Submitting Jobs Documentation
Software Documentation
The following software is reported as available on Anvil Notebook by the Software Documentation Service.
Available Software
| Application | Description | Research Discipline |
|---|---|---|
| amber | Amber is a suite of highly extensible molecular simulation programs. It is designed for simulations of biomolecules such as proteins, nucleic acids, and carbohydrates, and can also be used for small molecules. | Biological Sciences |
| ambertools | AmberTools is a suite of software for molecular dynamics simulations, energy minimization, and trajectory analysis in the field of computational chemistry. It provides tools for the refinement and analysis of biomolecular structures. | Biological Sciences |
| amd uprof | AMD uProf is a performance analysis tool that provides insights into CPU and memory usage for applications running on AMD processors. It helps developers optimize their code for better performance. | Computer Science |
| amdblis | Amdblis is a computational software for analyzing and visualizing single-molecule data, particularly for biophysical studies. | Biological Sciences |
| amdfftw | An AMD optimized version of FFTW. FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. Description Source: https://www.fftw.org/ | |
| amdlibflame | AMD LIBFLAME is an open-source software library that provides a high-performance implementation of the dense linear algebra routines on CPUs. It aims to offer efficient and robust algebraic computations for numerical linear algebra applications. | Computer & Information Sciences |
| amdlibm | AMDlibm is a software library provided by AMD that offers mathematical functions specifically optimized for high performance on AMD processors. It provides a collection of mathematical functions designed to exploit the advanced features of AMD processors for enhanced numerical computation. | Engineering & Technology |
| amdscalapack | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. | |
| anaconda | Anaconda is a free and open-source distribution of Python and R programming languages for scientific computing, that aims to simplify package management and deployment. | Computer and Information Sciences |
| aocc | The AMD Optimizing C/C++ Compiler (AOCC) is a high performance compiler suite with support for C, C++, and Fortran programming languages. | Computer & Information Sciences |
| arpack-ng | ARPACK (ARnoldi PACKage) is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The ARPACK-ng project is a re-implementation of the original ARPACK with the goal of improving its usability, maintainability, and performance across a wide range of modern hardware platforms. | Physical Sciences |
| aws-cli tool | The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts. | Computer Science |
| bamtools | BamTools is a software toolkit for manipulating BAM (Binary Alignment Map) files. It provides both a C++ API for BAM file input and output, and a command-line tool for performing various operations on BAM files. | Biological Sciences |
| beagle | Beagle is a high-performance software library for phylogenetic inference using maximum likelihood methods. It can be used for reconstructing large phylogenetic trees from molecular sequence data with high efficiency and accuracy. | Biological Sciences |
| beast2 | BEAST2 is a cross-platform program for Bayesian evolutionary analysis of molecular sequences. It is widely used for estimating species trees, gene trees, divergence times, substitution rates, and demographic parameters using various models of sequence evolution. | Biological Sciences |
| berkeley-db | Berkeley DB is a high-performance database library that provides developers with a variety of data management capabilities, including support for key/value pairs, transactions, and concurrency control. | Computer Science |
| biocontainers | BioContainers is a project that provides bioinformatics tools and workflows in a containerized format, making it easier to package, distribute, and run bioinformatics software in a reproducible manner. | Biological Sciences |
| bismark | Bismark is a software tool specifically designed for aligning bisulfite treated DNA sequencing reads and methylation calls. It is widely used in epigenetics research to analyze DNA methylation patterns. | Biological Sciences |
| blast-plus | BLAST+ is a suite of programs designed to allow researchers to compare nucleotide or protein sequences to sequence databases and identify similarities. | Genomics |
| blis | BLAS (Basic Linear Algebra Subprograms) implemented in native C and suitable for high-performance implementations. BLIS is capable of achieving high levels of performance on various architectures. | Computer & Information Sciences |
| boost | Boost is a set of C++ libraries that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It aims to extend the functionality of C++ programming language and make it more efficient and powerful. | Computer & Information Sciences |
| bowtie2 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly well-suited for aligning sequencing reads of DNA sequences, such as those generated by high-throughput sequencing technologies. | Biological Sciences |
| bwa | Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW, and BWA-MEM. The BWA-backtrack algorithm is designed for Illumina sequence reads up to 100bp, while BWA-SW and BWA-MEM are for longer Illumina reads, including 100bp reads produced by the HiSeq 2000 platform. | Biological Sciences |
| bzip2 | bzip2 is a free and open-source file compression program that uses the Burrows-Wheeler algorithm for compression and Huffman coding for decompression. It is designed to be fast and efficient in compressing large files while retaining a high compression ratio. | Computer & Information Sciences |
| cairo | Cairo is a 2D graphics library with support for multiple output devices. It provides a vector-based rendering engine for high-quality graphics with full support for transparency and anti-aliasing. | Computer & Information Sciences |
| cdo | Climate Data Operators (CDO) is a collection of command-line operators for manipulating and analyzing climate and numerical weather prediction (NWP) model data. | Earth & Environmental Sciences |
