Package: abs-guide Description-md5: c70e528b8b624e5738bdbd1b89e8b349 Description-en: The Advanced Bash-Scripting Guide An in-depth exploration of the art of shell scripting. . This tutorial assumes no previous knowledge of scripting or programming, but progresses rapidly toward an intermediate/advanced level of instruction ... all the while sneaking in little snippets of UNIX(R) wisdom and lore. It serves as a textbook, a manual for self-study, and a reference and source of knowledge on shell scripting techniques. The exercises and heavily-commented examples invite active reader participation, under the premise that the only way to really learn scripting is to write scripts. . This book is suitable for classroom use as a general introduction to programming concepts. Package: abyss Description-md5: 7c736de2ab206e6ade42c9f95ff44b4a Description-en: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. Package: autodir Description-md5: 0b6913d4b30fa8f1270054260e535bdb Description-en: Automatically creates home and group directories for LDAP/NIS/SQL/local accounts A modular and thread-enabled tool to create and/or mounting and managing automagically and transparently user/group home directories, on demand. . It can work with any authentication framework (e.g. system files, NIS, LDAP or SQL) and does not require PAM, which is a required feature for session-less service such as smtp servers. . Automounter version 4 (autofs4) has to be enabled when compiling the kernel. Debian packaged kernels have it enabled as module. Package: beast-mcmc Description-md5: 347f87629165216c55313b0035e8c195 Description-en: Bayesian MCMC phylogenetic inference BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. Package: beast-mcmc-examples Description-md5: c63bad5feea098eb39bb86db8b6f8d33 Description-en: Bayesian MCMC phylogenetic inference - example data BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains the example data. Package: clustalx Description-md5: a79728f91dcfed21b62f89dea1743319 Description-en: Multiple alignment of nucleic acid and protein sequences (graphical interface) This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade. . The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. . An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Package: darkice Description-md5: 1912539adeede843fe4a648780292b75 Description-en: Live audio streamer DarkIce is an IceCast, IceCast2 and ShoutCast live audio streamer. It takes audio input from a sound card, encodes it into mp3 and/or Ogg Vorbis, and sends the mp3 stream to one or more IceCast and/or ShoutCast servers, the Ogg Vorbis stream to one or more IceCast2 servers. DarkIce uses lame as a shared object as its mp3 encoder, and the Ogg Vorbis as its Ogg Vorbis encoder. . A legacy SYSV init script is provided for existing configurations. You have to set RUN=yes in /etc/default/darkice to run darkice as a daemon. With modern systems, this is not needed as realtime scheduling is available to normal users. Package: darksnow Description-md5: 2141573fbbeacbd9c89de6914798e19b Description-en: simple graphical user interface to darkice DarkSnow is a graphical interface written in GTK+2 for the darkice live streamer. Package: devede Description-md5: a80b48eb4e84ed4081919926d540e84b Description-en: simple application to create Video DVDs DeVeDe is a program to create video DVDs, suitable for home players, from any number of video files, in any of the formats supported by Mplayer. . It allows the user to create subtitles and even menus. Package: dvd-slideshow Description-md5: 980a2a115f819879a10ed6533ae6f66f Description-en: set of tools to create DVD slideshows with menus DVD Slideshow consists in a set of tools which allows one to create slideshows-style videos from a collection of pictures. This package provides the following programs: * dir2slideshow: Generates a listing of the pictures in a given directory for easy input to dvd-slideshow. * dvd-slideshow: This is the main script. It generates a DVD-compatible MPEG2 video file with audio from a text file input listing of pictures and effects. * dvd-menu: Creates a simple DVD menu with buttons that link to MPEG2 files generated with dvd-slideshow or ones created by the user. * gallery1-to-slideshow: Generates a text file listing of the pictures visible in a given "Gallery" (http://gallery.sourceforge.net) photo album in order to easily pass the