Differences between revisions 43 and 93 (spanning 50 versions)
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 * [http://cdd.alioth.debian.org/science/tasks/typesetting.php Sentinel page]
 * [[http://blends.alioth.debian.org/science/tasks/typesetting.html|Sentinel page]]
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== Editors ==
 * emacs ([[http://lists.debian.org/debian-science/2005/08/msg00002.html|Andre Lehovich]], [http://lists.debian.org/debian-science/2005/08
 * xemacs ([[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]])
 * bluefish ([[http://lists.debian.org/debian-science/2005/08/msg00006.html|Kenward Vaughan]]) /msg00170.html Filippo Rusconi], [[http://lists.debian.org/debian-science/2005/08/msg00005.html|Enrico Zini]])
 * kile ([[http://lists.debian.org/debian-science/2005/07/msg00006.html|Helen Faulkner]], [[http://lists.debian.org/debian-science/2005/08/msg00017.html|JD Rogers]])
 * [[http://packages.debian.org/unstable/tex/texmaker|texmaker]] A Cross-Platform LaTeX Editor
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 * bluefish ([http://lists.debian.org/debian-science/2005/08/msg00006.html Kenward Vaughan])
 * emacs ([http://lists.debian.org/debian-science/2005/08/msg00002.html Andre Lehovich], [http://lists.debian.org/debian-science/2005/08/msg00170.html Filippo Rusconi], [http://lists.debian.org/debian-science/2005/08/msg00005.html Enrico Zini])
 * kile ([http://lists.debian.org/debian-science/2005/07/msg00006.html Helen Faulkner], [http://lists.debian.org/debian-science/2005/08/msg00017.html JD Rogers])
 * LaTeX ([http://lists.debian.org/debian-science/2005/07/msg00006.html Helen Faulkner], [http://lists.debian.org/debian-science/2005/08/msg00002.html Andre Lehovich], [http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz], [http://lists.debian.org/debian-science/2005/08/msg00170.html Filippo Rusconi])
 * openoffice.org ([http://lists.debian.org/debian-science/2005/07/msg00006.html Helen Faulkner], [http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz], [http://lists.debian.org/debian-science/2005/08/msg00008.html Carlo Segre], [http://lists.debian.org/debian-science/2005/08/msg00006.html Kenward Vaughan], [http://lists.debian.org/debian-science/2005/08/msg00005.html Enrico Zini])
 * pdflatex ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * rubber ([http://lists.debian.org/debian-science/2005/08/msg00035.html Gorjanc Gregor], [http://lists.debian.org/debian-science/2005/08/msg00032.html Jukka Suomela])
 * scribus ([http://lists.debian.org/debian-science/2005/08/msg00001.html Yaroslav Halchenko])
=== TeX/LaTeX ===
 * [[http://packages.debian.org/unstable/tex/texlive|TeXLive]] TeX Live: A decent selection of the TeX Live packages
  * [[http://packages.debian.org/unstable/tex/texlive-bibtex-extra|texlive-bibtex-extra]] TeX Live: Extra BibTeX styles
  * [[http://packages.debian.org/unstable/tex/texlive-math-extra|texlive-math-extra]]TeX Live: Advanced math typesetting
  * [[http://packages.debian.org/unstable/tex/texlive-publishers|texlive-publishers]] TeX Live: Support for publishers
  * [[http://packages.debian.org/unstable/tex/texlive-science|texlive-science]] TeX Live: Typesetting for natural and computer sciences
 * LaTeX ([[http://lists.debian.org/debian-science/2005/07/msg00006.html|Helen Faulkner]], [[http://lists.debian.org/debian-science/2005/08/msg00002.html|Andre Lehovich]], [[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]], [[http://lists.debian.org/debian-science/2005/08/msg00170.html|Filippo Rusconi]])
 * pdflatex ([[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]])
 * [[http://packages.debian.org/sid/rubber|rubber]] an automated system for building LaTeX documents ([[http://lists.debian.org/debian-science/2005/08/msg00035.html|Gorjanc Gregor]], [[http://lists.debian.org/debian-science/2005/08/msg00032.html|Jukka Suomela]])
