Debian Science Typesetting packages

AUCTeX is a comprehensive customizable integrated environment for writing input files for TeX/LaTeX/ConTeXt/Texinfo using GNU Emacs. Currently XEmacs ships with its own AUCTeX version.

It supports processing source files by running TeX and related tools (such as output filters, post processors for generating indices and bibliographies, and viewers) from inside Emacs. AUCTeX allows browsing through the errors reported by TeX, while it moves the cursor directly to the reported error, and displays some documentation for that particular error. This will even work when the document is spread over several files.

AUCTeX can automatically indent LaTeX source, either line by line or for an entire document, and has a special outline feature which can greatly assist in getting an overview of a document.

AUCTeX is written entirely in Emacs Lisp, and may therefore be enhanced with new features for specific needs. It comes with a large range of handy Emacs macros. It is a GNU project, and documentation for all its features is accessible via the Emacs info browser.

Bibus is a bibliographic database which has been developed with 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.

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.

This package provides command line tools bib2xml, copac2xml, end2xml endx2xml, isi2xml, med2xml, ris2xml which convert to MODS XML format, modsclean which reformats MODS XML, and a matching set of commands xml2ads, xml2bib, xml2end, xml2isi, xml2ris, xml2wordbib which convert from MODS XML.

Dia is an editor for diagrams, graphs, charts etc. There is support for UML static structure diagrams (class diagrams), Entity-Relationship diagrams, network diagrams and much more. Diagrams can be exported to postscript and many other formats.

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.

FeynMF is a LaTeX package for easy drawing of professional-quality Feynman diagrams, illustrations that depict the fundamental interactions of subatomic particles. The diagrams may be created using either the Metafont or MetaPost programs. FeynMF lays out most diagrams satisfactorily from the structure of the graph without any need for manual intervention. Nevertheless all the power of Metafont or MetaPost is available for more obscure cases.

Note that you will need the texlive-metapost package in order to use the MetaPost-based version of FeynMF.

A set of utilities for manipulating DSC compliant postscript. The following programs are included:

impose: A preprocessor to pstops for creating 2-up printouts. It tries to remove white space from the printout by probing the original postscript for the printed area's bounding box. This makes the output more esthetic than a simplistic layout of non-cropped original pages.

bboxx: Extracts the bounding boxes of a postscript file, with the option of entering the bounding box into the file. This program uses the ghostscript bbox device.

fixtd: Sets options in a Postscript file asking the printer to turn on tumbling or duplex printing.

psbl: Rearranges pages in a file to create booklets.

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 ressources (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.

latexdiff compares two LaTeX files and marks up significant differences between them (i.e. a diff for LaTeX files). It generates a new LaTeX file containing the annotated differences.

Various options are available for visual markup using standard LaTeX packages such as 'color.sty'. Changes not directly affecting visible text, for example in formatting commands, are still marked in the LaTeX source.

A rudimentary revision facilility is provided by another Perl script, 'latexrevise', which accepts or rejects all changes. Manual editing of the difference file can be used to override this default behaviour and accept or reject selected changes only.

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. Since LyX supports LaTeX's concept of general mark-ups, it is even easier and faster to create professional quality documents with it than with usual word processors. It is also possible to use LaTeX commands within LyX, so nothing of LaTeX's power is lost.

You can extend the functionality of LyX by installing these packages:

• chktex: check for typographical errors
• dvipost: display tracked changes in DVI format output
• gnuhtml2latex: import HTML documents
• groff: improved table formatting in plain text exports
• linuxdoc-tools: export SGML LinuxDoc documents
• noweb: import noweb files
• rcs: integrated version control
• sgmltools-lite: export SGML DocBook documents
• tex4ht, elyxer, hevea, tth, or latex2html: export HTML documents
• texlive-latex-extra: more styles and packages
• wv: import MS Word documents

Mlpost is an OCaml library for scientific drawing. It relies on Metapost, giving the possibility to include (La)TeX fragments. Mlpost users can use the full power of OCaml to generate their diagrams, including static typing and the possibility to use any OCaml library. Moreover, Mlpost promotes a declarative style quite different from existing tools.

This package contains the library itself, and a command-line tool to ease the generation of PostScript or PDF figures directly from .ml files.

It currently supports BibTeX, Medline, Ovid and Refer files. It is useful for viewing, editing and searching, but also to convert bibliographic databases into HTML pages for example.

Note that this version of pybliographer DOES NOT SUPPLY ANY END-USER TOOLS YET. The version in unstable is almost certainly preferable for non-development work.