| clusterbot | ||
| cmake | CMake is an open-source, cross-platform family of tools designed to build, test, and package software. It is used to control the software compilation process using simple platform and compiler-independent configuration files. | Engineering & Technology |
| conda | Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. It is designed to quickly install, run, and update packages and their dependencies. | Computer Science |
| cp2k | CP2K is an open-source quantum chemistry and solid state physics software package designed to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It can be used to study a wide range of properties, including electronic structures, molecular dynamics, and vibrational spectra. | Physical Sciences |
| cue-login-env | Cue-login-env is a Python library that provides an easy way to configure user-specific environments within shared servers or computing clusters. It helps users manage their environment variables, aliases, and paths without interfering with the system-wide configurations. | Computer & Information Sciences |
| cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. | Biological Sciences |
| curl | curl is a command-line tool and library for transferring data with URLs. It supports various protocols including HTTP, HTTPS, FTP, FTPS, SCP, SFTP, and more. It is widely used in scripting and automation tasks, as well as for debugging network issues. | Computer & Information Sciences, Other Computer & Information Sciences |
| duckdb | DuckDB is an in-process SQL OLAP database management system designed for analytical query workloads. It is optimized for fast query execution and supports a wide variety of data formats. | Computer Science |
| eigen | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | Computer & Information Sciences |
| emacs | Emacs is a highly customizable, extensible, and self-documenting text editor. It is known for its powerful editing capabilities, which include content-aware editing, syntax highlighting, and a wide range of plugins and extensions. | Computer & Information Sciences |
| expat | Expat is an XML parser library written in C. It is a fast and lightweight library that is designed for high-performance applications. | Computer & Information Sciences |
| fastqc | FastQC is a quality control tool for high throughput sequence data. It provides a detailed overview of the quality and potential issues in sequencing data generated by high throughput sequencing pipelines. | Biological Sciences |
| fasttree | FastTree is a tool for inferring approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a few thousand sequences and has been designed to make trees with the minimum scale up to 100,000 sequences faster by approximating maximum-likelihood with heuristics. | Biological Sciences |
| fastx-toolkit | The fastx-toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. The tools simplify and streamline various tasks related to quality control, adapter trimming, and format conversion of next-generation sequencing data. | Biological Sciences |
| ffmpeg | FFmpeg is a free and open-source software project consisting of a large suite of libraries and programs for handling video, audio, and other multimedia files and streams. | Computer Science |
| fftw | FFTW is a fast C library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is widely used in areas such as signal processing, data compression, and solving partial differential equations. | Mathematics |
| font-util | font-util is a command-line utility for inspecting and manipulating font files. It provides tools to list font metadata, convert font formats, subset fonts, and perform various font-related operations useful for developers and typographers. | Software Engineering, Systems, and Development |
| fontconfig | Fontconfig is a library designed to provide system-wide font configuration, customization, and management for user interfaces and text display on Linux and other Unix-like operating systems. It allows applications to discover and access fonts, and provides settings for font selection, aliasing, subsetting, and caching. | Engineering & Technology |
| freetype | FreeType is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in various applications that require text rendering, such as operating systems, web browsers, desktop publishing tools, and more. | Computer & Information Sciences |
| gatk | The Genome Analysis Toolkit (GATK) is a widely used software package for variant discovery and genotyping analysis in high-throughput sequencing data. Developed by the Broad Institute, GATK provides a robust and comprehensive set of tools for processing raw sequencing data into accurate variant calls. | Biological Sciences |
| gcc | GNU Compiler Collection (GCC) is a free and open-source compiler system that supports various programming languages and platforms. It is widely used for compiling high-level programming languages into executable code for a variety of computer architectures. | Computer Science |
| gdal | GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license. It is a collection of geospatial data manipulation libraries that support raster and vector data formats, and includes protocols to access geospatial data sources. | Earth & Environmental Sciences, Engineering & Technology |
| gdb | GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes or what another program was doing at the moment it crashed. | Computer & Information Sciences |
| gdbm | GNU dbm (GDBM) is a library that provides an abstraction for a simple database manager. It allows for the creation and manipulation of key/value pairs in a persistent database, with support for fast lookup, retrieval, insertion, and deletion operations. | Computer & Information Sciences |
| geos | Geos is an open-source geometry engine that provides C++ software libraries and tools for processing spatial data. It is a key component of the PostGIS spatial database extender and is used in various GIS software applications. | Computer & Information Sciences |