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 * texi2dvi ([http://lists.debian.org/debian-science/2005/08/msg00035.html Gorjanc Gregor])  * texi2dvi ([[http://lists.debian.org/debian-science/2005/08/msg00035.html|Gorjanc Gregor]])
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 * xemacs ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * [[http://packages.debian.org/unstable/doc/diploma|diploma]] Write scientific papers with Debian - Debian GNU/Linux is widely used at universities to do research and to write papers with LaTeX. The package diploma contains examples which illustrate the possible ways to do this effectively with Debian GNU/Linux. Each example consists of a source tree where you can do "make" in the top level directory and then the source code is compiled, the measurement data are processed, and the results are converted into nice figures. Then the text is processed and combined with the figures to a print file.
=== Wysiwyg ===
 * openoffice.org ([[http://lists.debian.org/debian-science/2005/07/msg00006.html|Helen Faulkner]], [[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]], [[http://lists.debian.org/debian-science/2005/08/msg00008.html|Carlo Segre]], [[http://lists.debian.org/debian-science/2005/08/msg00006.html|Kenward Vaughan]], [[http://lists.debian.org/debian-science/2005/08/msg00005.html|Enrico Zini]])
 * scribus ([[http://lists.debian.org/debian-science/2005/08/msg00001.html|Yaroslav Halchenko]])
 * [[http://packages.debian.org/unstable/editors/lyx|LyX]] ([[http://www.lyx.org/|upstream]]) LyX is an almost WYSIWYG-frontend for LaTeX. It makes the power and typesetting quality of LaTeX available for people who are used to word processors.
 * [[http://packages.debian.org/unstable/editors/texmacs|texmacs]] WYSIWYG mathematical text editor using TeX fonts
  * [[http://packages.debian.org/unstable/editors/texmacs-extra-fonts|texmacs-extra-fonts]] extra fonts for the mathematical text editor TeXmacs
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 * gv ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * xpdf ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * gv ([[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]])
 * xpdf ([[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]])
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 * a0poster ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * prosper ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * textpos ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * latex-beamer (debian package exists) [http://latex-beamer.sourceforge.net/ upstream]
 * [[DebianScience/ConferenceTools#slides]] Tools for producing slides
 * [[DebianScience/ConferenceTools#posters]] Tools for producing posters
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 * preview-latex ([http://lists.debian.org/debian-science/2005/08/msg00002.html Andre Lehovich])
 * whizzytex ([http://lists.debian.org/debian-science/2005/08/msg00002.html Andre Lehovich])
 * [[http://packages.debian.org/stable/auctex|AUCTeX]] ([[http://www.gnu.org/software/auctex/|upstream]]) Integrated document editing environment for TeX etc. One component of AUCTeX that LaTeX users will find attractive is: [[http://packages.debian.org/stable/preview-latex-style|preview-latex]], a combination of folding and in-source previewing that provides true "What You See Is What You Get" experience in your sourcebuffer, while letting you retain full control.
 * [[http://packages.debian.org/stable/whizzytex|whizzytex]] ([[http://lists.debian.org/debian-science/2005/08/msg00002.html|Andre Lehovich]])
 * reftex mode - included with emacs helps with cross references.
 * flyspell mode - on the fly spell checking - included with emacs
