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: afio Description-md5: ca88467cccd23b8f150ff01185566a6c Description-en: archive file manipulation program Afio manipulates groups of files, copying them within or between filesystems and an afio archive. . Afio archives are portable as they contain only ASCII-formatted header information. Afio makes cpio-format archives. Afio deals somewhat gracefully with input data corruption. Afio supports multi-volume archives during interactive operation. Afio can make compressed archives that are much safer than compressed tar or cpio archives. . Afio is best used as an `archive engine' in a backup script. 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: brain2mesh-demos Description-md5: e9f024807779a12817de357606f053ea Description-en: sample files and demo scripts for Brain2Mesh This package contains sample JNIfTI sample data and meshing script to demonstrate the basic functionalities of the Brain2Mesh Toolbox. 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: 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: d72252cb79d6984abc60544ef6e91af5 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: 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: 008f9d9e702bd6987f254cc2cff6d5dd 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-ibm-plex Description-md5: 487af0a2145ab95bafd9ec231ff04447 Description-en: extensive typeface family designed by IBM IBM Plex is an extensive font family developed by IBM. It comes in four subfamilies (Sans, Sans Condensed, Mono and Serif) and 8 weights (Thin, Extralight, Light, Regular, Text, Medium, Semibold, Bold), with true italics to complement them. A variable-weight counterpart of IBM Plex Sans is also available. . The four basic subfamilies support most of the languages using the Latin alphabet (including Vietnamese), the Cyrillic writing system and monotonic Greek. Hebrew (including cantillation marks), Thai (both looped and loopless), Devanagari and Arabic are supported as separate typefaces. . There is also support for common mathematical and currency symbols as well as ligatures and stylistic alternates. . This package contains the TrueType (CFF) flavored OpenType fonts and the WOFF/WOFF2 web fonts. Package: gentle Description-md5: 8be9c34902838801e85217c491d8f282 Description-en: suite for molecular cloning and sequence analysis GENtle is an open-source tool designed to facilitate molecular cloning, DNA/RNA sequence analysis, and plasmid design. It provides an intuitive graphical interface for visualizing and editing nucleotide sequences, creating and managing cloning projects, and simulating restriction digests. GENtle supports multiple formats for sequence import/export and includes features for primer design, sequence alignment, and annotation, sequencer data import, calculators, gel image display, PCR, and much more. Package: ifeffit Description-md5: 910f116c8e14fa8d361b031b45896347 Description-en: Interactive XAFS analysis program IFEFFIT is an interactive program for XAFS analysis. It combines the high- quality analysis algorithms of AUTOBK and FEFFIT with graphical display of XAFS data and general data manipulation. . IFEFFIT comes as a command-line program, but the underlying functionality is available as a programming library. The IFEFFIT library can be used from C, Fortran, Tcl, and Perl. Package: ifeffit-doc Description-md5: 23588aa725d1361238e782379bbed9bc Description-en: IFEFFIT examples and documentation This package contains all the available documentation for IFEFFIT and its component programs. Example files for EXAFS data analysis are also provided as tutorials. 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: iso2mesh-demos Description-md5: 90b91382c05547d48c75972da0d46964 Description-en: sample files and demo scripts for Iso2Mesh toolbox This package contains sample meshing script and data files for testing and showcasing Iso2Mesh functions. The main functions demonstrated in this package include surface-based mesh generation via s2m/surf2mesh, volume- based mesh generation via v2m/vol2mesh, mesh smoothing (sms), boolean operations (surfboolean), downsampling (meshsample) and remeshing (remeshsurf). Package: iso2mesh-tools Description-md5: 3b89ffbe6b8b0aee8bbafebce5518870 Description-en: 3D mesh generation and repairing utilities This package contains 3D mesh generation and repairing tools that can be used independently and invoked inside iso2mesh. . These tools include cgalmesh (3D mesh generation from volumetric images), `cgalpoly` (3D mesh generation from polyhedral surfaces), `cgalsimp2` (triangular surface simplification), `meshfix` (3D surface cleaning and repairing), and `jmeshlib` (3D surface cleaning). Package: jhove Description-md5: febe0cb6a55fdf2af5baf3d3965883ac Description-en: JSTOR/Harvard Object Validation Environment Perform format-specific identification, validation, and characterization of digital objects. Package: jnifti-demos Description-md5: 7445791185a3b5db029339474eb2fce6 Description-en: sample files and demo scripts for JNIfTI toolbox This package contains sample NIfTI-1/2 data files as well as text and binary JNIfTI files. Package: ldraw-mklist Description-md5: 7f0b36129c83247e98ea1e2416fd0862 Description-en: LDraw mklist program 3D CAD programs and rendering programs using the LDraw parts library of LEGO parts rely on a file called parts.lst containing a list of all available parts. The program ldraw-mklist is used to generate this list from a directory of LDraw parts. 