information to dvd_slideshow. * jigl2slideshow: Does the same thing as gallery2slideshow, but works on a jigl gallery. Package: eigensoft Description-md5: 2245ac8a80e3acb8bcf1427468278197 Description-en: reduction of population bias for genetic analyses The EIGENSOFT package combines functionality from the group's population genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Package: f2j Description-md5: 166f686ad8732369697da87e1906ecd3 Description-en: Fortran to Java compiler The package contains a Fortran to Java converter, also used to create the libf2j-java package. It converts Fortran file to Java source and class files. Package: fasta3 Description-md5: 0c5f0c74fdf5df990b61c52bee98824e Description-en: tools for searching collections of biological sequences The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . * Protein - Protein-protein FASTA - Protein-protein Smith-Waterman (ssearch) - Global Protein-protein (Needleman-Wunsch) (ggsearch) - Global/Local protein-protein (glsearch) - Protein-protein with unordered peptides (fasts) - Protein-protein with mixed peptide sequences (fastf) . * Nucleotide - Nucleotide-Nucleotide (DNA/RNA fasta) - Ordered Nucleotides vs Nucleotide (fastm) - Un-ordered Nucleotides vs Nucleotide (fasts) . * Translated - Translated DNA (with frameshifts, e.g. ESTs) vs Proteins (fastx/fasty) - Protein vs Translated DNA (with frameshifts) (tfastx/tfasty) - Peptides vs Translated DNA (tfasts) . * Statistical Significance - Protein vs Protein shuffle (prss) - DNA vs DNA shuffle (prss) - Translated DNA vs Protein shuffle (prfx) . * Local Duplications - Local Protein alignments (lalign) - Plot Protein alignment "dot-plot" (plalign) - Local DNA alignments (lalign) - Plot DNA alignment "dot-plot" (plalign) . This software is often used via a web service at the EBI with readily indexed reference databases at http://www.ebi.ac.uk/Tools/fasta/. Package: fasta3-doc Description-md5: d8363a90c1f3049dede1153f13813e53 Description-en: user guide for FASTA tools The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . The use of the package's many binaries and the equally representated conceptual approaches towards sequence analyses are summarised in this PDF. Package: fonts-cns11643-kai Description-md5: ba10a1118a63ddf6a3e4788e30208e6f Description-en: Chinese TrueType font, TW-Kai The CNS 11643 character set (Chinese National Standard 11643), also officially known as the "Chinese Standard Interchange Code", is officially the standard character set of the Republic of China. (In practice, variants of Big5 are de facto standard.) . TW-Kai is released by RDEC, Executive Yuan, ROC. It covers the characters plane 1 to 9 defined by CNS11643. Package: fonts-cns11643-sung Description-md5: 0a0ab68df6c4d455c3b831f8ca434996 Description-en: Chinese TrueType font, TW-Sung The CNS 11643 character set (Chinese National Standard 11643), also officially known as the "Chinese Standard Interchange Code", is officially the standard character set of the Republic of China. . TW-Sung is released by RDEC, Executive Yuan, ROC. It covers the characters plane 1 to 9 defined by CNS11643. Package: fonts-mononoki Description-md5: 06be19e2222ba9b53ec6c87f791c70a0 Description-en: font for programming and code review This package provides a font designed for enhancing the code formatting. . The font has following features * Works on high and low resolution display * Every character is clearly distinguishable from other similar looking characters. Package: gentle Description-md5: 60adf1620c650c216b9ae673b5d248ca Description-en: suite to plan genetic cloning GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. Package: gmap Description-md5: d1daaf58e59d1f735c184407a7d778b3 Description-en: spliced and SNP-tolerant alignment for mRNA and short reads This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA. Package: ipadic Description-md5: eff1ec5477c7b450aa8e1a4494f38faf Description-en: Dictionaries for ChaSen (Binary data) Dictionaries for ChaSen, a morphological analysis system to segment and tokenize Japanese text string. It provides many additional information (pronunciation, semantic information, and others). . It is based on ICOT dictionary. . This package contains architecture dependent binary data. Package: jajuk Description-md5: 19e51f9051264cf8be50536b3ba60b93 Description-en: advanced jukebox and music organizer Jajuk is software that organizes