Home Page: http://www.pybliographer.org/

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

The TeX Live software distribution offers a complete TeX system. It encompasses programs for typesetting, previewing and printing of TeX documents in many different languages, and a large collection of TeX macros and font libraries.

This metapackage provides a decent selection of the TeX Live packages which should suffice for the most common tasks.

The distribution also includes extensive general documentation about TeX, as well as the documentation accompanying the included software packages.

Additional BibTeX styles and bibliography databases.

This package includes the following CTAN packages:

 aichej -- Bibliography style file for the AIChE Journal.
 amsrefs -- A LaTeX-based replacement for BibTeX.
 apacite -- Citation style following the rules of the APA.
 apalike2 -- Bibliography style that approaches APA requirements.
 beebe --
 bibarts -- "Arts"-style bibliographical information.
 bibhtml -- BibTeX support for HTML files.
 biblist -- Print a BibTeX database.
 bibtopic -- Include multiple bibliographies in a document.
 bibtopicprefix -- Prefix references to bibliographies produced by bibtopic.
 bibunits -- Multiple bibliographies in one document.
 cell -- Bibliography style for Cell.
 chicago -- A "Chicago" bibliography style.
 chicago-annote -- Chicago-based annotated BibTeX style.
 chembst -- A collection of BibTeX files for chemistry journals.
 collref -- Collect blocks of references into a single reference.
 compactbib -- Multiple thebibliography environments.
 custom-bib -- Customised BibTeX styles.
 din1505 -- Bibliography styles for German texts.
 dk-bib -- Danish variants of standard BibTeX styles.
 doipubmed -- Special commands for use in bibliographies.
 elsevier-bib -- BibTeX styles to be used in Elsevier preprints.
 fbs -- BibTeX style for Frontiers in Bioscience.
 figbib -- Organize figure databases with BibTeX.
 footbib -- Bibliographic references as footnotes.
 harvard -- Harvard citation package for use with LaTeX 2e.
 harvmac -- Macros for scientific articles.
 ijqc -- BibTeX style file for the Intl. J. Quantum Chem.
 inlinebib -- Citations in footnotes.
 iopart-num -- Numeric citation style for IOP journals.
 jneurosci -- BibTeX style for the Journal of Neuroscience.
 jurabib -- Extended BibTeX citation support for the humanities and legal
  texts.
 listbib -- Lists contents of BibTeX files.
 margbib -- Display bibitem tags in the margins.
 multibib -- Multiple bibliographies within one document.
 munich -- An alternative authordate bibliography style.
 notes2bib -- Integrating notes into the bibliography.
 perception -- BibTeX style for the journal Perception.
 rsc -- BibTeX style for use with RSC journals.
 sort-by-letters -- Bibliography styles for alphabetic sorting.
 splitbib -- Split and reorder your bibliography.
 urlbst -- Web support for BibTeX.

Extra math

This package includes the following CTAN packages:

 12many -- Generalising mathematical index sets.
 amstex -- American Mathematical Society plain TeX macros.
 boldtensors -- Bold latin and greek characters through simple prefix
  characters.
 bosisio -- A collection of packages by Francesco Bosisio.
 ccfonts -- Support for Concrete text and math fonts in LaTeX.
 commath -- Mathematics typesetting support.
 concmath -- Concrete Math fonts.
 concrete -- Concrete Roman fonts.
 extarrows -- Extra Arrows beyond those provided in AMSmath
 extpfeil -- Extensible arrows in mathematics.
 faktor -- Typeset quotient structures with LaTeX.
 ionumbers -- Restyle numbers in maths mode.
 isomath -- Mathematics conformant to ISO 31.
 mathcomp -- Text symbols in maths mode.
 mattens -- Matrices/tensor typesetting.
 mhequ -- Multicolumn equations, tags, labels, sub-numbering.
 multiobjective -- Symbols for multibojective optimisation etc.
 nath -- Natural mathematics notation.
 proba -- Shortcuts commands to symbols used in probability texts.
 shuffle -- A symbol for the shuffle product.
 statex2 -- Statistics style.
 stex -- An Infrastructure for Semantic Preloading of LaTeX Documents.
 stmaryrd -- St Mary Road symbols for theoretical computer science.
 susy -- Macros for SuperSymmetry-related work.
 syllogism -- Typeset syllogisms in LaTeX.
 synproof -- Easy drawing of syntactic proofs.
 tablor -- Create tables of signs and of variations.
 tensor -- Typeset tensors.
 tex-ewd -- Macros to typeset calculational proofs and programs in
  Dijkstra's style.
 thmbox -- Decorate theorem statements.
 turnstile -- Typeset the (logic) turnstile notation.
 venn -- Creating Venn diagrams with MetaPost.
 yhmath -- Extended maths fonts for LaTeX.