| gettext | GNU gettext is a package providing a framework for internationalization and localization of software. It includes tools for extracting translatable strings from source code, for generating message catalogs (pot files), and for translating the strings into different languages. | Computer & Information Sciences |
| gfms | Generalized Finite Element Method Software for structural mechanics simulations. Load this first to make GFMs application modules available. | |
| ghostscript | Ghostscript is a versatile software suite for viewing, converting, and printing PostScript and PDF files. It is widely used for rasterizing files for high-quality printing and viewing on a variety of devices. | Computer & Information Sciences, Engineering & Technology |
| glib | GLib is a general-purpose utility library for the C programming language. It provides data structure handling for lists, trees, hashes, memory allocation, and other commonly needed functionality. | Computer & Information Sciences |
| gmp | The GNU Multiple Precision Arithmetic Library (GMP) is a free library for arbitrary-precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. | Mathematics |
| gmt | The Generic Mapping Tools (GMT) is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots through contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports over 40 map projections and transformations and comes with support data such as coastlines, rivers, and political boundaries. | Earth & Environmental Sciences |
| gnuplot | Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. It is capable of producing interactive plots and supports various output formats. | Physical Sciences |
| grads | GrADS (Grid Analysis and Display System) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. It is particularly popular in meteorology and climatology for analyzing and plotting meteorological data. | Earth & Environmental Sciences |
| gromacs | GROMACS (GROningen MAssive Parallel MD for Molecular Dynamics) is a versatile package for molecular dynamics simulations with a strong emphasis on high-performance computing capabilities. | Biological Sciences |
| gsl | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It provides a wide range of mathematical routines such as special functions, linear algebra, interpolation, numerical integration, random numbers, and more. | Other Mathematics |
| gstreamer | GStreamer is a multimedia framework that allows the construction of graphs of media-handling components, ranging from simple Ogg/Vorbis playback to complex audio (mixing) and video (non-linear editing) processing. It is designed to be easily extended with new plugins that provide new functionality. | Computer & Information Sciences |
| gurobi | Gurobi Optimization is a high-performance mathematical programming solver for linear programming (LP), mixed-integer programming (MIP), and other related optimization problems. | Mathematics |
| hadoop | Hadoop is an open-source framework used for distributed storage and processing of large sets of data on computer clusters using simple programming models. | Computer & Information Sciences |
| hdf | HDF (Hierarchical Data Format) is a flexible and extensible file format for storing and managing large amounts of data. It supports various data types, attributes, and metadata, making it suitable for a wide range of scientific and engineering applications. | Other Computer & Information Sciences |
| hdf5 | HDF5 (Hierarchical Data Format version 5) is a file format and a suite of tools developed by the HDF Group for managing and storing large and complex data. It is designed to store and organize large amounts of data efficiently, enabling fast data access and sharing. | Computer Science |
| hpctoolkit | HPCToolkit is a performance analysis tool for high-performance computing applications. It provides a comprehensive suite of tools for profiling, tracing, and analyzing the performance of parallel applications. | Computer Science |
| hwloc | hwloc, the Portable Hardware Locality (hwloc), is an open-source hierarchical machine topology library used to provide abstract representation of the hierarchical topology of modern architectures. | Computer & Information Sciences |
| hypershell | hypershell is a cross-platform, high-throughput computing utility designed to process shell commands over a distributed, asynchronous queue. It enables scalable, parallel execution of shell tasks with support for distributed environments, facilitating efficient workload management and execution. | Computer Science |
| impi | impi is a high-performance message passing library that provides asynchronous messaging and queuing functionalities for parallel computing applications. | Engineering & Technology |
| intel-mkl | Intel Math Kernel Library (MKL) is a library of optimized math routines for science, engineering, and financial applications. | Numerical Analysis |
| intel-parallel-studio | Intel Parallel Studio is a suite of development tools for creating high-performance applications. It includes compilers, libraries, and performance analysis tools to optimize code for Intel architectures. | Computer Science |
| julia | Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and extensive mathematical function libraries. | Computer & Information Sciences |
| jupyter | Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. It supports over 40 programming languages, including Python, R, and Julia, and is widely used in data science, scientific computing, and machine learning projects. | Computer & Information Sciences |
| keras | Keras is an open-source neural network library written in Python. It is capable of running on top of TensorFlow, Microsoft Cognitive Toolkit, Theano, or PlaidML. Designed with user-friendliness and modularity as its guiding principles, Keras is known for its ease of use and flexibility, allowing users to experiment with deep neural networks. | Computer & Information Sciences |
| krb5 | Kerberos is a network authentication protocol designed to provide strong authentication for client/server applications through secret-key cryptography. | Computer Science |