and plays music. Jajuk is designed to be intuitive, fast and provide multiple ways to perform the same operation. It is a fully-featured application geared towards advanced users with very large or scattered music collections. Package: lgeneral Description-md5: d3cd338c86e0144cd187ecea33e57ef8 Description-en: strategy game in the tradition of Panzer General LGeneral is a turn-based strategy game heavily inspired by Panzer General. You play single scenarios or whole campaigns turn by turn against a human player or the AI. . Entrenchment, rugged defense, defensive fire, surprise contacts, surrender, unit supply, weather influence, reinforcements and other implementations contribute to the tactical and strategic depth of the game. . This is the game engine only. LGeneral requires lgeneral-data or lgc-pg, which converts the game data of the original Panzer General game, to function properly. Package: libf2j-java Description-md5: 545bcec4a65e2d974a0e300c0f193fa5 Description-en: Java library port of Fortran numerical libraries The package provides the Java library (APIS) to numerical libraries originally written in Fortran (particularly BLAS and LAPACK). Package: libforms-doc Description-md5: 2d31b9908f0fcc2b4d5add43805bddf9 Description-en: Documentation for the XForms graphical interface library This package contains PDF and HTML documentation for the XForms library. Package: libgxr-dev Description-md5: 759b8733daf913cc5139a97faf41ca06 Description-en: GLib / C wrapper for OpenVR - development headers Development files for the libgxr library. . This package contains the header and development files which are needed for building OpenVR/GLib applications. Package: libjlapack-java Description-md5: 4ea83703e8aa7420f895fb1264b3ddc9 Description-en: LAPACK numerical subroutines translated from their Fortran 77 source The package provides the LAPACK numerical subroutines translated from their subset Fortran 77 source into class files, executable by the Java Virtual Machine (JVM) and for use by Java programmers. . This makes it possible for Java applications or applets, distributed on the World Wide Web to use established legacy numerical code that was originally written in Fortran. The translation is accomplished using a special purpose Fortran-to-Java (source-to-source) compiler. Package: libmtj-java Description-md5: 83d51bf9bf17c051b3fb647b16f73a89 Description-en: Java library for developing numerical applications MTJ is designed to be used as a library for developing numerical applications, both for small and large scale computations. The library is based on BLAS and LAPACK for its dense and structured sparse computations, and on the Templates project for unstructured sparse operations. . MTJ uses the netlib-java project as a backend, which can be set up to use machine-optimised BLAS libraries for improved performance of dense matrix operations, falling back to a pure Java implementation. This ensures perfect portability, while allowing for improved performance in a production environment. Package: libmtj-java-doc Description-md5: 380f48555fc36f4067152bb8caad7db7 Description-en: Java library for developing numerical applications (documentation) MTJ is designed to be used as a library for developing numerical applications, both for small and large scale computations. The library is based on BLAS and LAPACK for its dense and structured sparse computations, and on the Templates project for unstructured sparse operations. . MTJ uses the netlib-java project as a backend, which can be set up to use machine-optimised BLAS libraries for improved performance of dense matrix operations, falling back to a pure Java implementation. This ensures perfect portability, while allowing for improved performance in a production environment. . This package contains the javadoc documentation files. Package: libnetlib-java Description-md5: 65016fe7e4efe90ed5b9d15484c91570 Description-en: collection of mission-critical software components for linear algebra systems Netlib is a collection of mission-critical software components for linear algebra systems (i.e. working with vectors or matrices). . Netlib libraries are written in C, Fortran or optimised assembly code. This package provides a Java translation but it does not take advantage of optimised system libraries. Package: libnucleotidelikelihoodcore0 Description-md5: 2beeba75259cb25079c34eef520b0bde Description-en: