From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: org-mode in the wild Date: Sat, 2 Nov 2013 20:25:59 -0400 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=001a113630e0fbd08f04ea3ad7d9 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59352) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclVz-0003HC-5h for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:26:04 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VclVx-00008Q-MK for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:26:03 -0400 Received: from mail-pb0-x22e.google.com ([2607:f8b0:400e:c01::22e]:41842) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclVx-00008J-Dt for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:26:01 -0400 Received: by mail-pb0-f46.google.com with SMTP id un15so767995pbc.33 for ; Sat, 02 Nov 2013 17:25:59 -0700 (PDT) List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "emacs-orgmode@gnu.org" --001a113630e0fbd08f04ea3ad7d9 Content-Type: text/plain; charset=ISO-8859-1 Hi everyone, We had another manuscript written in org-mode accepted in Topics in Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! Check out references 14, 39 and 40 ;) The supporting information seems to be freely available ( http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf) was also prepared in org-mode. It is probably best read with the Adobe PDF reader. This file is an interesting hybrid of data sharing methods. Some of the data is in the pdf, some of it is embedded in the pdf, including the org-mode files for the manuscript and the supporting information file itself. Anyone interested in seeing how we did it can check it out. 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 --001a113630e0fbd08f04ea3ad7d9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi everyone,

We had another manuscr= ipt written in org-mode accepted in Topics in Catalysis (http://link.springer= .com/article/10.1007%2Fs11244-013-0166-3)!=A0 Check out references 14, = 39 and 40 ;)

The supporting information seems to be freely available (http://link.springer.com/content/esm/= art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.p= df) was also prepared in org-mode. It is probably best read with the Ad= obe PDF reader. This file is an interesting hybrid of data sharing methods.= Some of the data is in the pdf, some of it is embedded in the pdf, includi= ng the org-mode files for the manuscript and the supporting information fil= e itself. Anyone interested in seeing how we did it can check it out.

John

-------------------= ----------------
John Kitchin
Associate Professor
Doherty Hall A20= 7F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