| lammps | LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code designed for simulating large-scale atomistic systems. It is highly versatile and can be used to model a wide range of materials and complex molecular structures. | Chemical Sciences |
| launcher | Launcher is a software application that provides a centralized platform for accessing and managing various files, programs, and tools on a computer system. It serves as a customizable tool for organizing shortcuts and quick access to frequently used resources. | |
| learning | The learning module loads the prerequisites (such as anaconda and cudnn ) and makes ML applications visible to the user | |
| libbsd | libbsd is a library that provides functions typically found in the BSD operating systems. It aims to offer a more portable solution for developers needing BSD functions on non-BSD systems. | Computer & Information Sciences |
| libfabric | libfabric is a high-performance library for fabric interfaces, designed to abstract fabric communication resources to applications while providing flexibility to applications that need to bypass the fabric interfaces. It provides fabric-agnostic interfaces for communication in high-performance computing (HPC) environments. | Engineering & Technology |
| libffi | libffi is a library that provides a portable, high-level programming interface to various calling conventions. It allows a C function to be called from a language other than C without having to hand-write assembly code. | Computer & Information Sciences |
| libflame | libflame is a portable library for dense matrix computations, providing high-performance implementations of the BLAS and LAPACK interfaces. | Mathematics |
| libiconv | libiconv is a library that provides character set conversion support. It converts text data between different character encoding schemes. | Computer & Information Sciences |
| libmd | libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials. | Physical Sciences |
| libmesh | Libmesh is a C++ finite element library designed to provide a framework for the numerical simulation of partial differential equations in high dimensions. It supports 1D, 2D, and 3D mesh generation, provides a wide range of finite element types, and includes solvers for various types of PDEs. | Other Mathematics |
| libpng | Libpng is the official PNG reference library, used to support the PNG (Portable Network Graphics) format for storing raster images. It provides a set of functions for creating, reading, and manipulating PNG image files. | Computer & Information Sciences |
| libpthread-stubs | The libpthread-stubs package provides weak aliases for pthread functions not provided in libc or otherwise available by default. | |
| libszip | libszip is a compression library for large datasets used in scientific computing and research. It provides support for efficient and high-speed compression and decompression of large data files, particularly in formats commonly used in scientific applications. | Other Natural Sciences |
| libtiff | libtiff is a library for reading and writing TIFF (Tagged Image File Format) files. It provides support for handling images and documents in various uncompressed and compressed formats. | Computer & Information Sciences |
| libtirpc | libtirpc is an open-source library that provides an implementation of Sun's Transport-Independent RPC (TI-RPC) protocol. | Computer & Information Sciences |
| libv8 | libv8 is an open-source C++ library that provides a fast and efficient JavaScript engine for embedding in various applications and tools. | Computer & Information Sciences |
| libx11 | libX11 is the X Window System protocol client library which provides an interface to the X Window System core protocol and provides higher-level functions for building window systems on top of the X Window System core. | Computer & Information Sciences, Computer Science |
| libxau | libXau is a library that provides authentication data for Xlib-based client programs. | Computer & Information Sciences |
| libxcb | libxcb is a C language library for the X Window System's X protocol, providing a replacement for the traditional Xlib API. It allows for more efficient communication between X clients and the X server by reducing round-trip requests. | Computer & Information Sciences |
| libxdmcp | libxdmcp is the X Display Manager Control Protocol library. It provides an API for the X Display Manager Control Protocol (XDMCP) for both the client and server side. | Computer & Information Sciences |
| libxext | libXext is an extension library for the X Window System that provides additional functionality to the core Xlib library. | Computer and Information Sciences |
| libxml2 | Libxml2 is a software library for parsing, validating, and manipulating XML and HTML documents. It provides a tree-based API for working with XML data and supports various standards such as XML 1.0, XPath, XInclude, XPointer, and XML Catalogs. | Computer & Information Sciences |
| libxrender | libXrender is a library that provides an interface to the X Rendering Extension, which allows for the rendering of images and shapes in a more efficient manner than traditional X11 methods. | Computer and Information Sciences |
| libxscrnsaver | libxscrnsaver is a library that provides an X Window System client interface to the X11 MIT-SCREEN-SAVER extension. It allows applications to inhibit the screensaver and screen blanking in a standardized way. | Computer & Information Sciences |
| libxslt | Libxslt is the XSLT C library developed for the GNOME project. It is used for transforming XML documents into other formats using XSLT stylesheets. Libxslt is based on libxml2, the XML C parser and toolkit. | Computer & Information Sciences |
| matlab | MATLAB is a high-performance language for technical computing and visualization. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. | Mathematics, Applied Mathematics |
| meep | Meep (or MIT Electromagnetic Equation Propagation) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. | Physical Sciences |
| mesa-glu | mesa-gl is an open-source implementation of the OpenGL specification, a system for rendering interactive 3D graphics, and a widely used and versatile graphics library. mesa-glu is the OpenGL Utility Library (GLU) component of Mesa, providing useful functions for building OpenGL applications. | |