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: libamgcl-dev Description-md5: ec65c5ece2e2ac48e9fba2a354789071 Description-en: Solves large sparse linear systems with algebraic multigrid method AMG is one of the most effective iterative methods for solution of equation systems arising, for example, from discretizing PDEs on unstructured grids. The method can be used as a black-box solver for various computational problems, since it does not require any information about the underlying geometry. AMG is often used not as a standalone solver but as a preconditioner within an iterative solver (e.g. Conjugate Gradients, BiCGStab, or GMRES). . AMGCL builds the AMG hierarchy on a CPU and then transfers it to one of the provided backends. This allows for transparent acceleration of the solution phase with help of OpenCL, CUDA, or OpenMP technologies. Users may provide their own backends which enables tight integration between AMGCL and the user code. . AMG is a header-only C++ library, with the headers provided by this package. 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: 590651c9a4c18a23907183a8e45c2fe6 Description-en: Documentation for the XForms graphical interface library This package contains PDF and HTML documentation for the XForms library. . XForms is a GUI toolkit based on Xlib for X Window Systems. It features a rich set of objects, such as buttons, scrollbars, and menus etc. integrated into an easy and efficient object/event callback execution model that allows fast and easy construction of X-applications. In addition, the library is extensible and new objects can easily be created and added to the library. Package: libifeffit-perl Description-md5: e6edcbfcf9214ca2748ec5d9024356e5 Description-en: Perl extensions for IFEFFIT IFEFFIT is an interactive program for XAFS analysis. It combines the high- quality analysis algorithms of AUTOBK and FEFFIT with graphical display of XAFS data and general data manipulation. . This package provides an interface to IFEFFIT from Perl. 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: libopenzwave1.6-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: libopenzwave1.6t64 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: libprimus-vk1 Description-md5: 9cc616059b790cb11afff2f1a5f393d2 Description-en: vulkan layer library for the primus-vk layer This library implements the primus-vk layer. It decides which GPU the individual Vulkan API calls should go against and does the image copying. Package: llm Description-md5: a2fcaf5b441d6324ee1b96a3e87cf59a Description-en: CLI utility and Python library for interacting with Large Language Models A CLI utility and Python library for interacting with Large Language Models, both via remote APIs and models that can be installed and run on your own machine. . This allows users to interact with various language models. Its primary target is obviously the OpenAI API, but it also supports local models like Llama 2, Ollama, and MLC, and other online models like Claude, GEmini and Mistral. Package: mame-extra Description-md5: 61c8a776b23245377e3a697ae118ac3d 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: matlab-iso2mesh Description-md5: 70c13d5376ac1a8d098638a8deed9e4e Description-en: 3D surface and volumetric mesh generator for MATLAB Iso2Mesh is a MATLAB/Octave-based mesh generation toolbox, designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, working either independently or interacting with external free meshing utilities. Iso2Mesh toolbox can directly convert a 3D image stack, including binary, segmented or gray-scale images such as MRI or CT scans, into quality volumetric meshes. This makes it particularly suitable for multi-modality medical imaging data analysis and multi-physics modeling. Iso2Mesh is cross-platform and is compatible with both MATLAB and GNU Octave. . This package contains the MATLAB support for iso2mesh. Package: mp3diags Description-md5: 16800a1a67b245d0fda22211b5a3e69a 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: notion Description-md5: 09e7f6a1881d70d8ecd78d22041a49b7 Description-en: tiling tabbed window manager designed for keyboard users Notion divides the screen into tiles and places windows in these tiles by default. Each tile has a set of tabs for the windows within it. It also allows windows to be made 'floating' and placed freely. Notion can be controlled through the keyboard alone or together with a mouse. . Notion can be configured and extended using the Lua language. It also supports extension modules written in C. Package: notion-dev Description-md5: cc63e31ab5c2f3d12f04e0160cfd72ff Description-en: Notion development files Notion divides the screen into tiles and places windows in these tiles by default. Each tile has a set of tabs for the windows within it. It also allows windows to be made 'floating' and placed freely. Notion can be controlled through the keyboard alone or together with a mouse. . This package contains the files necessary for building extension modules to the Notion window manager 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: nvtop Description-md5: 0beb511f9e4ada1ca897f74ecf2e2072 Description-en: Neat Videocard TOP NVTOP stands for Neat Videocard TOP, a (h)top like task monitor for AMD, Intel and NVIDIA GPUs. It can handle multiple GPUs and print information about