 * [[ftp://ftp.tex.ac.uk/tex-archive/support/ite/index.html|ite]] (ITP: DebianBug:492651) Position figure labels interactively. [[http://sites.google.com/site/ralexowen/debian-packages|Preliminary Package]]
=== Vim addons for LaTeX ===
 * [[http://package.debian.org/stable/vim-latexsuite|VIM LaTeX-suite]] ([[http://vim-latex.sourceforge.net/|upstream]]) view, edit and compile LaTeX document from VIM. Provides a lot of very useful macros to insert symbols, environments, and to type mathematical formulas. Offers similar features as Auctex to VI users.
=== Vector diagrams ===
 * [[http://packages.debian.org/unstable/graphics/dia|dia]] [[http://live.gnome.org/Dia|upstream]] Dia is an editor for diagrams, graphs, charts etc.
 * [[http://packages.debian.org/unstable/graphics/xfig|xfig]] Facility for Interactive Generation of figures under X11
  * [[http://packages.debian.org/unstable/graphics/transfig|transfig]] Utilities for converting XFig figure files
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 * See also [http://www.debian.org/devel/debian-med/doc debian-med/doc]
 * [[http://packages.qa.debian.org/s/skribe.html|skribe]] ''[[http://www-sop.inria.fr/mimosa/fp/Skribe/|upstream]]'' ([[http://lists.debian.org/debian-science/2005/08/msg00171.html|Brett Viren]])
 * See also [[http://www.debian.org/devel/debian-med/doc|debian-med/doc]]
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 * epsmerge ([http://lists.debian.org/debian-science/2005/07/msg00007.html Victor Munoz])
 * [http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=205392 jabref] ''[http://jabref.sourceforge.net/ upstream]'' ([http://lists.debian.org/debian-science/2005/08/msg00032.html Jukka Suomela]) [http://www.toastfreeware.priv.at/debian/ unofficial packages]
 * pyblink (already packaged by [http://lists.debian.org/debian-science/2005/08/msg00001.html Yaroslav Halchenko]): it is for those who have to struggle in OO and write anything which includes bibliographies. pyblink would help you to interact OO with pybliographic and have references done in easier way.
 * Sweave ''[http://www.ci.tuwien.ac.at/~leisch/Sweave/ upstream]'' ([http://lists.debian.org/debian-science/2005/08/msg00035.html Gorjanc Gregor]) very powerful combination of LaTeX and R in one file. This is based on Noweb ideology.
 * yzis ''[http://www.yzis.org/ upstream]'' For vi-like users.
 * [[http://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=use..typesetting;users=debian-science@lists.debian.org|Packages being worked on]].
 * epsmerge ([[http://lists.debian.org/debian-science/2005/07/msg00007.html|Victor Munoz]])
 * pyblink (already packaged by [[http://lists.debian.org/debian-science/2005/08/msg00001.html|Yaroslav Halchenko]]): it is for those who have to struggle in OO and write anything which includes bibliographies. pyblink would help you to interact OO with pybliographic and have references done in easier way.
 * Sweave ''[[http://www.ci.tuwien.ac.at/~leisch/Sweave/|upstream]]'' ([[http://lists.debian.org/debian-science/2005/08/msg00035.html|Gorjanc Gregor]]) very powerful combination of LaTeX and R in one file. This is based on Noweb ideology.
 * yzis ''[[http://www.yzis.org/|upstream]]'' For vi-like users.
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 * FeynmanGraph ''[http://www.physics.odu.edu/~musatov/ upstream]''.
 * JaxoDraw ''[http://jaxodraw.sourceforge.net/ upstream]''
 * FeynmanGraph ''[[http://www.physics.odu.edu/~musatov/|upstream]]''.
 * JaxoDraw ''[[http://jaxodraw.sourceforge.net/|upstream]]''
 * [[http://packages.debian.org/unstable/tex/feynmf|feynmf]] set of LaTeX macros for creating Feynman diagrams
=== Printing utilities ===
 * [[http://packages.debian.org/unstable/text/impose+|impose+]] Postscript utilities for two-up printing, bbox, etc
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 * Bibus ''[http://bibus-biblio.sourceforge.net/ upstream]'' ([http://lists.debian.org/debian-science/2005/08/msg00164.html Stephan Gromer])