| modtree | ModTree is a software tool for the reconstruction of modular trees of mRNA transcripts and alternative splicing events. It is designed to identify and visualize the modular organization of alternative splicing events within a transcriptome. | Biological Sciences |
| monitor | A monitor is an electronic visual display for computers. It usually consists of a screen, circuitry, and casing. The display device in modern monitors is typically a thin film transistor liquid crystal display (TFT-LCD) or a flat panel LED display, while older monitors used a cathode ray tube (CRT). Monitors are used to display output from the computer's graphics card, allowing users to interact with the computer and its software. | |
| mpc | MPC, short for Multi-Party Computation, is a cryptographic protocol that allows multiple parties to jointly compute a function over their inputs while keeping those inputs private. It ensures data privacy and security in collaborative computations. | Computer & Information Sciences |
| mpfr | The GNU MPFR (Multiple Precision Floating-Point Reliable) library is a C library for arbitrary-precision arithmetic on floating-point numbers that guarantees correctly rounded results. | Mathematics |
| mrbayes | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It employs Markov chain Monte Carlo methods to estimate the posterior distribution of model parameters. | Biological Sciences |
| mvapich2 | MVAPICH2 is an open-source MPI implementation for InfiniBand, iWARP, and RoCE communication protocols which delivers high performance and scalability on a wide variety of HPC systems. | Physical Sciences |
| namd | NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is optimized for the simulation of biomolecular systems containing millions of atoms. | Biochemistry and Molecular Biology |
| ncl | The NCAR Command Language (NCL) is a scripting language designed specifically for the analysis and visualization of scientific data. It is widely used in the atmospheric and related sciences. | Earth & Environmental Sciences |
| nco | NCO (NetCDF Operators) is a suite of programs designed to help manipulate and analyze netCDF and HDF4 files. It provides a range of powerful tools for processing and analyzing climate and weather data stored in netCDF format. | Earth & Environmental Sciences |
| ncurses | ncurses is a programming library providing an API that allows the programmer to write text-based user interfaces on a terminal. | Computer & Information Sciences |
| ncview | ncview is a visual browser for netCDF format files used for earth system data. It provides functionalities for viewing, analyzing, and interacting with data stored in netCDF files. | Earth and Environmental Sciences |
| netcdf-c | NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Other Natural Sciences |
| netcdf-cxx4 | netcdf-cxx4 is a C++ library for accessing netCDF-4 classic and extended model data formats. It provides a high-level interface for reading and writing netCDF-4 data files in C++. | Computer & Information Sciences |
| netcdf-fortran | NetCDF-Fortran is a set of Fortran interfaces to the NetCDF library providing an easy-to-use, high-level access to the NetCDF file format for storing and sharing scientific data. | Other Natural Sciences |
| netlib-lapack | Netlib LAPACK (Linear Algebra PACKage) is a widely-used library for numerical linear algebra. It provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. | Computer & Information Sciences |
| nextflow | Nextflow is a powerful workflow manager that enables the writing of parallel and scalable computational workflows using native, containerized, or cloud-enabled execution environments. | Biological Sciences |
| nf-core | NF-core is a collection of community curated Nextflow pipelines available for genomics, transcriptomics, and other bioinformatics analyses. It provides a collection of best practices workflows that are highly optimized, scalable, and easy to use. | Biological Sciences |
| nltk | NLTK, or Natural Language Toolkit, is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning. | Computer & Information Sciences |
| numactl | Numactl is a set of tools that allows you to have more control over NUMA (Non-Uniform Memory Access) systems. It provides utilities for memory placement and migration of processes and controlling the NUMA policy of a process. | Engineering & Technology |
| nwchem | NWChem is an open-source computational chemistry package designed for high-performance simulations of large-scale molecular systems. It provides various tools and algorithms for both classical and quantum chemical calculations. | Chemical Sciences |
| octave | Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems and has extensive graphics capabilities for data visualization and manipulation. | Computer & Information Sciences |
| oneapi | OneAPI is a unified programming model that aims to simplify development across diverse architectures such as CPUs, GPUs, FPGAs, and other accelerators. It provides a single programming interface for developers to efficiently target and deploy applications in heterogeneous computing environments. | Computer & Information Sciences |
| onnx | ONNX (Open Neural Network Exchange) is an open-source format for AI models. It enables interoperability between different frameworks, making it easier to move models between various tools and platforms. | Computer & Information Sciences |
| openblas | OpenBLAS is an open-source implementation of the Basic Linear Algebra Subprograms (BLAS) library with optimized functions for matrix operations and linear algebra computations. It provides fast and efficient routines for common linear algebra operations. | Computer & Information Sciences |
| opencv | OpenCV (Open Source Computer Vision Library) is an open-source computer vision and machine learning software library. It provides a wide range of functionalities for real-time computer vision, including image processing, object detection, object tracking, and machine learning algorithms. | Computer & Information Sciences |