them in a htop-familiar way. Package: octave-brain2mesh Description-md5: 63af1c41e2154d307ea77a403e3ba7f9 Description-en: automated brain tetrahedral mesh generation toolbox for Octave The Brain2Mesh toolbox provides a streamlined matlab function to convert a segmented brain volumes and surfaces into a high-quality multi-layered tetrahedral brain/full head mesh. Typical inputs include segmentation outputs from SPM, FreeSurfer, FSL etc. This tool does not handle the segmentation of MRI scans, but examples of how commonly encountered segmented datasets can be used to create meshes can be found in the package named brain2mesh-demos. Package: octave-iso2mesh Description-md5: ce676342413ec36338c3beea8b44f3e9 Description-en: 3D surface and volumetric mesh generator for Octave Iso2Mesh is a MATLAB/Octave-based mesh generation toolbox, designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, working either independently or interacting with external free meshing utilities. Iso2Mesh toolbox can directly convert a 3D image stack, including binary, segmented or gray-scale images such as MRI or CT scans, into quality volumetric meshes. This makes it particularly suitable for multi-modality medical imaging data analysis and multi-physics modeling. Iso2Mesh is cross-platform and is compatible with both MATLAB and GNU Octave. . This package contains the Octave support for iso2mesh. Package: octave-jnifti Description-md5: af5a7cdee58d2facd39837138556d1d6 Description-en: fast NIfTI-1/2 reader and NIfTI-to-JNIfTI converter This is a fully functional NIfTI-1/2 reader/writer that supports both MATLAB and GNU Octave, and is capable of reading/writing both non- compressed and compressed NIfTI files (.nii, .nii.gz) as well as two-part Analyze7.5/NIfTI files. . More importantly, this is a toolbox that converts NIfTI data to its JSON- based replacement, JNIfTI (.jnii for text-based and .bnii for binary- based), defined by the JNIfTI specification http://github.com/fangq/jnifti. JNIfTI is a much more flexible, human- readable and extensible file format compared to the more rigid and opaque NIfTI format, making the data much easier to manipulate and share. Package: openttd-opensfx Description-md5: 107eb65077f6c64d7c21a0c757480def Description-en: sound set for use with the OpenTTD game OpenSFX is a replacement for the original TTD (Transport Tycoon Deluxe) base sounds used by OpenTTD, distributed under a restrictive license. The main goal of OpenSFX therefore is to provide a set of sounds, available free of charge, which make it possible to play OpenTTD without requiring the user to pay for the original Transport Tycoon Deluxe game for its sound set. 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: primus-vk Description-md5: f31384e21e05aff86907e8c0495ecc4f Description-en: Vulkan layer for GPU offloading Typically you want to display an image rendered on a more powerful GPU on a display managed by an internal GPU. The layer in this package will direct rendering commands to a dedicated, more powerful GPU an when such an image is displayed it will be copied to the integrated CPU for displaying. . The user can activate offloading for individual applications by launching them with the "pvkrun" program. Package: python3-amgcl Description-md5: ecbb9c7c4315244c6b65581f6b220a1f Description-en: Solves large sparse linear systems with algebraic multigrid method AMG is one of the most effective iterative methods for solution of equation systems arising, for example, from discretizing PDEs on unstructured grids. The method can be used as a black-box solver for various computational problems, since it does not require any information about the underlying geometry. AMG is often used not as a standalone solver but as a preconditioner within an iterative solver (e.g. Conjugate Gradients, BiCGStab, or GMRES). . AMGCL builds the AMG hierarchy on a CPU and then transfers it to one of the provided backends. This allows for transparent acceleration of the solution phase with help of OpenCL, CUDA, or OpenMP technologies. Users may provide their own backends which enables tight integration between AMGCL and the user code. . This package provides the Python interface Package: python3-django-anymail Description-md5: 71574dff1b20374349634eb78eb46791 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), MailerSend, Mailgun, Mailjet, Mandrill (MailChimp transactional), Postal (self-hosted ESP, requires python3-cryptography), Postmark, SendinBlue, SendGrid, and SparkPost. . 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-llm-anthropic Description-md5: b1d64f62457680b144d1d1f4dcb809ba Description-en: LLM access to models by Anthropic, including the Claude series This is a plugin for the llm command that provides access to the large language models provided by Anthropoic, like Claude, Sonnet, etc. Package: python3-pyvkfft-cuda Description-md5: 57ea98ebe636a6b0393437bac86d8b5e Description-en: Binding to the CUDA backends of VkFFT - Python3 pyvkfft offers a simple python interface to the CUDA and OpenCL backends of VkFFT, compatible with pyCUDA, CuPy and pyOpenCL. . This package installs the CUDA backend. Package: python3-sparkpost Description-md5: 1337738f2301f622817dd90a4362c9a4 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. 