RInfrastructure
ReadCube Papers
A reference-management and reading platform with literature search, annotation, sharing, and citation tools.
reference managementannotation
View entry RESEARCH INFRASTRUCTURE
Research infrastructure
Software, frameworks, and platforms for scientific computing, data processing, visualization, experiment management, and reproducible workflows. Inclusion does not imply that a resource itself uses AI. The database currently includes 138 entries in this section.
LInfrastructure
LiquidText
A document workspace for connecting excerpts, annotations, and notes across multiple sources.
deep readingannotation
View entry RInfrastructure
Rayyan
A review-management platform for screening records, collaborating with reviewers, resolving conflicts, and handling duplicates.
systematic reviewscreening
View entry CInfrastructure
Covidence
A systematic-review platform covering citation screening, full-text review, data extraction, and risk-of-bias assessment.
systematic reviewdata extraction
View entry DInfrastructure
DistillerSR
A workflow platform for systematic reviews, literature surveillance, and regulatory evidence management.
systematic reviewworkflow
View entry SInfrastructure
Sysrev
A collaborative review platform for screening documents, defining labels, and extracting structured information.
screeningdata extraction
View entry ZInfrastructure
Zotero
An open-source reference manager for collecting, organizing, annotating, citing, and synchronizing research materials.
reference managementcitations
View entry EInfrastructure
EndNote
A commercial reference-management application for collecting literature, sharing libraries, and formatting citations.
reference managementcitation styles
View entry OInfrastructure
Overleaf
A collaborative, browser-based LaTeX editor for papers, reports, and technical documents.
LaTeXcollaboration
View entry WInfrastructure
Wolfram Mathematica
A technical computing system for symbolic mathematics, numerical methods, modeling, and visualization.
symbolic computationscientific computing
View entry MInfrastructure
MATLAB
A programming and numerical-computing environment used for algorithm development, data analysis, simulation, and engineering models.
numerical computingengineering
View entry JInfrastructure
JupyterLab
An open-source interactive computing environment that combines code, data, narrative, and visual output.
notebooksopen source
View entry KInfrastructure
KNIME Analytics Platform
An analytics platform for assembling data access, transformation, modeling, and machine-learning workflows from visual nodes.
visual workflowsdata analysis
View entry OInfrastructure
Orange Data Mining
An open-source visual programming application for data exploration, machine learning, and teaching.
visual programmingmachine learning
View entry GInfrastructure
GraphPad Prism
A desktop application that combines biostatistical analysis, curve fitting, and scientific graphing.
biostatisticsscientific graphs
View entry PInfrastructure
Plotly
Open-source graphing libraries for interactive visualization in Python, R, and JavaScript, with related application tooling.
interactive chartsPython
View entry RInfrastructure
RAWGraphs
An open-source web application that converts tabular data into a range of conventional and less common visual forms.
open sourcecharts
View entry DInfrastructure
Datawrapper
A browser-based tool for creating and publishing charts, maps, and tables without programming.
chartsmaps
View entry FInfrastructure
Flourish
A template-based platform for interactive visualizations, animated charts, maps, and data stories.
data storiesinteractive graphics
View entry TInfrastructure
Tableau
A visual analytics platform for connecting data, exploring relationships, building dashboards, and sharing results.
visual analyticsdashboards
View entry OInfrastructure
OriginPro
A Windows application for scientific data analysis, curve fitting, and publication-oriented graphing.
scientific graphingcurve fitting
View entry GInfrastructure
ggplot2
An open-source R package based on a grammar of graphics for building reproducible statistical visualizations.
Ropen source
View entry MInfrastructure
Matplotlib
An open-source Python library for static, animated, and interactive visualizations.
Pythonopen source
View entry BInfrastructure
Benchling
A cloud platform for biotechnology research that combines electronic lab records, sequence tools, and research data management.
electronic lab notebooksequence design
View entry DInfrastructure
DeepChem
An open-source Python library for applying machine learning to drug discovery, quantum chemistry, biology, and materials problems.
drug discoverymachine learning
View entry NInfrastructure
NVIDIA BioNeMo
A collection of frameworks, models, and deployment tools for generative AI in biomolecular and drug research.
biomolecular AIdrug research
View entry NInfrastructure
NCBI BLAST
NCBI sequence-search tools for finding local similarity between nucleotide or protein queries and sequence databases.
sequence searchbioinformatics
View entry GInfrastructure
Galaxy
An open web platform for running, documenting, and sharing reproducible computational biology workflows.
bioinformaticsreproducible workflows
View entry CInfrastructure
CellProfiler
Open-source software for building pipelines that measure cellular and other biological features in microscopy images.
microscopycell analysis
View entry MInfrastructure
MONAI
An open-source framework built on PyTorch for developing and deploying deep-learning workflows in medical imaging.
medical imagingdeep learning
View entry CInfrastructure
ChemDraw
A professional chemistry application for drawing structures and reactions and working with chemical information.
chemical drawingstructures
View entry RInfrastructure
RDKit
An open-source cheminformatics toolkit for molecular representations, descriptors, substructure search, and modeling workflows.
cheminformaticsPython
View entry QInfrastructure
Quantum ESPRESSO
An open-source suite for electronic-structure calculations and materials modeling based on plane waves and pseudopotentials.