implementation of LikelihoodCore for nucleotides used by beast-mcmc BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package provides an implementation of LikelihoodCore for nucleotides that calls native methods for maximum speed. Package: libopenzwave-doc Description-md5: 1391b189d7f13f6d41b4a88932ed605b Description-en: documentation for the openzwave library OpenZWave is an open-source, cross-platform library designed to enable anyone to add support for Z-Wave home-automation devices to their applications, without requiring any in depth knowledge of the Z-Wave protocol. . This package contains documentation. Package: libopenzwave1.5 Description-md5: 6fd563f922d2ce455d13cf7e75020bb2 Description-en: API to use a Z-Wave controller OpenZWave is an open-source, cross-platform library designed to enable anyone to add support for Z-Wave home-automation devices to their applications, without requiring any in depth knowledge of the Z-Wave protocol. . This package contains the library. Package: libopenzwave1.5-dev Description-md5: eb57b245ab8d94734acd74b03f165761 Description-en: header files for the openzwave library OpenZWave is an open-source, cross-platform library designed to enable anyone to add support for Z-Wave home-automation devices to their applications, without requiring any in depth knowledge of the Z-Wave protocol. . This package contains files for developing. Package: libpgplot-perl Description-md5: 0bcad72bb03a82fdbdd15f1eaf307200 Description-en: perl interface to the pgplot plotting library The PGPLOT module provides a perl interface to the pgplot libraries used for plotting and visualizing scientific data. It is particularly popular for plotting astronomical data. Compared to using pgplot from C or FORTRAN, these Perl bindings allow for a faster, more interactive development. Package: libthrust-dev Description-md5: 5c04cf9edc908ae75dc0cc67ca840a33 Description-en: Thrust - Parallel Algorithms Library Thrust is a parallel algorithms library which resembles the C++ Standard Template Library (STL). Thrust's high-level interface greatly enhances programmer productivity while enabling performance portability between GPUs and multicore CPUs. Interoperability with established technologies (such as CUDA, TBB, and OpenMP) facilitates integration with existing software. Package: libxrdesktop-0.13-0 Description-md5: cec400a2918cc041e18e9e052b2b69bb Description-en: XR desktop interaction library library for XR interaction with classical desktop compositors. . This package includes the loader library. Package: libxrdesktop-dev Description-md5: 6115dcd13048c891450d047d79f18a32 Description-en: XR desktop interaction library -- development files library for XR interaction with classical desktop compositors. . This package includes files needed for development. Package: maelstrom Description-md5: c76f02beb9cd36d79668013b8d163109 Description-en: Arcade-style game resembling Asteroids This is a port of the high-resolution "asteroids" style arcade game written by Andrew Welch for the Macintosh. Package: mame-extra Description-md5: 35baa04e70a76083d21e320c835f737b Description-en: Additional files for the Multiple Arcade Machine Emulator (MAME) MAME is a hardware emulator: it faithfully reproduces the behavior of many arcade machines (it is not a simulation). This program is not a game but can directly, through ROM images, run the complete system of these old arcade machines. These ROMs are subject to copyright and it is in most of the cases illegal to use them if you do not own the arcade machine. . This package provides additional data files for the MAME arcade emulator: nplayers.ini -- provide information about multi-player support history.dat -- provides a brief historical overview of each game Package: mp3diags Description-md5: 27a41b67e8f0c1d350bd807507e1bc57 Description-en: find issues in MP3 files and help to solve them MP3 Diags is a GUI-based application that allows end-users to identify issues with their MP3 files, fix some of the issues and make other changes, like adding track information. It also allows user to "look inside" an MP3 file. . Unlike some programs that are designed to deal with a single topic (like fixing VBR headers or adding cover art), MP3 Diags is a one stop solution that identifies more than 50 different issues in MP3 files and provides the means to fix many of them. . Some of the more important issues