 * [http://packages.debian.org/unstable/text/impose+ impose+] ([http://lists.debian.org/debian-science/2005/08/msg00001.html Yaroslav Halchenko])
 * [http://packages.qa.debian.org/s/skribe.html skribe] ''[http://www-sop.inria.fr/mimosa/fp/Skribe/ upstream]'' ([http://lists.debian.org/debian-science/2005/08/msg00171.html Brett Viren])
 * [[http://packages.debian.org/sid/jabref|jabref]] JabRef is a GUI to manage BibTeX databases, the standard LaTeX bibliography reference format. JabRef is built to be platform independent (requires Java 1.5). It merges and extends the functionalities of BibKeeper (Morten O. Alver) and JBibtexManager (Nizar Batada).
 * [[http://packages.debian.org/bibus|Bibus]] ([[http://bibus-biblio.sourceforge.net/wiki/index.php/Main_Page|upstream]]) is a bibliographic database written in Python and working together with OpenOffice.org.
 * [[http://packages.debian.org/unstable/text/bibutils|bibutils]] ([[http://www.scripps.edu/~cdputnam/software/bibutils/|upstream]]) Convert between the following bibliographic data formats: BibTeX, COPAC, EndNote refer, EndNote XML,
 * [[http://packages.debian.org/unstable/text/cb2bib|cb2bib]] ([[http://www.molspaces.com/d_cb2bib-overview.php/|upstream]]) Extract unformatted or unstandardized bibliographic references from email alerts, journal Web pages, and PDF files. Manage huge BibTeX bibliographies.
Pubmed XML, ISI web of science, US Library of Congress MODS XML, RIS, and Word 2007 bibliography.
 * [[http://packages.debian.org/unstable/kde/kbibtex|kbibtex]] ([[http://www.unix-ag.uni-kl.de/~fischer/kbibtex/|upstream]] BibTeX editor for KDE
 * [[http://packages.debian.org/unstable/gnome/pybliographer|pybliographer]] ([[http://www.pybliographer.org/|pybliographer]] tool for manipulating bibliographic databases
 * [[http://packages.debian.org/unstable/gnome/referencer|referencer]] ([[http://icculus.org/referencer/index.html|upstream]]) Referencer is a GNOME application to organise documents or references, and ultimately generate a BibTeX bibliography file.
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||Name||Task||Licence||Package||
||[http://www.scripps.edu/~cdputnam/software/bibutils/bibutils.html bibutils]||converting bibliographies||GPL||[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=452577 ITP#452577]||
||[http://bibus-biblio.sourceforge.net/
Bibus]||Managing citations in an OpenOffice document||GPL||[http://bibus-biblio.sourceforge.net/html/en/introduction.html#mozTocId157381 unofficial]||
||[http://quaneko.sourceforge.net/ Quaneko]||Indexing||GPL||[http://mentors.debian.net/debian/pool/main/q/quaneko/ mentors]||
||[http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=
69446 Biomail] ''[http://biomail.sourceforge.net/biomail/ upstream]''||Surveying||GPL|| ||
||[http://refdb.sourceforge.net/ RefDB]||Database||GPL||[http://refdb.sourceforge.net/install.html#debian upstream]||
||[http://www.cs.usyd.edu.au/~tapted/bib2endnote.html bib2endnote]||Converter||GPLv2||depens on Java||
||[http://bioinformatics.org/librarian/ Librarian]||PDF article indexing||GPL||depends on php/mysql/apache||
||Name ||Task ||Licence ||Package ||
||Biomail (DebianBug:69446) ''[[http://biomail.sourceforge.net/biomail/|upstream]]'' ||Surveying ||GPL || ||
||[[http://refdb.sourceforge.net/|RefDB]] ||Database ||GPL ||[[http://refdb.sourceforge.net/install.html#debian|upstream]] ||
||[[http://www.cs.usyd.edu.au/~tapted/bib2endnote.html|bib2endnote]] ||Converter ||GPLv2 ||depens on Java ||
||[[http://bioinformatics.org/librarian/|Librarian]] ||PDF article indexing ||GPL ||depends on php/mysql/apache ||
||[[http://gpapers.org/|gPapers]] ||Bibliography management ||GPL ||depends on python ||
||[[http://www.zotero.org/|zotero]] || bibliography management as a web browser addon || || ||

