Debian Med Project
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Summary
Typesetting
Debian Med support for typesetting and publishing

This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Typesetting packages

Official Debian packages with high relevance

King
interactive system for three-dimensional vector graphics
Versions of package king
ReleaseVersionArchitectures
sid2.23.161103+dfsg1-1all
wheezy2.21.120420-2all
jessie2.21.120420+dfsg-1all
stretch2.23.161103+dfsg1-1all
buster2.23.161103+dfsg1-1all
Popcon: 14 users (11 upd.)*
Versions and Archs
License: DFSG free
Git

KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research. KiNG builds on Mage, JavaMage, and the "kinemage" (kinetic image) concept to deliver a full-featured Java application with a user-friendly interface and integrated editing features. The KiNG jar file can be used within a web page as a Java applet or Java object to promote easy access to kinemages or coordinate files from a web browser.

Texlive-latex-extra
??? missing short description for package texlive-latex-extra :-(
Versions of package texlive-latex-extra
ReleaseVersionArchitectures
squeeze2009-10+squeeze1all
wheezy2012.20120611-2all
jessie2014.20141024-1all
stretch2016.20170123-5all
buster2017.20170809-1all
sid2017.20170809-1all
Debtags of package texlive-latex-extra:
made-offont, tex
roleapp-data
usetypesetting
works-withfont, text
works-with-formatpdf, tex
Popcon: 3672 users (3343 upd.)*
Versions and Archs
License: DFSG free
Remark of Debian Med team: For biologists specifically texshade.sty is interesting

The texlive-latex-extra package contains a lot of interesting LaTeX styles for different purposes. As a biologist you are most probably interested in

 TeXShade: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/texshade.htm

You might like to install texlive-latex-extra-doc as well and read the documents in

 /usr/share/doc/texlive-latex-extra-doc/latex/texshade/
Texlive-science
??? missing short description for package texlive-science :-(
Versions of package texlive-science
ReleaseVersionArchitectures
buster2017.20170809-1all
squeeze2009-10+squeeze1all
stretch2016.20170123-5all
wheezy2012.20120611-2all
jessie2014.20141024-1all
sid2017.20170809-1all
Debtags of package texlive-science:
fieldbiology, chemistry, electronics, mathematics, physics
made-oftex
roleapp-data
sciencepublishing
usetypesetting
works-withgraphs, text
works-with-formattex
Popcon: 2675 users (1438 upd.)*
Versions and Archs
License: DFSG free
Remark of Debian Med team: For biologists specifically biotex.sty and textopo.sty are interesting

The texlive-science package contains a lot of interesting LaTeX styles for different sciences. As a biologist you are most probably interested in

 TeXTopo: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/textopo.htm

You might like to install texlive-science-doc as well and read the documents in

 /usr/share/doc/texlive-science-doc/latex/textopo/

Official Debian packages with lower relevance

Biber
Much-augmented BibTeX replacement for BibLaTeX users
Versions of package biber
ReleaseVersionArchitectures
stretch2.7-2all
sid2.7-2all
buster2.7-2all
wheezy0.9.9+release-1all
jessie1.9-3+deb8u1all
Popcon: 343 users (344 upd.)*
Versions and Archs
License: DFSG free
Git

The biblatex package by Philipp Lehman is becoming the definitive citation management tool for LaTeX users. Biblatex has relied on the venerable BibTeX program only for sorting and generating a very generic .bbl file without any formatting instruction. Everything else is taken care of by biblatex, which provides a powerful and flexible macro interface for authors of citation styles.

Biber offers a large superset of BibTeX functionality for BibLaTeX users. In addition it offers full UTF-8 (Unicode 6.0) capabilities, fully customisable sorting, output to GraphViz to help visualise complex crossrefs, support for remote data sources, structural validation of the data against the (customisable) data model, and a lot more.

