Differences between revisions 83 and 93 (spanning 10 versions)
Revision 83 as of 2008-10-17 15:01:13
Size: 9159
Editor: ?ChristopherWalker
Comment: Add more texlive packages
Revision 93 as of 2012-05-24 13:19:56
Size: 10385
Editor: ?FilippoRusconi
Comment:
Deletions are marked like this. Additions are marked like this.
Line 4: Line 4:
 * [http://cdd.alioth.debian.org/science/tasks/typesetting.html Sentinel page]
 * [[http://blends.alioth.debian.org/science/tasks/typesetting.html|Sentinel page]]
Line 7: Line 6:
Line 9: Line 7:

* 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])
 * 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
Line 16: Line 13:
Line 18: Line 14:
 * [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])
 * 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])
 
 * [[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]])
Line 30: Line 24:
 * 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]])
Line 32: Line 26:
 * [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.   * [[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.
Line 34: Line 28:
 * 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. 
 * 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
Line 38: Line 34:
 * 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]])
Line 42: Line 37:
 * [:DebianScience/ConferenceTools#slides:] Tools for producing slides
 * [:DebianScience/ConferenceTools#posters:] Tools for producing posters
 * [[DebianScience/ConferenceTools#slides]] Tools for producing slides
 * [[DebianScience/ConferenceTools#posters]] Tools for producing posters
Line 46: Line 40:
 * [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])
 
 * [[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]])
Line 52: Line 43:
 * flyspell mode - on the fly spell checking - included with emacs

 * [ftp://ftp.tex.ac.uk/tex-archive/support/ite/index.html ite] ([http://bugs.debian.org/492651 ITP:#492651]) Position figure labels interactively. [http://sites.google.com/site/ralexowen/debian-packages Preliminary Package]
 * 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.
Line 57: Line 48:
 * [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
 * [[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
Line 61: Line 52:
 * [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]
 * [[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]]
Line 64: Line 55:
 * [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.
 * [[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.
Line 72: Line 61:
 * 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
 * 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
Line 77: Line 65:
 * [http://packages.debian.org/unstable/text/impose+ impose+] Postscript utilities for two-up printing, bbox, etc
 * [[http://packages.debian.org/unstable/text/impose+|impose+]] Postscript utilities for two-up printing, bbox, etc
Line 81: Line 68:
 * [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/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, 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.  
 * [[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.
Line 89: Line 77:
||Name||Task||Licence||Package||
||[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||
||[http://gpapers.org/ gPapers]||Bibliography management||GPL||depends on python||
||[http://bibus-biblio.sourceforge.net/wiki/index.php/Main_Page bibus]|| Bibliography management -works with OpenOffice|| ||[http://bibus-biblio.sourceforge.net/wiki/index.php/Installation#Debian unofficial package] ||
||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