This package includes the following CTAN packages:

 ANUfinalexam -- LaTeX document shell for ANU final exam
 IEEEconf -- Macros for IEEE conference proceedings.
 IEEEtran -- Document class for IEEE Transactions journals and conferences.
 aastex -- Macros for Manuscript Preparation for AAS Journals.
 acmconf -- Class for ACM conference proceedings.
 acmtrans -- Class and BibTeX style for ACM Transactions.
 active-conf -- Class for typesetting ACTIVE conference papers.
 afthesis -- Air Force Institute of Technology thesis class.
 aguplus -- Styles for American Geophysical Union.
 aiaa -- Typeset AIAA conference papers.
 ametsoc -- Official American Meteorological Society Latex Template.
 apa -- American Psychological Association format.
 arsclassica -- A different view of the ClassicThesis package.
 asaetr -- Transactions of the ASAE.
 ascelike -- Bibliography style for the ASCE.
 beamer-FUBerlin -- Beamer, using the style of FU Berlin.
 chem-journal -- Various BibTeX formats for journals in Chemistry.
 classicthesis -- A "classically styled" thesis package.
 confproc -- A set of tools for generating conference proceedings.
 ebsthesis -- Typesetting theses for economics
 economic -- BibTeX support for submitting to Economics journals.
 elsevier -- Classes for Elsevier Science journals.
 erdc -- Style for Reports by US Army Corps of Engineers.
 estcpmm -- Style for Munitions Management Project Reports.
 euproposal -- A class for preparing FP7 proposals.
 gaceta -- A class to typeset La Gaceta de la RSME.
 gatech-thesis -- Georgia Institute of Technology thesis class
 har2nat -- Replace the harvard package with natbib.
 icsv -- Class for typesetting articles for the ICSV conference.
 ieeepes -- IEEE Power Engineering Society Transactions.
 ijmart -- LaTeX Class for the Israel Journal of Mathematics.
 imac -- International Modal Analysis Conference format.
 imtekda -- IMTEK thesis class.
 jhep -- Class for JHEP.
 jpsj -- Document Class for Journal of the Physical Society of Japan.
 kluwer --
 lps -- Class for "Logic and Philosophy of Science".
 macqassign -- Typeset assignments for Macquarie University.
 mentis -- A basis for books to be published by Mentis publishers.
 muthesis -- Classes for University of Manchester Dept of Computer Science.
 nature -- Prepare papers for the journal Nature.
 nddiss -- Notre Dame Dissertation format class.
 nih -- A class for NIH grant applications.
 nostarch -- LaTeX class for No Starch Press.
 nrc -- Class for the NRC technical journals.
 philosophersimprint -- Typesetting articles for "Philosophers' Imprint".
 powerdot-FUBerlin -- Powerdot, using the style of FU Berlin.
 pracjourn -- Typeset articles for PracTeX.
 procIAGssymp -- Macros for IAG symposium papers.
 ptptex -- Macros for 'Progress of Theoretical Physics'.
 psu-thesis -- Package for writing a thesis at Penn State University.
 revtex -- Styles for various Physics Journals.
 sageep -- Format papers for the annual meeting of EEGS.
 siggraph -- SIGGRAPH conference class.
 spie -- Support for formatting SPIE Proceedings manuscripts.
 stellenbosch -- Stellenbosch thesis bundle.
 sugconf -- SAS(R) user group conference proceedings document class.
 thesis-titlepage-fhac -- Little style to create a standard titlepage for
  diploma thesis
 thuthesis -- Thesis template for Tsinghua University.
 toptesi -- Bundle of files for typsetting theses.
 tugboat -- LaTeX macros for TUGboat articles.
 tugboat-plain -- Plain TeX macros for TUGboat.
 uaclasses -- University of Arizona thesis and dissertation format.
 ucdavisthesis -- A thesis/dissertation class for University of California
  Davis.
 ucthesis -- University of California thesis format.
 uiucthesis -- UIUC thesis class.
 umthesis -- Dissertations at the University of Michigan.
 umich-thesis -- University of Michigan Thesis LaTeX class.
 ut-thesis -- University of Toronto thesis style.
 uwthesis -- University of Washington thesis class.
 vancouver -- Bibliographic style file for Biomedical Journals.
 vxu -- Document classes for Vaxjo University
 york-thesis -- A thesis class file for York University, Toronto.