| openfoam | OpenFOAM (Open Source Field Operation and Manipulation) is a free, open-source computational fluid dynamics (CFD) software package developed by the OpenFOAM Foundation. It is widely used for simulating complex fluid flows in various industries and academic research. | Physical Sciences |
| openjdk | OpenJDK (Open Java Development Kit) is a free and open-source implementation of the Java Platform, Standard Edition (Java SE). It is developed under the OpenJDK project as a collaboration between several companies and the open-source community. | Computer & Information Sciences |
| openmpi | OpenMPI is an open-source Message Passing Interface (MPI) library that allows parallel computing on a distributed memory system. It enables high performance computing (HPC) by facilitating communication and coordination between processes running on multiple nodes. | Computer & Information Sciences |
| openssl | OpenSSL is a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library. | Computer & Information Sciences, Other Computer & Information Sciences |
| ovito | OVITO (Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data. It is designed to visualize and analyze large-scale molecular dynamics and Monte Carlo simulation results. | Computational Materials Science |
| papi | PAPI (Performance Application Programming Interface) is a portable and efficient API that provides a consistent interface and methodology for collecting performance counter data from the underlying hardware. | Computer Science |
| parafly | Parafly is a Python library for parallelizing and distributing task execution across multiple cores or nodes, aimed at improving computational efficiency for high-performance computing applications. | Computer & Information Sciences |
| parallel | GNU Parallel is a command-line tool for Unix-like operating systems that allows the user to execute shell scripts or commands in parallel. It is designed to simplify parallel job execution on single or multiple processors without the need for complex scripting. | Computer & Information Sciences |
| parallel-netcdf | Parallel-NetCDF is a library providing high-performance I/O in parallel environments for big data applications with large scientific datasets. It offers parallel I/O capabilities for NetCDF files, which are commonly used in climate modeling, weather forecasting, and other scientific disciplines. | Physical Sciences |
| paraview | ParaView is an open-source, multi-platform data analysis and visualization application. It is designed to handle large data sets and offers a wide range of visualization techniques to analyze and interact with the data. | Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences |
| pcre | Perl Compatible Regular Expressions (PCRE) is a library for pattern matching with regular expressions. It implements the functionality of the regular expression library in Perl and provides support for Perl-style regular expressions in many programming languages. | Computer & Information Sciences |
| pelican | Pelican is an open-source software platform for building data federations that works by connecting a broad range of data repositories under a unified architecture. Whether data lives on a POSIX filesystem, in S3, or behind an HTTP server, Pelican aims to bring this data together and simplify its access by abstracting away the need to know where it comes from. | |
| perl | Perl is a high-level, general-purpose, interpreted, dynamic programming language known for its powerful text-processing features and used for a wide range of tasks including web development, system administration, and network programming. | Computer & Information Sciences |
| perl-bioperl | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. | Biological Sciences |
| petsc | PETSc, the Portable, Extensible Toolkit for Scientific Computation, is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | Natural Sciences |
| picard | Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. It is primarily used for processing and analyzing next-generation sequencing (NGS) data in genomics. | Biological Sciences |
| pixman | Pixman is a low-level software library for pixel manipulation, providing software acceleration for numerous rendering operations. It is used primarily by projects requiring high-quality rendering such as the X server, Cairo, the GTK+ toolkit, and more. | Computer & Information Sciences |
| proj | PROJ is a standard Unix filter function designed to convert geographic longitude and latitude coordinates into Cartesian coordinates. It is widely used in geospatial applications for coordinate transformation and map projection. | Other Natural Sciences |
| protobuf | Protocol buffers are a language- and platform-neutral extensible mechanism for serializing structured data. It enables you to define data structures in a JSON-like format and automatically generate code to serialize and deserialize them in a variety of languages. | Computer & Information Sciences |
| py-cutadapt | py-cutadapt is a Python package for preprocessing high-throughput sequencing data. It trims adapter sequences, removes low-quality bases, and filters out reads that do not meet specified quality thresholds. | Biological Sciences |
| py-gpaw | GPAW is an open-source software package for electronic structure calculations based on density functional theory (DFT). It uses the real-space grid method and is designed for high-performance computing environments. | Quantum Chemistry |
| py-htseq | Py-htseq is a high-throughput sequencing (HTS) analysis tool in Python designed to process and analyze mapped sequence data, particularly for RNA-seq experiments. It facilitates gene expression analysis by counting reads that align to features in the reference genome or transcriptome. | Biological Sciences |
| py-mpi4py | py-mpi4py is a Python interface to the Message Passing Interface (MPI) standard for parallel computing, allowing users to utilize MPI functionality within Python scripts and applications. | Computer & Information Sciences |
| python | Python is a high-level, interpreted programming language known for its simplicity and readability. It supports multiple programming paradigms and has a vast ecosystem of libraries and frameworks. | Computer & Information Sciences, Software Engineering, Systems & Development |