that are found: . * Broken tags / headers / audio. * Duplicate tags / headers. * Incorrect placement of tags / headers (ID3V2, ID3V1, LAME, Xing, etc). * Low quality audio. * Missing VBR header. * Missing track info / cover art. * Broken track info / cover art. * Missing normalization data. * Character encoding issues (for languages other than English). . Some of the fixes and changes that MP3 Diags can do: . * Adding / fixing track info, including album cover; information can be retrieved from several sources: Internet, clipboard, file name, local files, and (obviously) keyboard. * Correcting files that show incorrect song duration. * Correcting files in which the player cannot seek correctly. * Converting characters for non-English names. * Adding composer name to the artist field, for players that don't handle the composer field. * Renaming files based on their fields. * Changing word case for track info. Package: mp3fs Description-md5: 8f548d5affaa2e87ffd6a47cb0cd77db Description-en: FUSE filesystem for transcoding FLAC to MP3 on the fly MP3FS is a read-only FUSE filesystem which transcodes audio formats (currently FLAC) to MP3 on the fly when opened and read. . It is also a novel alternative to traditional mp3 encoder applications. Users can use their favorite file browser to select the files they want encoded and copy them somewhere. Package: nvpy Description-md5: c44576128342ce7083deace26854b8d0 Description-en: Simplenote-syncing note-taking tool nvpy is a simplenote-syncing note-taking tool inspired by Notational Velocity (and a little bit by nvALT too) on OSX and ResophNotes on Windows. It is significantly uglier, but it is cross-platform. Package: onionshare Description-md5: 63cc3bc204fe484d34a28935c4bdb26d Description-en: Share a file over Tor Hidden Services anonymously and securely OnionShare lets you securely and anonymously share a file of any size with someone. It works by starting a web server, making it accessible as a Tor hidden service, and generating an unguessable URL to access and download the file. It doesn't require setting up a server on the Internet somewhere or using a third party filesharing service. You host the file on your own computer and use a Tor hidden service to make it temporarily accessible over the Internet. The other user just needs to use the Tor Browser and to enter the URL to download the file from you. Package: openlugaru Description-md5: db884766fbb0af653ae84909ccef976a Description-en: transitional package This is a transitional package. It can be safely removed. Package: openlugaru-data Description-md5: 2f95d4eb2927c8374b1eb7d8c9c34a67 Description-en: transitional package - data This is a transitional package for the data. It can be safely removed. Package: openzwave Description-md5: 442706df5b6e40fa2ad015dc3c3b824c Description-en: Sample Program for libopenzwave OpenZWave is an open-source, cross-platform library designed to enable anyone to add support for Z-Wave home-automation devices to their applications, without requiring any in depth knowledge of the Z-Wave protocol. Package: python3-chargebee Description-md5: a6f9c94e445ea3f0d774ca82a07247db Description-en: Python library for integrating with Chargebee (Python 3/API v1) The Python library for integrating with Chargebee Recurring Billing and Subscription Management solution. . Chargebee now supports two API versions - V1 and V2. This library is for the older API version V1. . This package conflicts with python3-chargebee2 which provides the V2 API in the same Python module namespace. . This is the Python 3 version of the package. Package: python3-chargebee2 Description-md5: ba1d1147e3fbeb4e9cd0b06acbd83f02 Description-en: Python library for integrating with Chargebee (Python 3/API v2) The Python library for integrating with Chargebee Recurring Billing and Subscription Management solution. . Chargebee now supports two API versions - V1 and V2. This library is for the newer API version V2. . This package conflicts with python3-chargebee which provides the V1 API in the same Python module namespace. . This is the Python 3 version of the package. Package: python3-django-anymail Description-md5: 0ecb2257b28dea89d0db0037b3a6741a Description-en: Django email backend for multiple ESPs (Python 3) Anymail integrates several transactional email service providers (ESPs) into Django, with a consistent API that lets you use ESP-added features