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: 46e64c1847bcc09b85d7cb58e07f3ef1 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: 028949954f0ca7a5c48fdc6b9eabf37e Description-en: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) . A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) . For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) and Meyer and Held (2014) . twinSIR() models the susceptible-infectious- recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) . twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) . A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) . 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: reform-handbook Description-md5: d2b5fc03c4b1e694346af7f4991d28f8 Description-en: MNT Reform Operator Handbook The HTML and PDF version of the operator handbook for the MNT Reform open hardware laptop. It contains topics like: . * Linux basics (terminal, shell, filesystem, managing software with apt) * the graphical desktops sway and wayfire with waybar * MNT Reform specific software and scripts * the hardware (case, motherboard, processor modules, keyboard, trackball, trackpad, battery packs) * advanced topics (serial via uart, u-boot) - hardware schematics and bill of materials Package: ruby-pgplot Description-md5: cf08efc3d00267462ecffbd245d9bf82 Description-en: Ruby interface to the PGPLOT graphics library Ruby/PGPLOT is the Ruby interface to the PGPLOT graphics library. PGPLOT is a FORTRAN library to draw line/scatter/histogram plot, error bar, contour/image/vector map, etc. Supports various output devices including Postscript, PNG, X-Window, etc. Package: seaview Description-md5: a82e7d5dbc9d5aa2cf6662e48d7aa245 Description-en: Multiplatform interface for sequence alignment and phylogeny SeaView is a viewer and editor of multiple sequence alignments, i.e. DNA or protein sequences are positioned each in their own separate line, such that the nucleotide/amino acid at a particular position (column) is presumed to have the same biochemical property. . 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: steam-devices Description-md5: c6f7755a92af38b81ec981d94314c124 Description-en: Device support for Steam-related hardware Installing this package configures udev to allow logged-in local users to access various gaming-related hardware devices, such as: . - Valve devices such as the Steam Controller and Steam Deck - Microsoft Xbox gamepads (Xbox 360 or newer) - Sony Playstation gamepads (Playstation 3 or newer) - Nintendo Switch gamepads - third-party "clone" gamepads compatible with those devices - virtual reality and XR peripherals such as the HTC Vive . It also allows input device emulation via /dev/uinput, which is required by some Steam features such as Steam Input and Steam Remote Play. . These udev rules represent a trade-off between functionality and security, and this package should not be installed on systems that are expected to have malicious local users. The security risks and mitigations are discussed in more detail in . Package: svtools Description-md5: b7a54428f60e646164c05acb6574152b Description-en: utilities for daemontools and multilog This package provides some convenient utilities to handle multilog log files and maintain supervised services: . mlcat - output concatenated multilog files; mlhead - output the first part of multilog files; mltail - output the last part of multilog files; svdir - find the daemontools service directory; svinfo - get information about a supervised process; svinitd - wrap init.d commands for daemontools services; svinitd-create - create an init.d script for a supervised process; svsetup - set up a service for daemontools. Package: tightvnc-java Description-md5: 40a38acc917ddb191772cd544459f689 Description-en: TightVNC java applet and command line program VNC stands for Virtual Network Computing. It is, in essence, a remote display system which allows you to view a computing `desktop' environment not only on the machine where it is running, but from anywhere on the Internet and from a wide variety of machine architectures. . This is the vnc java applet file that the tightvncserver can distribute to the client. In addition a command line program that starts the java based vnc viewer locally is included. 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: ugene Description-md5: 9a10717d68a69dfaff1354fa2282b503 Description-en: integrated bioinformatics toolkit Unipro UGENE is a cross-platform visual environment for DNA and protein sequence analysis. UGENE integrates the most important bioinformatics computational algorithms and provides an easy-to-use GUI for performing complex analysis of the genomic data. One of the main features of UGENE is a designer for custom bioinformatics workflows. Package: ugene-data Description-md5: a0c0756b3f7b317ece195fedee3dde50 Description-en: required data for UGENE - integrated bioinformatics toolkit Unipro UGENE is a cross-platform visual environment for DNA and protein sequence analysis. . This package contains various data and example files for UGENE. Package: videotrans Description-md5: 811c3c615baaa5fcb4270a865d32a1c6 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: wdq2wav Description-md5: bb5df72836bb6620b3380cb6182d33a7 Description-en: Converts a WinDAQ channel to sound .wav file This program extracts a channel from a WinDAQ file and produces a .wav file that can be played. This is helpful when recording a chatter channel for a WinDAQ session with multiple A/D channels. 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.