charles C. Berry                            Dept of Family/Preventive Medicine
>> cberry at ucsd edu                          UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901
>>
>>
>
>

-- 
Thomas S. Dye
http://www.tsdye.com

Re: how do scientists use org mode?

[Christopher W. Ryan]

Just tried a similar thing on my computer at work: WinXP, emacs-22.3.1,
org-mode 7.7.  I tried both R and python.  With this in my .emacs file:

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (python . t)
   ))

Here are the contents of the org file I am playing with:

#+begin_src R
rnorm(10)
#+end_src

#+begin_src python
print "Hello, World!"
#+end_src


C-c C-c the first block results in a message like this:

Evaluate this R code block on your system? (yes or no)

Answering yes yields:

No org-babel-execute function for R!

Trying the same in the python block yields the same results, except with
"python" substituted for "R" in all the messages.

Any suggestions where I am going wrong?

Thanks.

--Chris Ryan

Re: how do scientists use org mode?

[Simon Thum]

Hi Christopher,

to add my 2c: I'm using org-mode to track our participation in a 
mid-sized project (9 Partners, ~30 People, 3 Years). I'm not 
coordinating, in which case I'd probably look for more project 
management centric tools, and thus found org-mode to be very useful.

I use it to track the project state, not hard data (which is typically 
massive), our commitments and other's compliance with their commitments, 
and all the rest that comes up and needs project context: Ideas, tasks, 
deadlines, project reports & what not. The outline of this file reflects 
the project structure. I have tags for partners and people in that file, 
so e.g. when I speak someone I can easily check for further things to 
discuss.

Big projects get their own file, for smaller projects and commitments I 
have a few more files. I'm not using the attachments as it's 
unfortunately a very microsoft-wordey project where git won't help much, 
but plan to use them privately. Ah yes, I use org-mode for private stuff 
too. It's the first tool that I use for more than a month.

I use export (tags) to inform my supervisor and other people on the 
project about certain aspects, which usually works OK. I also found the 
custom links to be helpful, as we have multiple web frontends for 
project-specific matters whose contents I can link in easily this way.

The whole thing synced to a server using git, which saved my shiny a few 
times. This is something I wouldn't recommend anyone to put off, even if 
your backup schedule is in minutes.

HTH,

Simon


On 01/30/2012 06:37 PM, Christopher W. Ryan wrote:
> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
> started to dabble in Org mode in the past couple of weeks. Just as
> Christoph is, I'm trying to decide whether/how Org-mode might be useful
> in organizing and carrying out research projects, presentations, etc. So
> this thread has been very useful and timely.
>
> I'm trying to envision what a small research project, managed via a
> single Org file, might look like. There would be notes from meetings,
> thoughts from brainstorming sessions, scheduled appointments, data, R
> code, R output, and manuscript/presentation prose. Some of this might be
> destined for a manuscript, some for a beamer presentation, and some only
> for "internal consumption." How are all these pieces differentiated in
> the Org file, so that Org knows what to put in the
> presentation/manuscript, and what not to? Could anyone share or point to
> a short, perhaps fictional, example?
>
> Thanks very much.
>
> --Chris
> Christopher W. Ryan, MD
> SUNY Upstate Medical University Clinical Campus at Binghamton
> 425 Robinson Street, Binghamton, NY  13904
> cryanatbinghamtondotedu
>
> "Observation is a more powerful force than you could possibly reckon.
> The invisible, the overlooked, and the unobserved are the most in danger
> of reaching the end of the spectrum. They lose the last of their light.
>> From there, anything can happen . . ."  [God, in "Joan of Arcadia,"
> episode entitled, "The Uncertainty Principle."]
>
> Tomas Grigera wrote:
>> Hi Cristoph
>>
>> On Fri, Jan 27, 2012 at 15:27, John Hendy<jw.hendy@gmail.com>  wrote:
>>> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph 13<christoph-13@gmx.net>  wrote:
>>>> Hi
>>>> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way.
>>>
>>> [...]
>>
>> Thomas, Eric and John gave very useful answers, I just want to add my
>> $0.02 as a physicist who recently (about a year ago) started using Org
>> mode.  I started mainly looking for a workflow organization system,
>> but slowly discovered it has many other possibilities. For research, I
>> find org-babel is a great tool. It allows you to have a document
>> collecting together thoughts and discussion along with data, data
>> analysis, scripts for data manipulations and plots (Org tables are
>> actually more like a spreadsheet since Org supports quite complex
>> formulas and even plotting directly from the table).  The many export
>> possibilities mean that you can share your notes with colleagues not
>> using Org (or even Emacs).
>>
>> I have also discovered it is a great tool for drafting presentations
>> and then actually producing your slides via Latex- Beamer export.
>>
>> HTH,
>>
>> Tomas
>>
>
>

Re: how do scientists use org mode?