without locking your code to a particular ESP. . It currently fully supports Amazon SES (requires python3-boto3), Mailgun, Mailjet, Postmark, SendinBlue, SendGrid, and SparkPost, and has limited support for Mandrill . Anymail normalizes ESP functionality so it "just works" with Django's built-in `django.core.mail` package. It includes: . * Support for HTML, attachments, extra headers, and other features of Django's built-in email * Extensions that make it easy to use extra ESP functionality, like tags, metadata, and tracking, with code that's portable between ESPs * Simplified inline images for HTML email * Normalized sent-message status and tracking notification, by connecting your ESP's webhooks to Django signals * "Batch transactional" sends using your ESP's merge and template features . This is the Python 3 version of the package. Package: python3-sparkpost Description-md5: c5cd3eb61351c9c9549c69e845f48a6d Description-en: SparkPost Python API client (Python 3) Super-mega-official Python package for using the SparkPost API. . Python and Python-Django integration with SparkPost's email transmission API. . This is the Python 3 version of the package. Package: python3-vertica Description-md5: e4fe2897df4016619c5c391f68a42c8a Description-en: native Python client for the Vertica database (Python 3) HP Vertica is a commercial column-oriented database. . This package provides all the source, examples and documentation you need to easily connect to and interact with Vertica. . This is the Python 3 version of the package. Package: qcomicbook Description-md5: 5e1e59ae80d5250683bcf393eda201bc Description-en: qt viewer for comic book archives (cbr/cbz/cba/cbg/cbb) QComicBook is a viewer for comic book archives containing jpeg/png images, which aims at convenience and simplicity. Features include: automatic decompression, full-screen mode, page scaling, mouse or keyboard navigation etc. . QComicBook for now supports archives: - cbr - rar-compressed - cbz - zip-compressed - cba - ace-compressed - cbg - targzipped - cbb - tarbzip2ped Package: r-cran-surveillance Description-md5: 3206ab392e2d1549a03174efb7d99d18 Description-en: GNU R package for the Modeling and Monitoring of Epidemic Phenomena Implementation of statistical methods for the modeling and change-point detection in time series of counts, proportions and categorical data, as well as for the modeling of continuous-time epidemic phenomena, e.g., discrete-space setups such as the spatially enriched Susceptible-Exposed- Infectious-Recovered (SEIR) models, or continuous-space point process data such as the occurrence of infectious diseases. Main focus is on outbreak detection in count data time series originating from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics or social sciences. . Currently, the package contains implementations of many typical outbreak detection procedures such as Farrington et al (1996), Noufaily et al (2012) or the negative binomial LR-CUSUM method described in Höhle and Paul (2008). A novel CUSUM approach combining logistic and multinomial logistic modelling is also included. Furthermore, inference methods for the retrospective infectious disease models in Held et al (2005), Held et al (2006), Paul et al (2008), Paul and Held (2011), Held and Paul (2012), and Meyer and Held (2014) are provided. . Continuous self-exciting spatio-temporal point processes are modeled through additive-multiplicative conditional intensities as described in Höhle (2009) ('twinSIR', discrete space) and Meyer et al (2012) ('twinstim', continuous space). . The package contains several real-world data sets, the ability to simulate outbreak data, visualize the results of the monitoring in temporal, spatial or spatio-temporal fashion. . Note: Using the 'boda' algorithm requires the 'INLA' package, which is available from . Package: raster3d Description-md5: 7017e40afb8a84c7aca1cff9519d06ba Description-en: tools for generating images of proteins or other molecules Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel. Package: raster3d-doc Description-md5: c1fa8477bbb4f0ad2b3ab28130533382 Description-en: documents and example files for Raster3D Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel. . This package contains documents and example files for the raster3d package. Package: seaview Description-md5: 6956ccec0b723eeec1ee5d454b5a86f8 Description-en: Multiplatform interface for