<= /div>
--001a113630e0fbd08f04ea3ad7d9-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: William Denton Subject: Re: org-mode in the wild Date: Sat, 2 Nov 2013 20:55:24 -0400 (EDT) Message-ID: References: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="658601964-1826569960-1383440124=:13500" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33771) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclyT-0000Dl-Jl for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VclyP-0007Dy-90 for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:29 -0400 Received: from shell.miskatonic.org ([65.39.236.119]:36923) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VclyP-0007Di-4j for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:25 -0400 Received: from wtd (helo=localhost) by shell.miskatonic.org with local-esmtp (Exim 4.72) (envelope-from ) id 1VclyO-0003WC-1a for emacs-orgmode@gnu.org; Sat, 02 Nov 2013 20:55:24 -0400 In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "emacs-orgmode@gnu.org" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --658601964-1826569960-1383440124=:13500 Content-Type: TEXT/PLAIN; charset=UTF-8; format=flowed Content-Transfer-Encoding: QUOTED-PRINTABLE On 2 November 2013, John Kitchin wrote: > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! > Check out references 14, 39 and 40 ;) Lovely! Here's the start of section 4, "Manuscript Preparation Method:" "This manuscript was prepared in a manner sufficiently different than=20 standard methods that we feel it warrants discussion. In this work, we=20 have prepared a single document containing all of the raw data, the=20 analysis of the raw data that has led to the figures and conclusions in=20 the manuscript, and the manuscript itself. The document is in plain text=20 format, marked up using org-mode syntax [14]. Org-mode is a lightweight=20 text markup language that enables intermingling of narrative text, data=20 and analysis code in an active document [39] when viewed in the editor=20 Emacs (http://www.gnu.org/software/emacs/). This approach is known as=20 literate programming and reproducible research [40]. Notably, files in=20 org-mode syntax can be exported to a variety of other formats including=20 LaTEX, PDF and html. The export can be done selectively to include only=20 portions of the complete document. The published manuscript was exported=20 from this document to create LaTEX source which was submitted to this=20 journal. The Supplementary information file is the document itself, which= =20 includes all of the data used in the analysis. All analysis was done using= =20 Python (http://python.org), and figures were generated with Matplotlib=20 [24]. All of these software packages are open-source and freely=20 available." The citations: 14. Dominik C (2010) The Org Mode 7 Reference Manual: Organize your life wi= th GNU Emacs. Network Theory, UK. 39. Schulte E, Davison D (2011) Active documents with org-mode. Comput Sci = Eng 13(3):66=E2=80=9373 40. Schulte E, Davison D, Dye T, Dominik C (2012) A multi-language computin= g environment for literate programming and reproducible research. J Stat So= ftw 46(3):1=E2=80=9324 Bill --=20 William Denton Toronto, Canada http://www.miskatonic.org/ --658601964-1826569960-1383440124=:13500-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: tsd@tsdye.com (Thomas S. Dye) Subject: Re: org-mode in the wild Date: Sat, 02 Nov 2013 19:48:42 -1000 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59562) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VcqYi-00053D-Jw for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 01:49:18 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VcqYd-0000sM-8A for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 01:49:12 -0400 Received: from outbound-ss-47.bluehost.com ([66.147.245.65]:51726) by eggs.gnu.org with smtp (Exim 4.71) (envelope-from ) id 1VcqYd-0000sB-0Z for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 01:49:07 -0400 In-Reply-To: (John Kitchin's message of "Sat, 2 Nov 2013 20:25:59 -0400") List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: John Kitchin Cc: "emacs-orgmode@gnu.org" Aloha John, This is wonderful! The pdf file is a user-friendly entry into the Org mode compendium *and* an effective way to distribute it. Thanks for your pioneering efforts. All the best, Tom John Kitchin writes: > Hi everyone, > > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! > Check out references 14, 39 and 40 ;) > > The supporting information seems to be freely available ( > http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf) > was also prepared in org-mode. It is probably best read with the Adobe PDF > reader. This file is an interesting hybrid of data sharing methods. Some of > the data is in the pdf, some of it is embedded in the pdf, including the > org-mode files for the manuscript and the supporting information file > itself. Anyone interested in seeing how we did it can check it out. > > 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 > Hi everyone, > > We had another manuscript written in org-mode accepted in Topics in > Catalysis > (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! Check > out references 14, 39 and 40 ;) > > The supporting information seems to be freely available > (http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_ > 2013_166_MOESM1_ESM.pdf) was also prepared in org-mode. It is probably > best read with the Adobe PDF reader. This file is an interesting > hybrid of data sharing methods. Some of the data is in the pdf, some > of it is embedded in the pdf, including the org-mode files for the > manuscript and the supporting information file itself. Anyone > interested in seeing how we did it can check it out. > > 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 > > -- Thomas S. Dye http://www.tsdye.com From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rasmus Subject: Re: org-mode in the wild Date: Sun, 03 Nov 2013 14:37:21 +0100 Message-ID: <87txftfvxq.fsf@gmx.us> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58394) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Vcxs1-0007JJ-4P for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 08:37:42 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Vcxrw-0003RX-2x for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 08:37:37 -0500 Received: from plane.gmane.org ([80.91.229.3]:49180) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Vcxrv-0003RR-SY for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 08:37:32 -0500 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1Vcxru-0004L8-FX for emacs-orgmode@gnu.org; Sun, 03 Nov 2013 14:37:30 +0100 Received: from dynamic-adsl-94-34-145-254.clienti.tiscali.it ([94.34.145.254]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Sun, 03 Nov 2013 14:37:30 +0100 Received: from rasmus by dynamic-adsl-94-34-145-254.clienti.tiscali.it