[Christopher W. Ryan]

Thanks everyone for the advice and ideas. I see lots of potential, and 
also lots to learn.

I made my first attempt at an R code block in an Org file. I'm running 
Ubuntu 10.04 LTS. Synaptic tells me that I have emacs 23.1+1-4ubuntu7.2, 
and Org 6.34c-1.

I added this to my .emacs:

;; active Babel languages
(org-babel-do-load-languages
  'org-babel-load-languages
  '((R . t)
    ))

Here is the source block:

#+begin_src R
getwd()
dd <- read.csv("cars.csv", sep=",", header=TRUE)
head(dd)
str(dd)
dd$date <- as.Date(as.character(dd$Date), format="%d-%b-%y")
names(dd)[4] <- "city"
table(is.na(dd$date))
min(dd$date, na.rm=TRUE); max(dd$date, na.rm=TRUE)
#+end_src

emacs seems to do the syntax highlighting properly, so I guess it is 
recognizing this as a code block.

When I put point inside the block and type C-c C-c, emacs gives me this 
message:

C-c C-c can do nothing useful at this location.

I wonder if I have Babel? Is it "built in" to the emacs or Org versions 
that I have?

Thanks.

--Chris Ryan

Simon Thum wrote:
> Hi Christopher,
>
> to add my 2c: I'm using org-mode to track our participation in a
> mid-sized project (9 Partners, ~30 People, 3 Years). I'm not
> coordinating, in which case I'd probably look for more project
> management centric tools, and thus found org-mode to be very useful.
>
> I use it to track the project state, not hard data (which is typically
> massive), our commitments and other's compliance with their commitments,
> and all the rest that comes up and needs project context: Ideas, tasks,
> deadlines, project reports & what not. The outline of this file reflects
> the project structure. I have tags for partners and people in that file,
> so e.g. when I speak someone I can easily check for further things to
> discuss.
>
> Big projects get their own file, for smaller projects and commitments I
> have a few more files. I'm not using the attachments as it's
> unfortunately a very microsoft-wordey project where git won't help much,
> but plan to use them privately. Ah yes, I use org-mode for private stuff
> too. It's the first tool that I use for more than a month.
>
> I use export (tags) to inform my supervisor and other people on the
> project about certain aspects, which usually works OK. I also found the
> custom links to be helpful, as we have multiple web frontends for
> project-specific matters whose contents I can link in easily this way.
>
> The whole thing synced to a server using git, which saved my shiny a few
> times. This is something I wouldn't recommend anyone to put off, even if
> your backup schedule is in minutes.
>
> HTH,
>
> Simon
>
>
> On 01/30/2012 06:37 PM, Christopher W. Ryan wrote:
>> I'm fairly experienced with emacs, ESS, Sweave, and R, but I've only
>> started to dabble in Org mode in the past couple of weeks. Just as
>> Christoph is, I'm trying to decide whether/how Org-mode might be useful
>> in organizing and carrying out research projects, presentations, etc. So
>> this thread has been very useful and timely.
>>
>> I'm trying to envision what a small research project, managed via a
>> single Org file, might look like. There would be notes from meetings,
>> thoughts from brainstorming sessions, scheduled appointments, data, R
>> code, R output, and manuscript/presentation prose. Some of this might be
>> destined for a manuscript, some for a beamer presentation, and some only
>> for "internal consumption." How are all these pieces differentiated in
>> the Org file, so that Org knows what to put in the
>> presentation/manuscript, and what not to? Could anyone share or point to
>> a short, perhaps fictional, example?
>>
>> Thanks very much.
>>
>> --Chris
>> Christopher W. Ryan, MD
>> SUNY Upstate Medical University Clinical Campus at Binghamton
>> 425 Robinson Street, Binghamton, NY 13904
>> cryanatbinghamtondotedu
>>
>> "Observation is a more powerful force than you could possibly reckon.
>> The invisible, the overlooked, and the unobserved are the most in danger
>> of reaching the end of the spectrum. They lose the last of their light.
>>> From there, anything can happen . . ." [God, in "Joan of Arcadia,"
>> episode entitled, "The Uncertainty Principle."]
>>
>> Tomas Grigera wrote:
>>> Hi Cristoph
>>>
>>> On Fri, Jan 27, 2012 at 15:27, John Hendy<jw.hendy@gmail.com> wrote:
>>>> On Thu, Jan 26, 2012 at 3:21 PM, GMX Christoph
>>>> 13<christoph-13@gmx.net> wrote:
>>>>> Hi
>>>>> this is my first post here and although I am evaluating org mode
>>>>> with great interest, I am also asking myself in which way other
>>>>> scientists are making use of org mode. It will take a while to get
>>>>> my head around how to accomplish certain things in org mode but for
>>>>> the moment I am intrigued by *why* one would want to approach the
>>>>> problem of organizing one's research with org mode and in which way.
>>>>
>>>> [...]
>>>
>>> Thomas, Eric and John gave very useful answers, I just want to add my
>>> $0.02 as a physicist who recently (about a year ago) started using Org
>>> mode. I started mainly looking for a workflow organization system,
>>> but slowly discovered it has many other possibilities. For research, I
>>> find org-babel is a great tool. It allows you to have a document
>>> collecting together thoughts and discussion along with data, data
>>> analysis, scripts for data manipulations and plots (Org tables are
>>> actually more like a spreadsheet since Org supports quite complex
>>> formulas and even plotting directly from the table). The many export
>>> possibilities mean that you can share your notes with colleagues not
>>> using Org (or even Emacs).
>>>
>>> I have also discovered it is a great tool for drafting presentations
>>> and then actually producing your slides via Latex- Beamer export.
>>>
>>> HTH,
>>>
>>> Tomas
>>>
>>
>>
>