| pytorch | PyTorch is an open-source machine learning library used for numerical computations and building deep learning models. | Computer & Information Sciences |
| qemu | QEMU is a generic and open-source machine emulator and virtualizer that supports executing different operating systems and programs on a host operating system. It provides full system simulation, allowing users to run virtual machines with various architectures (x86, ARM, PowerPC, etc.) on a wide range of host platforms. QEMU can be used for various purposes such as development, testing, debugging, and virtualization. | Computer & Information Sciences |
| qgis | QGIS is a free and open-source cross-platform desktop geographic information system (GIS) application that supports viewing, editing, and analysis of geospatial data. | Earth & Environmental Sciences |
| qt | Qt is a cross-platform C++ framework for application development. It provides a comprehensive set of libraries and tools for building graphical user interfaces, as well as for developing applications with network support, database integration, and more. | Engineering & Technology |
| quantum-espresso | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. | Condensed Matter Physics |
| r | R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows, and MacOS. | Computer Science |
| rclone | Rclone is a command-line program to manage files on cloud storage. It is a powerful tool that supports various cloud storage services and allows users to sync files between different storage locations. | Computer Science |
| readline | GNU Readline is a free software library that provides line-editing and history capabilities for interactive programs with a command-line interface. It allows users to edit command lines as they are typed in, recall and re-edit previous input, and perform basic character manipulations. | Computer & Information Sciences |
| renderproto | renderproto is a protocol specification for the Render extension to the X Window System (X11). It defines the wire protocol for rendering operations such as compositing, transformations, and anti-aliased rendering of images and glyphs on X servers that support the Render extension. | |
| rstudio | RStudio is an integrated development environment (IDE) for R, a programming language and environment widely used for statistical computing and graphics. RStudio provides an intuitive and productive user interface for R, allowing users to efficiently write, execute, and debug R code. | Other Natural Sciences |
| samtools | Samtools is a suite of programs for interacting with high-throughput sequencing data generated in sequence alignment/map (SAM) format, such as those produced by the Short Read Mapping (SHRiMP) or Burrows-Wheeler Aligner (BWA) aligners. It allows various operations on SAM/BAM files, including indexing, sorting, merging, and manipulating sequence alignments. | Biological Sciences |
| spark | Apache Spark is an open-source distributed computing system that provides an interface for programming entire clusters with implicit data parallelism and fault tolerance. | Computer & Information Sciences |
| spice-server | spice-server is the server component of the SPICE (Simple Protocol for Independent Computing Environments) remote desktop protocol. It provides a high-quality remote access solution for virtualized desktops and virtual machines, enabling users to interact with graphical desktop environments over a network with low latency and rich multimedia support. | Computer Science |
| sqlite | SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most widely deployed SQL database engine in the world. The source code for SQLite is in the public domain. | Computer & Information Sciences |
| sratoolkit | The SRA Toolkit is a collection of tools for working with data in the Sequence Read Archive (SRA). It allows users to download, convert, and manipulate sequencing data from the SRA. | Genomics |
| swig | SWIG (Simplified Wrapper and Interface Generator) is a software development tool that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, Tcl, and more. It simplifies the process of creating interfaces for these languages, enabling developers to easily incorporate C/C++ code into their scripting language-based projects. | Computer & Information Sciences, Software Engineering, Systems & Development |
| tar | tar is a software utility used for packaging files together into an archive file often referred to as a "tarball". It is commonly used in Unix-like operating systems for creating, storing, and managing files in a single file. | Computer & Information Sciences |
| tcl | Tool Command Language (Tcl) is a dynamic programming language often used for creating scripts, applications, and embedded control systems. It provides a simple scripting language and a powerful code execution environment for various platforms. | Computer & Information Sciences |
| tensorflow | TensorFlow is an open-source machine learning library developed by Google to build and train deep learning models. | Computer & Information Sciences |
| texlive | TeX Live is a comprehensive distribution of TeX and related programs, providing a complete environment for typesetting documents. | Computer Science |
| tk | Tkinter is a standard GUI toolkit for Python. It is included with most Python installations and is widely used for building desktop applications in Python. | Computer & Information Sciences, Computer Science, Software Engineering, Systems & Development |
| tophat | Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to the genome using the Bowtie aligner and then analyzes the mapping results to identify splice junctions between exons. | Biological Sciences |
| totalview | TotalView is a comprehensive parallel debugging and performance analysis solution. It provides developers with advanced tools to effectively find and fix bugs, optimize code, and improve application performance for HPC, big data, and machine learning applications. | Computer Science |