Bibus
bibliographic database
Versions of package bibus
ReleaseVersionArchitectures
squeeze1.5.1-3all
wheezy1.5.2-1all
buster1.5.2-4all
stretch1.5.2-4all
jessie1.5.2-4all
sid1.5.2-4all
Debtags of package bibus:
interfacex11
roleprogram
sciencebibliography, publishing
uitoolkitwxwidgets
useorganizing, typesetting
works-with-formatbib, odf
x11application
Popcon: 27 users (15 upd.)*
Versions and Archs
License: DFSG free
Svn

Bibus is a bibliographic database which has been developed with LibreOffice/ OpenOffice.org in mind. It can directly insert citations and format the bibliographic index in an open OpenOffice.org Writer document. The main features are

  • hierarchical organization of the references with user-defined keys
  • designed for multiuser-environments (share databases between users)
  • a search engine supporting live queries
  • on-line PubMed access
  • import of PubMed (Medline), EndNote/Refer, RIS and BibTeX records.

Bibus will use an SQLite-database by default for storage (via the SQLite3 module available in Python >2.5). But it also supports MySQL-databases. If you want to use a MySQL-database, make sure, that you have the python-mysqldb package installed.

Screenshots of package bibus

Desktop tools that help inserting references in LibreOffice, or help managing PDF collections. This list is probably incomplete.

Jabref-plugin-oo
LibreOffice plugin for JabRef (transitional dummy package)
Maintainer: gregor herrmann
Versions of package jabref-plugin-oo
ReleaseVersionArchitectures
squeeze0.7.4+ds-3all
wheezy0.9+ds-2all
jessie2.10+ds-3all
Debtags of package jabref-plugin-oo:
roleplugin
sciencebibliography
suiteopenoffice
works-with-formatbib
Popcon: 0 users (0 upd.)*
Versions and Archs
License: DFSG free
Git

This is a transitional dummy package to upgrade to a newer jabref package, which now includes the LibreOffice plugin.

It can safely be removed after upgrading jabref to at least 2.9~beta1.

Desktop tools that help inserting references in LibreOffice, or help managing PDF collections. This list is probably incomplete.

Kbibtex
BibTeX editor for KDE
Versions of package kbibtex
ReleaseVersionArchitectures
jessie0.4-4amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
squeeze0.2.3.90-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
wheezy0.4-4amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
stretch0.4-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
buster0.4-4amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
sid0.4-4amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
experimental0.4.1-1amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
Debtags of package kbibtex:
interfacex11
roleprogram
uitoolkitqt
useediting
works-withdtp, text
works-with-formatbib
x11application
Popcon: 68 users (56 upd.)*
Versions and Archs
License: DFSG free
Git

An application to manage bibliography databases in the BibTeX format. KBibTeX can be used as a standalone program, but can also be embedded into other KDE applications (e.g. as bibliography editor into Kile).

KBibTeX can query online resources (e.g. Google scholar) via customizable search URLs. It is also able to import complete datasets from NCBI Pubmed. It also supports tagging references with keywords and manages references to local files.

BibTeX files can be exported into HTML, XML, PDF, PS and RTF format using a number of citation styles.

Screenshots of package kbibtex
R-cran-qqman
R package for visualizing GWAS results using Q-Q and manhattan plots
Versions of package r-cran-qqman
ReleaseVersionArchitectures
sid0.1.4-2all
stretch0.1.2-1all
buster0.1.2-1all
Popcon: 5 users (7 upd.)*
Versions and Archs
License: DFSG free
Git

qqman is an add-on package for the R statistical environment. This package provides functions for visualizing Genome-Wide Association Studies (GWAS) results using Manhattan plots and Quantile-Quantile plots.

Referencer
GNOME Document Organiser
Versions of package referencer
ReleaseVersionArchitectures
sid1.2.2-2amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,powerpc,ppc64el,s390x
buster1.2.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
stretch1.2.2-2amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
jessie1.2.2-1amd64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x
wheezy1.1.6-2amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
squeeze1.1.6-1amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc
Debtags of package referencer:
interfacex11
roleprogram
scopeutility
uitoolkitgtk
useorganizing
x11application
Popcon: 36 users (20 upd.)*
Versions and Archs
License: DFSG free

Referencer is a GNOME application to organise documents or references, and ultimately generate a BibTeX bibliography file. Referencer includes a number of features to make this process easier:

  • Automatic metadata retrieval from PubMed, CrossRef and ArXiv
  • Smart web links
  • Import from BibTeX, Reference Manager and EndNote
  • Tagging
Screenshots of package referencer

Desktop tools that help inserting references in LibreOffice, or help managing PDF collections. This list is probably incomplete.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 195306