Re: how do scientists use org mode?

[Nick Dokos]

Christopher W. Ryan <cryan@binghamton.edu> wrote:

> Thanks everyone for the advice and ideas. I see lots of potential, and 
> also lots to learn.
> 
> I made my first attempt at an R code block in an Org file. I'm running 
> Ubuntu 10.04 LTS. Synaptic tells me that I have emacs 23.1+1-4ubuntu7.2, 
> and Org 6.34c-1.
> 
> I added this to my .emacs:
> 
> ;; active Babel languages
> (org-babel-do-load-languages
>   'org-babel-load-languages
>   '((R . t)
>     ))
> 
> Here is the source block:
> 
> #+begin_src R
> getwd()
> dd <- read.csv("cars.csv", sep=",", header=TRUE)
> head(dd)
> str(dd)
> dd$date <- as.Date(as.character(dd$Date), format="%d-%b-%y")
> names(dd)[4] <- "city"
> table(is.na(dd$date))
> min(dd$date, na.rm=TRUE); max(dd$date, na.rm=TRUE)
> #+end_src
> 
> emacs seems to do the syntax highlighting properly, so I guess it is 
> recognizing this as a code block.
> 
> When I put point inside the block and type C-c C-c, emacs gives me this 
> message:
> 
> C-c C-c can do nothing useful at this location.
> 
> I wonder if I have Babel? Is it "built in" to the emacs or Org versions 
> that I have?
> 

You probably have babel, but not the ob-R.el module - that came in 6.36+:

,----
| $ git blame -L1,1 lisp/ob-R.el
| 07388931 lisp/babel/langs/ob-R.el (Eric Schulte 2010-06-11 16:02:42 -0700 1) ;;; ob-R.el --- org-babel functions for R code evaluation
| $ git describe 07388931
| release_6.36-324-g0738893
`----

You can use some other language (elisp, shell, python probably all
existed in 6.34). But you will be happier I think with a more recent
version of org: visit http://orgmode.org/org-mode-download.html
and choose your poison.

o Many people update to the latest development version fairly frequently,
  using git.

o Many others use the standard distribution (7.8.03 as of this writing):
  download a .zip or .tgz file and install it.  Alternatively, you can
  use the Emacs package manager (ELPA): there are several entries in the
  FAQ

    http://orgmode.org/worg/org-faq.html#keeping-current-with-Org-mode-development

  that describe these methods in more detail.

o Many others use whatever is bundled with their emacs (invariably an
  ancient org version that causes problems to everybody involved: org-mode
  is moving very fast).

Nick

Re: how do scientists use org mode?