| trimmomatic | Trimmomatic is a flexible and efficient tool for trimming raw next-generation sequencing data. It provides several trimming modes and options to cater to different sequencing platforms and quality control requirements. | Biological Sciences |
| udunits | UDUNITS supports conversion of unit specifications between formatted, human-readable strings and machine-friendly structures. In addition, UDUNITS defines functions that can be used to identify whether pairs of units are conformable for mathematical operations, to convert numerical values from one unit to another, and to generate strings representing the units of quantities. | Computer and Information Sciences |
| util-linux-uuid | util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique. | Computer & Information Sciences |
| valgrind | Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. It can also be used for cache and thread error detection. | Computer & Information Sciences |
| vasp | VASP (Vienna Ab-initio Simulation Package) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. | Physical Sciences, Engineering & Technology |
| vcftools | VCFtools is a software package for manipulating and analyzing genetic variation data stored in Variant Call Format (VCF) files. It provides a wide range of tools for quality control, filtering, summarization, and other analyses of genetic variants. | Biological Sciences |
| visit | Visit is an open-source interactive parallel visualization and graphical analysis tool. It is designed to handle very large data set visualization and enable users to visualize and analyze data from a variety of sources. | Computer & Information Sciences |
| visual studio code | Visual Studio Code is a source-code editor developed by Microsoft. It includes support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. | Computer Science |
| vlc player | VLC media player is a free and open-source multimedia player and framework that plays most multimedia files, as well as DVDs, audio CDs, VCDs, and various streaming protocols. | Computer Science |
| vmd | Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | Biological Sciences |
| vtk | The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK offers a wide range of functionality for tasks such as scientific visualization, medical imaging, computational fluid dynamics, and more. | Physical Sciences |
| wannier90 | Wannier90 is a tool used for the computation of maximally-localized Wannier functions, which are spatially compact and localized functions that provide a natural description of the electronic structure of a solid. These functions are often used in condensed matter physics calculations to study the electronic properties of materials. | Physical Sciences |
| xalt | XALT (XALT Accounting for Loadable and Transient Objects) is a tool designed to track the detailed usage of HPC systems by monitoring library dependencies and executables during job executions. It captures information on modules, compilers, libraries, and executables used in each job, providing detailed insights into the software stack and usage patterns on the HPC system. | Engineering & Technology |
| xcb-proto | Protocol descriptions used to generate language bindings for the X Window System XCB library. | |
| xcb-util-image | The xcb-util-image library provides a number of functions used for manipulating and creating XCB format images, including loading and saving images to disk in various formats. | Computer & Information Sciences |
| xcb-util-keysyms | The xcb-util-keysyms library provides utility functions for obtaining the keysyms keycode values, as used in the X Window System, as well as common XKB functions. It is part of the X C Bindings (XCB) utility libraries which provide a number of convenience functions and interfaces for usage with XCB. | Computer & Information Sciences |
| xcb-util-renderutil | A set of libraries which provide a convenient API for rendering text with XCB. | Computer & Information Sciences |
| xcb-util-wm | xcb-util-wm is a set of utility functions for interfacing with the X Window Manager (WM) extension of the XCB library. It provides a number of functions that are useful to XCB WM clients. | |
| xextproto | X11 Extension protocols and auxiliary headers | Computer & Information Sciences |
| xproto | X Window System protocol development files. | Computer & Information Sciences |
| xz | xz is a free and open-source data compression tool that uses the LZMA compression algorithm. It is designed to be an efficient and high-performance compression utility. | Computer & Information Sciences |
| zlib | zlib is a software library for data compression that provides functions for file compression and decompression using the DEFLATE compression algorithm. It is widely used in various applications for reducing file size and conserving storage space. | Computer & Information Sciences |
No software matches that name.
Storage Documentation
File System
| Directory | Path | Quota | Purge | Backup | Notes |
|---|---|---|---|---|---|
| Home | $HOME | 25 GB | Never purged | Snapshots only, retained 60 days | ZFS. Area for personal software, scripts, compiling and editing. There is no limit on the number of files. Snapshots live on the same hardware as the primary copy and are not a backup - back up anything you cannot lose. |
| Scratch | $SCRATCH | 100 TB, 1,048,576 files | Purged 30 days after last access | Not backed up | GPFS. Working space for job input and output, not long-term storage. Deletions here are silent and permanent - there is no warning email and no way to recover a file. |
| Projects | $PROJECT | 5 TB, 1,048,576 files | Purged 90 days after allocation expires | Snapshots only, retained 60 days | GPFS. Shared across your allocation for project data. Reached via $PROJECT or $WORK. Snapshots live on the same hardware as the primary copy and are not backups; backup anything you cannot lose. |
| Applications | /apps | See notes | Never purged | ZFS. Read-only area holding the software Anvil installs centrally. Not user storage, so no quota applies. | |
| Datasets | /anvil/datasets | See notes | Never purged | GPFS. Read-only collection of community datasets curated by Anvil. Not allocated to users and not counted against your quota. |