sequence alignment and phylogeny SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. Alignments can be manually edited. It drives the programs Muscle or Clustal Omega for multiple sequence alignment, and also allows one to use any external alignment algorithm able to read and write FASTA-formatted files. It computes phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or by maximum likelihood using the program PhyML 3.0. SeaView draws phylogenetic trees on screen or PostScript files, and allows one to download sequences from EMBL/GenBank/UniProt using the Internet. Package: spread-phy Description-md5: 3adb36b53159c17b4ca86e0ba4d0f573 Description-en: analyze and visualize phylogeographic reconstructions SPREAD is a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion. . There is a tutorial for SPREAD online at http://www.kuleuven.be/aidslab/ph ylogeography/tutorial/spread_tutorial.html . Originally this program is named "spread". However, there is just such a package inside Debian and thus a 'phy' for phylogeny was prepended. Package: svtools Description-md5: 0e1af3ce7283b30f537bf151c85ac7d0 Description-en: Utilities for daemontools and multilog This package provides some useful utilities to maintain supervised services and to handle multilog log files: . svdir: Find daemontools service directory. svinfo: Get infos about a supervised process. svinitd: init.d weapper for daemontools services. svinitd-create: Create an init.d-script for a supervices process. svsetup: Service setup tool for daemontools. mlcat: cat frontend for multilog files. mlhead: head frontend for multilog files. mltail: tail frontend for multilog files. Package: tiemu Description-md5: 1102e21f878c7b4ba0911b7e6e5634f0 Description-en: Texas Instruments calculators emulator (without GDB) TiEmu emulates Texas Instruments calculators TI-89/92/92+/V200PLT. . It is based on XTiger, the original TI emulator for Linux, which uses the 68k emulation core from UAE (The Ultimate Amiga Emulator). . You need to either dump the ROM of your calculator (you can do so with TiLP), or get a FLASH upgrade from Texas Instrument (see the software section concerning your calculator, then download the archive and extract the file) to use this emulator. There are *no* TI ROMs provided in this package, as they are copyrighted by Texas Instruments, Inc. . However, a free (as in speech) ROM is now provided with TiEmu, namely PedRom. Try it out! . This version includes a VTI-style assembly debugger. . Please note it exists another version (tiemu-gdb) not provided on Debian itself which includes a GDB-style assembly debugger for use with TIGCC and/or KTIGCC. Package: treeview Description-md5: ba1871fdfc7832e4ff41cecdd4a32563 Description-en: Java re-implementation of Michael Eisen's TreeView TreeView creates a matrix-like display of expression data, known as Eisen clustering. The original implementation was a Windows program named TreeView by Michael Eisen. This TreeView package, sometimes also referred to as jTreeView, was rewritten in Java under a free license. . Java TreeView is an extensible viewer for microarray data in PCL or CDT format. Package: videotrans Description-md5: e1f89ca2dddfd4e1fb8361b8e9ee4150 Description-en: DVD authoring utilities A collection of utilities and scripts designed to help with DVD authoring: * movie-to-dvd - convert video to MPEG2 + MP2 or AC3 * movie-title - combine video and title sequence into a menu * movie-make-title - create background video for DVD menu * movie-make-title-simple - create background image+audio for DVD menu * movie-rip-tv.com - gather information about TV series from tv.com * movie-rip-epg.data - convert EPG to .info for movie-title * movie-compare-dvd - verify if DVD was burned correctly Package: weirdx Description-md5: efd18efb16cda856c70bd010ee0ab87c Description-en: X server in Java A complete X server implementation in Java which can run standalone or as an applet. It supports remote X and (using libjsch-java) X forwarded over SSH. . Also includes a library for embedding WeirdX in other Java programs or Applets. Package: xsnow Description-md5: 50f83ae2081d9d64cb36576ded637c7a Description-en: brings Christmas to your desktop Xsnow is a X Window application that will snow on the desktop background. Santa and his reindeer will complete your festive-season feeling. Xsnow runs in GNOME, KDE, FVWM and desktops that are derived from those.