with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Sun, 03 Nov 2013 14:37:30 +0100 List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org John Kitchin writes: > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! > Check out references 14, 39 and 40 ;) Congrats! And thanks for sharing. > The supporting information seems to be freely available ( > http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf) > was also prepared in org-mode. It is probably best read with the Adobe PDF > reader. This file is an interesting hybrid of data sharing methods. Some of > the data is in the pdf, some of it is embedded in the pdf, including the > org-mode files for the manuscript and the supporting information file > itself. Anyone interested in seeing how we did it can check it out. With Evince 3.10, the GNOME document viewer, I'm able to save attachments. Do you use other features?. It's catching up. Supposedly, Okular is also quite feature-rich. On matplotlib: looks great! Are you aware that matplotlib now supports pgf out-of-the-box? You just specify it as an extension (pgf). .pgf is also recognized as an image in Org for a while. The main benefit is that fonts magically get the right size. –Rasmus -- Dung makes an excellent fertilizer From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rainer M Krug Subject: Re: org-mode in the wild Date: Mon, 04 Nov 2013 10:23:43 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40974) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VdGO9-0007Ca-MF for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 04:24:06 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VdGO4-00057E-G0 for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 04:24:01 -0500 Received: from plane.gmane.org ([80.91.229.3]:32933) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VdGO4-00056y-9c for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 04:23:56 -0500 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1VdGO3-0004pH-QZ for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 10:23:55 +0100 Received: from arn78-1-88-186-171-7.fbx.proxad.net ([88.186.171.7]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Mon, 04 Nov 2013 10:23:55 +0100 Received: from Rainer by arn78-1-88-186-171-7.fbx.proxad.net with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Mon, 04 Nov 2013 10:23:55 +0100 List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org John Kitchin writes: > Hi everyone, > > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3)! > Check out references 14, 39 and 40 ;) > > The supporting information seems to be freely available ( > http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/MediaObjects/11244_2013_166_MOESM1_ESM.pdf) > was also prepared in org-mode. It is probably best read with the Adobe PDF > reader. This file is an interesting hybrid of data sharing methods. Some of > the data is in the pdf, some of it is embedded in the pdf, including the > org-mode files for the manuscript and the supporting information file > itself. Anyone interested in seeing how we did it can check it out. Thanks - this is brilliant and gives quite a few ideas how to write paper, but especially how to do an analysis and graphs for a paper, in org. Incidently, we have just submitted a paper which was written by the main author in MS Office, but the graphs were generated and the analysis was doine using org. In a similar manner, I included the complete analysis in the supporting information. But I relly like the \attachfile{} - I'll add this to the supporting informateion as werll as a paragraph aboiut org. Cheers, Rainer > > 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 <#secure method=pgpmime mode=sign> -- Rainer M. Krug email: RMKruggmailcom From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: org-mode in the wild Date: Mon, 4 Nov 2013 18:35:27 -0500 Message-ID: References: <87txftfvxq.fsf@gmx.us> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7b6d933ef30bd504ea625e55 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37114) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VdTgB-0005IA-Qf for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 18:35:33 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VdTgA-000333-01 for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 18:35:31 -0500 Received: from mail-pa0-x22a.google.com ([2607:f8b0:400e:c03::22a]:53573) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VdTg9-00032m-7Y for emacs-orgmode@gnu.org; Mon, 04 Nov 2013 18:35:29 -0500 Received: by mail-pa0-f42.google.com with SMTP id kp14so7694453pab.1 for ; Mon, 04 Nov 2013 15:35:27 -0800 (PST) In-Reply-To: <87txftfvxq.fsf@gmx.us> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Rasmus Cc: "emacs-orgmode@gnu.org" --047d7b6d933ef30bd504ea625e55 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable I wasn't familiar with pgf at all. we are usually limited by what publishers will accept in terms of formats, which is usually pdf, eps, png or tiff where we publish. for other features in pdf, we did not use any for these manuscripts, but sometimes I use some adobe specific javascript for making interactive features in course notes(using acrotex). some of those do not work well in any other browser. 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 Sun, Nov 3, 2013 at 8:37 AM, Rasmus wrote: > John Kitchin writes: > > > We had another manuscript written in org-mode accepted in Topics in > > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3 > )! > > Check out references 14, 39 and 40 ;) > > Congrats! And thanks for sharing. > > > The supporting information seems to be freely available ( > > > http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/M= ediaObjects/11244_2013_166_MOESM1_ESM.pdf > ) > > was also prepared in org-mode. It is probably best read with the Adobe > PDF > > reader. This file is an interesting hybrid of data sharing methods. Som= e > of > > the data is in the pdf, some of it is embedded in the pdf, including th= e > > org-mode files for the manuscript and the supporting information file > > itself. Anyone interested in seeing how we did it can check it out. > > With Evince 3.10, the GNOME document viewer, I'm able to save > attachments. Do you use other features?. It's catching up. > Supposedly, Okular is also quite feature-rich. > > On matplotlib: looks great! > Are you aware that matplotlib now supports pgf out-of-the-box? You > just specify it as an extension (pgf). .pgf is also recognized as an > image in Org for a while. The main benefit is that fonts magically > get the right size. > > =96Rasmus > > -- > Dung makes an excellent fertilizer > > > --047d7b6d933ef30bd504ea625e55 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
I wasn't familiar with pgf at all. we are usually= limited by what publishers will accept in terms of formats, which is usual= ly pdf, eps, png or tiff where we publish.