[Bodhi]

GMX Christoph 13 <christoph-13 <at> gmx.net> writes:

> 
> Hi
> this is my first post here and although I am evaluating org mode with great
interest, I am also asking myself
> in which way other scientists are making use of org mode. It will take a while
to get my head around how to
> accomplish certain things in org mode but for the moment I am intrigued by
*why* one would want to approach
> the problem of organizing one's research with org mode and in which way. 
> Are you putting exclusively your todos in, well, your todo file and perhaps
keep project-related things,
> such as data and progress, notes, ideas etc. somewhere else? Or do you embed
your notes and todos within
> their original context, i.e. is org mode your one-stop solution for data
management? Do you maintain a
> separate file for every major project you are responsible for or involved in
or throw everything into one
> or few humungous  files and differentiate using hierarchies and tags? 
> In the past I have hit some road blocks not so much with other softwares but
rather concepts such as GTD, which
> I think is tailored to the needs of people outside science, so I would deeply
appreciate your views and experience.
> 
> If this list is geared towards the proximate aspects of development and less
towards philosophy of usage, I apologize
> 
> Christoph
> 
> 

Hey Christoph,
Welcome to orgmode!

Well, to put it simply: you can use orgmode for everything: right from making
notes, to writing papers, to designing websites and presentations, the list goes
on and on. For example, you can write your papers and orgmode will generate
LaTeX and pdfs automatically for you. It can also generate HTML files
automatically, in case you wish to publish something on your website, but lack
the time/enthusiasm/expertise to generate a decent looking webpage. Same goes
for presentation (orgmode uses Beamer). Bottom-line: all you write is plain
text, and everything else is auto-generated, seamlessly and without the user
bothering about what is happening at the back.

For example, I was recently a part of a team of a few Engineers and a bunch of
Research Assistants, and we always used to assign tasks, maintain timesheets,
generate reports, make presentations etc. using orgmode. 

For your questions on how to organize data and files: you can use orgmode to
link between files, directories and URLs. So it is up to you to decide how you
keep your files/folders. You just need to link them, and then use orgmode to
pull it up for you.


There are a bunch of tutorials
here:http://orgmode.org/worg/org-tutorials/index.html. Please feel free to look
at them, in order to gain some perspective on how efficiently orgmode can aid
you in your day-to-day activities.

Happy "document"-hacking,
Bodhi

PS: I hope you are using Emacs, as it seamlessly renders orgmode stuff. Other
editors just can't do it as nicely.

Re: how do scientists use org mode?

[Sven Bretfeld]

Hi Christoph

For my scientific work (I'm an Indologist) I use orgmode in three ways:

1. _Project planning and calendar management_

   That's just the normal thing. I use the GTD approach, extended by
   some specialties like the tags :BIGROCK: (most important project to
   work on this week) and :MIT: (most important thing of the day).

2. _Writing papers_

   To me this is one of the most important powers of orgmode: work on
   papers and have Todos inserted into the text directly. So, if you
   have referenced a book but you don't have it at hand at the moment,
   you can do:

   This is a paraphrase you need a reference for (Smith 2009: ??).
   TODO Check the page in Smith's book           :LIBRARY:

   I always add files with draft papers to org-agenda-files. Next time
   I'm at the library and have MobileOrg with me, the Todo shows up and
   I can check the book. I know of no other wordprocessor or editor
   which can do this.

3. _Collecting reference material_

   Whenever I read a book (since some months I usually read ebooks or
   pdfs on my tablet), I find passages I need for present or future
   papers. With the ezReader app (Android) you can mark these passages
   and send them to MobileOrg. When I come home, the new material has
   already synced and waits to be tagged and refiled. I use org-files
   for each paper I'm working on as databases for references. The header
   is a short description of the content of each reference. Keywords and
   bibliographic data are put into drawers that can be queried. I have
   an Emacs macro that automatically transforms the raw entry into the
   right markup.

Welcome to org

Sven

GMX Christoph 13 <christoph-13@gmx.net> writes:

> Hi
> this is my first post here and although I am evaluating org mode with great interest, I am also asking myself in which way other scientists are making use of org mode. It will take a while to get my head around how to accomplish certain things in org mode but for the moment I am intrigued by *why* one would want to approach the problem of organizing one's research with org mode and in which way. 
> Are you putting exclusively your todos in, well, your todo file and perhaps keep project-related things, such as data and progress, notes, ideas etc. somewhere else? Or do you embed your notes and todos within their original context, i.e. is org mode your one-stop solution for data management? Do you maintain a separate file for every major project you are responsible for or involved in or throw everything into one or few humungous  files and differentiate using hierarchies and tags? 
> In the past I have hit some road blocks not so much with other softwares but rather concepts such as GTD, which I think is tailored to the needs of people outside science, so I would deeply appreciate your views and experience.
>
> If this list is geared towards the proximate aspects of development and less towards philosophy of usage, I apologize
>
> Christoph