Typesetting for natural and computer sciences

This package includes the following CTAN packages:

 SIstyle -- Package to typeset SI units, numbers and angles.
 SIunits -- International System of Units.
 alg -- LaTeX environments for typesetting algorithms.
 algorithm2e -- Floating algorithm environment with algorithmic keywords.
 algorithmicx -- The algorithmic style you always wanted.
 algorithms -- A suite of tools for typesetting algorithms in pseudo-code.
 biocon -- Typesetting biological species names
 bpchem -- Typeset chemical names, formulae, etc.
 bytefield -- Create illustrations for network protocol specifications.
 chemarrow -- Arrows for use in chemistry.
 chemcompounds -- Simple consecutive numbering of chemical compounds.
 chemcono -- Support for compound numbers in chemistry documents.
 chemstyle -- Writing chemistry with style.
 clrscode -- Typesets pseudocode as in Introduction to Algorithms.
 complexity -- Computational complexity class names.
 computational-complexity -- Class for the journal Computational Complexity.
 digiconfigs -- Writing "configurations"
 dyntree -- Construct Dynkin tree diagrams.
 eltex -- Simple circuit diagrams in LaTeX picture mode.
 formula -- Typesetting physical units.
 fouridx -- Left sub- and superscripts in maths mode.
 functan -- Macros for functional analysis and PDE theory
 galois -- Typeset Galois connections.
 gastex -- Graphs and Automata Simplified in TeX.
 gene-logic -- Typeset logic formulae, etc.
 gu -- Typeset crystallographic group-subgroup-schemes.
 hep -- A "convenience wrapper" for High Energy Physics packages.
 hepnames -- Pre-defined high energy particle names.
 hepparticles -- Macros for typesetting high energy physics particle names.
 hepthesis -- A class for academic reports, especially PhD theses.
 hepunits -- A set of units useful in high energy physics applications.
 karnaugh -- Typeset Karnaugh-Veitch-maps.
 mhchem -- Typeset chemical formulae/equations and Risk and Safety phrases.
 mhs -- Historical mathematics.
 miller -- Typeset miller indices.
 objectz -- Macros for typesetting Object Z.
 pseudocode -- LaTeX environment for specifying algorithms in a natural way.
 scientificpaper -- Format a scientific paper for journal publication.
 sciposter -- Make posters of ISO A3 size and larger.
 sfg -- Draw signal flow graphs.
 siunitx -- A comprehensive (SI) units package.
 steinmetz -- Print Steinmetz notation.
 struktex -- Draw Nassi-Schneidermann charts
 t-angles -- Draw tangles, trees, Hopf algebra operations and other
  pictures.
 textopo -- Annotated membrane protein topology plots.
 ulqda -- Support of Qualitative Data Analysis.
 unitsdef -- Typesetting units in LaTeX.
 youngtab -- Typeset Young-Tableaux.

GNU TeXmacs is a free scientific text editor, which was both inspired by TeX and GNU Emacs.

The editor allows you to write structured documents via a WYSIWYG (what-you-see-is-what-you-get) and a user friendly interface. New styles may be created by the user. The program implements high-quality typesetting algorithms and TeX fonts, which help you to produce professionally looking documents.

The high typesetting quality still goes through for automatically generated formulas, which makes TeXmacs suitable as an interface for computer algebra systems. TeXmacs also supports the Guile/Scheme extension language, so that you may customize the interface and write your own extensions to the editor.

This package contains the architecture dependent files.

This package contains a reasonably complete set of Type 1 fonts for basic use of the mathematical text editor TeXmacs. Type 1 fonts may yield better printing results and are preferred by publishers.

TeXmacs also uses Type 1 fonts from the TeTeX distribution, but without a more complete set of Type 1 fonts, TeXmacs falls back to the Metafont system and needs to autogenerate fonts from a LaTeX distribution on demand, which takes a lot of time during editing.

This package brings the pregenerated Type 1 fonts that are part of the distribution of TeXmacs for Microsoft Windows and can't be found in other Debian packages.

 Homepage: [http://www.texmacs.org/](http://www.texmacs.org/)

This packages contains utilities (mainly fig2dev) to handle XFig (Facility for Interactive Generation of figures) files.

It can convert them to box, cgm, epic, eepic, eepicemu, emf, eps, gif, ibmgl, jpeg, latex, map (HTML image map), mf (MetaFont), mp (MetaPost), mmp (Multi-Meta-Post), pcx, pdf, pdftex, pdftex_t, pic, pictex, png, ppm, ps, pstex, pstex_t, ptk (Perl/tk), sld (AutoCad slide format), textyl, tiff, tk (Tcl/Tk), tpic, xbm and xpm.