Known users from DebianScience listed in parenthesis.

Typesetting

Editors

Typesetting tools already packaged in Debian

TeX/LaTeX

  • TeXLive TeX Live: A decent selection of the TeX Live packages

  • LaTeX (Helen Faulkner, Andre Lehovich, Victor Munoz, Filippo Rusconi)

  • pdflatex (Victor Munoz)

  • rubber an automated system for building LaTeX documents (Gorjanc Gregor, Jukka Suomela)

  • TeX
  • tex4ht
  • texi2dvi (Gorjanc Gregor)

  • texify
  • diploma Write scientific papers with Debian - Debian GNU/Linux is widely used at universities to do research and to write papers with LaTeX. The package diploma contains examples which illustrate the possible ways to do this effectively with Debian GNU/Linux. Each example consists of a source tree where you can do "make" in the top level directory and then the source code is compiled, the measurement data are processed, and the results are converted into nice figures. Then the text is processed and combined with the figures to a print file.

Wysiwyg

Viewers

Useful for slides and posters

Emacs extensions for LaTeX

  • AUCTeX (upstream) Integrated document editing environment for TeX etc. One component of AUCTeX that LaTeX users will find attractive is: preview-latex, a combination of folding and in-source previewing that provides true "What You See Is What You Get" experience in your sourcebuffer, while letting you retain full control.

  • whizzytex (Andre Lehovich)

  • reftex mode - included with emacs helps with cross references.
  • flyspell mode - on the fly spell checking - included with emacs
  • ite (ITP: 492651) Position figure labels interactively. Preliminary Package

Vim addons for LaTeX

  • VIM LaTeX-suite (upstream) view, edit and compile LaTeX document from VIM. Provides a lot of very useful macros to insert symbols, environments, and to type mathematical formulas. Offers similar features as Auctex to VI users.

Vector diagrams

  • dia upstream Dia is an editor for diagrams, graphs, charts etc.

  • xfig Facility for Interactive Generation of figures under X11

    • transfig Utilities for converting XFig figure files

Others

Publishing tools that could be considered for inclusion in Debian

  • Packages being worked on.

  • epsmerge (Victor Munoz)

  • pyblink (already packaged by Yaroslav Halchenko): it is for those who have to struggle in OO and write anything which includes bibliographies. pyblink would help you to interact OO with pybliographic and have references done in easier way.

  • Sweave upstream (Gorjanc Gregor) very powerful combination of LaTeX and R in one file. This is based on Noweb ideology.

  • yzis upstream For vi-like users.

Drawing Feynman diagrams

Printing utilities

  • impose+ Postscript utilities for two-up printing, bbox, etc

Bibliographies

Managing bibliographies

  • jabref ?JabRef is a GUI to manage BibTeX databases, the standard LaTeX bibliography reference format. ?JabRef is built to be platform independent (requires Java 1.5). It merges and extends the functionalities of ?BibKeeper (Morten O. Alver) and JBibtexManager (Nizar Batada).

  • Bibus (upstream) is a bibliographic database written in Python and working together with OpenOffice.org.

  • bibutils (upstream) Convert between the following bibliographic data formats: BibTeX, COPAC, ?EndNote refer, ?EndNote XML,

  • cb2bib (upstream) Extract unformatted or unstandardized bibliographic references from email alerts, journal Web pages, and PDF files. Manage huge BibTeX bibliographies.

Pubmed XML, ISI web of science, US Library of Congress MODS XML, RIS, and Word 2007 bibliography.

Tools for handling bibliographies that could be considered for inclusion in Debian

Name

Task

Licence

Package

Biomail (69446) upstream

Surveying

GPL

RefDB

Database

GPL

upstream

bib2endnote

Converter

GPLv2

depens on Java

Librarian

PDF article indexing

GPL

depends on php/mysql/apache

gPapers

Bibliography management

GPL

depends on python

zotero

bibliography management as a web browser addon