for other features = in pdf, we did not use any for these manuscripts, but sometimes I use some = adobe specific javascript for making interactive features in course notes(u= sing acrotex). some of those do not work well in any other browser.

John

-------= ----------------------------
John Kitchin
Associate Professor
Dohe= rty Hall A207F
Department of Chemical Engineering
Carnegie Mellon Uni= versity
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu

<= /div>

On Sun, Nov 3, 2013 at 8:37 AM, Rasmus <= span dir=3D"ltr"><ras= mus@gmx.us> wrote:
John Kitchin <jkitchin@andrew.cmu.edu> writes:

> We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2F= s11244-013-0166-3)!
> Check out references 14, 39 and 40 ;)

Congrats! =A0And thanks for sharing.

> The supporting information seems to be freely available (
> = http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file/Med= iaObjects/11244_2013_166_MOESM1_ESM.pdf)
> was also prepared in org-mode. It is probably best read with the Adobe= PDF
> reader. This file is an interesting hybrid of data sharing methods. So= me of
> the data is in the pdf, some of it is embedded in the pdf, including t= he
> org-mode files for the manuscript and the supporting information file<= br> > itself. Anyone interested in seeing how we did it can check it out.
With Evince 3.10, the GNOME document viewer, I'm able to save
attachments. =A0Do you use other features?. =A0It's catching up.
Supposedly, Okular is also quite feature-rich.

On matplotlib: looks great!
Are you aware that matplotlib now supports pgf out-of-the-box? =A0You
just specify it as an extension (pgf). =A0.pgf is also recognized as an
image in Org for a while. =A0The main benefit is that fonts magically
get the right size.

=96Rasmus

--
Dung makes an excellent fertilizer



--047d7b6d933ef30bd504ea625e55-- From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Julian M. Burgos" Subject: Re: org-mode in the wild Date: Tue, 05 Nov 2013 10:43:10 +0000 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48155) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Vde6b-0003sT-TZ for emacs-orgmode@gnu.org; Tue, 05 Nov 2013 05:43:34 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Vde6X-0002qb-91 for emacs-orgmode@gnu.org; Tue, 05 Nov 2013 05:43:29 -0500 Received: from hafgarpur.hafro.is ([130.208.64.48]:60515) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Vde6W-0002ox-TK for emacs-orgmode@gnu.org; Tue, 05 Nov 2013 05:43:25 -0500 In-reply-to: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: John Kitchin Cc: "emacs-orgmode@gnu.org" Thank you very much John!!! Your document contains a wealth of informatio= n on how to use org-mode for reproducible research! I really like the idea of embedding the supporting documents (bibliography, additional analysis) in= to the document. Very nice. Perhaps it would be good to have a repository of practices and examples for reproducible research, maybe a section in Worg? All the best, Julian John Kitchin writes: > Hi everyone, > > We had another manuscript written in org-mode accepted in Topics in > Catalysis (http://link.springer.com/article/10.1007%2Fs11244-013-0166-3= )! > Check out references 14, 39 and 40 ;) > > The supporting information seems to be freely available ( > http://link.springer.com/content/esm/art:10.1007/s11244-013-0166-3/file= /MediaObjects/11244_2013_166_MOESM1_ESM.pdf) > was also prepared in org-mode. It is probably best read with the Adobe = PDF > reader. This file is an interesting hybrid of data sharing methods. Som= e of > the data is in the pdf, some of it is embedded in the pdf, including th= e > org-mode files for the manuscript and the supporting information file > itself. Anyone interested in seeing how we did it can check it out. > > 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 --=20 Julian Mariano Burgos, PhD Hafranns=C3=B3knastofnun/Marine Research Institute Sk=C3=BAlagata 4, 121 Reykjav=C3=ADk, Iceland S=C3=ADmi/Telephone : +354-5752037 Br=C3=A9fs=C3=ADmi/Telefax: +354-5752001 Netfang/Email: julian@hafro.is From mboxrd@z Thu Jan 1 00:00:00 1970 From: Karl Voit Subject: Re: org-mode in the wild Date: Wed, 6 Nov 2013 16:19:56 +0100 Message-ID: <2013-11-06T16-19-19@devnull.Karl-Voit.at> References: Reply-To: news1142@Karl-Voit.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55527) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ve4u7-0002pV-9A for emacs-orgmode@gnu.org; Wed, 06 Nov 2013 10:20:28 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Ve4ty-0004sV-Ap for emacs-orgmode@gnu.org; Wed, 06 Nov 2013 10:20:23 -0500 Received: from plane.gmane.org ([80.91.229.3]:39141) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Ve4ty-0004sF-3o for emacs-orgmode@gnu.org; Wed, 06 Nov 2013 10:20:14 -0500 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1Ve4tw-0002xH-Uq for emacs-orgmode@gnu.org; Wed, 06 Nov 2013 16:20:12 +0100 Received: from mail.michael-prokop.at ([88.198.6.110]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Wed, 06 Nov 2013 16:20:12 +0100 Received: from news1142 by mail.michael-prokop.at with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Wed, 06 Nov 2013 16:20:12 +0100 List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org * Julian M. Burgos wrote: > Thank you very much John!!! Your document contains a wealth of information on how to > use org-mode for reproducible research! I really like the idea of > embedding the supporting documents (bibliography, additional analysis) into the > document. Very nice. A agree! > Perhaps it would be good to have a repository of practices and examples > for reproducible research, maybe a section in Worg? If would be very cool if John could link the repos and the PDF on: http://orgmode.org/worg/org-contrib/babel/uses.html#sec-6 -- mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode: > get Memacs from https://github.com/novoid/Memacs < https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on github