XFig is a menu-driven tool that allows the user to draw and manipulate objects interactively in an X window. The resulting pictures can be saved, printed on postscript printers, or converted to a variety of other formats (e.g. to allow inclusion in LaTeX documents or web pages) using the transfig program.

This package contains the xfig program itself.

You should think about installing the transfig package to export the graphics to several common formats. You should also think about installing xfig-doc, which contains the documentation and xfig-libs, which contains several clip art libraries.

csv2latex is a simple command-line file converter that converts a comma-separated-values file into a LaTeX table. It can guess exotic csv formats.

Dmaths is software that integrates with office suites OpenOffice (free), StarOffice and NeoOffice (Mac OS X) and which aids scientists and those who wish to edit mathematical formulas and / or scientists. It also directly use your favorite drawing software and incorporate graphs functions in a document.

This R package provides functions returning, displaying or writing to disk the LaTeX or HTML code associated with the supplied object of class xtable. The package also provides functions converting an R object to an xtable object, which can then be printed as a LaTeX or HTML table.

Tellico is a collection manager for KDE. It includes default collections for books, bibliographies, comic books, videos, music, coins, stamps, trading cards, and wines, and also allows custom collections; with unlimited user-defined fields allowed. Automatically formatted names, sorting by any property, filters, automatic ISBN validation and full customization for printing or display through XSLT files are some of the features present. It can import CSV, RIS, BibTeX, and BibTeXML files; and export CSV, HTML, BibTeX, BibTeXML, and PilotDB. Tellico can also import data from Amazon, IMDb, CDDB, or any US-MARC compliant z39.50 server.

The files are stored in XML format, avoiding the need for database server. It also makes it easy for other softwares to use the Tellico data.

Texmaker is a clean, highly configurable LaTeX editor with good hot key support and extensive LaTeX documentation. Texmaker integrates many tools needed to develop documents with LaTeX, in just one application. It has some nice features such as syntax highlighting, insertion of 370 mathematical symbols with only one click, and "structure view" of the document for easier navigation.

JabRef is a graphical Java application for editing bibtex (.bib) databases. JabRef lets you organize your entries into overlapping logical groups, and with a single click limit your view to a single group or an intersection or union of several groups. You can customize the entry information shown in the main window, and sort by any of the standard Bibtex fields. JabRef can autogenerate bibtex keys for your entries. JabRef also lets you easily link to PDF or web sources for your reference entries.

JabRef can import from and export to several formats, and you can customize export filters. JabRef can be run as a command line application to convert from any import format to any export format.

Quaneko is a tool that allows you to quickly search for keywords in the files and directories on the local hard disk. It creates indexes over the words in those files. For you, this means that a typical search query will only take seconds.

quaneko can not only search for words in plain text files but also in various other file formats, depending on its configuration (e.g. Word doc, pdf, html, xml,...)

Digital library manager. Think of it as an iTunes for your PDFs.

Zotero is an easy-to-use yet powerful research tool that helps you gather, organize, and analyze sources (citations, full texts, web pages, images, and other objects), and lets you share the results of your research in a variety of ways. An extension to the popular open-source web browser Firefox, Zotero includes the best parts of older reference manager software (like EndNote)—the ability to store author, title, and publication fields and to export that information as formatted references—and the best parts of modern software and web applications (like iTunes and del.icio.us), such as the ability to interact, tag, and search in advanced ways. Zotero integrates tightly with online resources; it can sense when users are viewing a book, article, or other object on the web, and—on many major research and library sites—find and automatically save the full reference information for the item in the correct fields. Since it lives in the web browser, it can effortlessly transmit information to, and receive information from, other web services and applications; since it runs on one’s personal computer, it can also communicate with software running there (such as Microsoft Word). And it can be used offline as well (e.g., on a plane, in an archive without WiFi).

• Automatic capture of citation information from web pages
• Storage of PDFs, files, images, links, and whole web pages
• Flexible notetaking with autosave
• Fast, as-you-type search through your materials
• Playlist-like library organization, including saved searches (smart collections) and tags
• Platform for new forms of digital research that can be extended with other web tools and services
• Formatted citation export (over 1100 styles and growing)
• Integration with Microsoft Word and OpenOffice
• Saves records and notes in several languages
• Integration with WordPress and other blogging software
• Remote library backup
• Advanced search and data mining tools
• Wide variety of import/export