electronic structurefirst principles
View entry BInfrastructure
Biopython
An open-source Python toolkit for computational biology, including sequence, structure, database, and file-format operations.
bioinformaticsPython
View entry SInfrastructure
Scanpy
An open-source Python toolkit for preprocessing, reducing, clustering, and visualizing single-cell gene-expression data.
single celltranscriptomics
View entry SInfrastructure
scvi-tools
An open-source Python package that provides probabilistic generative models and a shared interface for single-cell omics.
single cellprobabilistic models
View entry NInfrastructure
Nextflow
An open-source workflow system for portable and scalable computational pipelines, widely used in bioinformatics.
workflowsreproducible computing
View entry SInfrastructure
Snakemake
An open-source workflow manager that expresses analysis steps and their dependencies as rules.
workflowsdata pipelines
View entry NInfrastructure
nf-core
A community project that maintains Nextflow pipelines under shared development, testing, and release practices.
bioinformatics pipelinesNextflow
View entry NInfrastructure
napari
An open-source Python viewer for inspecting, annotating, and analyzing multidimensional scientific images.
multidimensional imagingannotation
View entry QInfrastructure
QuPath
Open-source desktop software for digital pathology and whole-slide image analysis.
digital pathologywhole-slide imaging
View entry FInfrastructure
Fiji
A distribution of ImageJ bundled with plugins and update sites for scientific image analysis, especially in life sciences.
scientific imagingImageJ
View entry OInfrastructure
OMERO
An open platform for managing, viewing, sharing, and analyzing microscopy images with their metadata.
image data managementmicroscopy
View entry AInfrastructure
AutoDock Vina
An open-source program for predicting and scoring candidate binding poses between small molecules and receptors.
molecular dockingvirtual screening
View entry OInfrastructure
OpenMM
An open-source molecular simulation toolkit with a Python API and support for GPU acceleration.
molecular dynamicsGPU
View entry OInfrastructure
OpenFE
An open-source toolkit and community project for setting up, running, and analyzing relative binding free-energy calculations.
binding free energydrug discovery
View entry PInfrastructure
pymatgen
An open-source Python library for representing, transforming, and analyzing materials structures and computational outputs.
materials informaticsPython
View entry AInfrastructure
Atomic Simulation Environment
An open-source Python toolkit for setting up, running, and analyzing atomistic simulations across multiple calculators.
atomistic simulationPython
View entry LInfrastructure
LAMMPS
An open-source parallel simulation engine for classical molecular dynamics and particle-based materials modeling.
molecular dynamicsparallel computing
View entry DInfrastructure
DeePMD-kit
An open-source package for training deep neural-network interatomic potentials and using them in molecular simulation.
machine-learned potentialsmolecular simulation
View entry SInfrastructure
SchNetPack
An open-source PyTorch toolbox for developing and training atomistic machine-learning models.
atomistic machine learningPyTorch
View entry PInfrastructure
ParaView
An open-source application for interactive analysis and visualization of large two- and three-dimensional scientific datasets.
3D visualizationscientific computing
View entry UInfrastructure
UCSF ChimeraX
Desktop software for visualization and analysis of molecular structures, density maps, and related biomedical data.
molecular visualizationstructural biology
View entry VInfrastructure
VMD
Software for displaying, analyzing, and rendering molecular systems and simulation trajectories.
molecular visualizationsimulation trajectories
View entry SInfrastructure
seaborn
An open-source Python statistical-graphics library built on Matplotlib with a high-level, data-frame-oriented interface.
statistical graphicsPython
View entry SInfrastructure
Seurat
An open-source R package for quality control, analysis, integration, and visualization of single-cell transcriptomic data.
single cellR
View entry BInfrastructure
Bioconductor
An open bioinformatics software ecosystem built around R, with analysis, annotation, experiment-data, and workflow packages.
bioinformaticsR
View entry GInfrastructure
GATK
An open-source genomics toolkit from the Broad Institute focused on variant discovery, genotyping, and related sequencing-data processing.
variant callinggenomics
View entry SInfrastructure
STAR
An open-source splice-aware aligner designed for RNA sequencing reads.
RNA-seqalignment
View entry SInfrastructure
Salmon
An open-source command-line tool for estimating transcript abundance from RNA-seq data using selective alignment or sketching methods.
RNA-seqquantification
View entry KInfrastructure
kallisto
An open-source tool that uses pseudoalignment to estimate transcript abundance from bulk or single-cell RNA-seq data.
RNA-seqpseudoalignment
View entry HInfrastructure
Hail
An open-source Python framework for scalable genomic data analysis across local, cloud, and Spark environments.
population genomicsdistributed computing
View entry PInfrastructure
PLINK 2
An open-source command-line toolset for genome-wide association studies, genotype quality control, and population-genetic analysis.
GWASgenotypes
View entry SInfrastructure
SAMtools
An open-source command-line suite for reading, converting, sorting, indexing, and summarizing SAM, BAM, and CRAM alignment files.
alignment filessequencing
View entry MInfrastructure
MultiQC
An open-source tool that aggregates outputs from many bioinformatics programs and samples into a unified quality-control report.
quality controlbioinformatics reports
View entry CInfrastructure
Cell Ranger
A set of 10x Genomics pipelines for processing Chromium single-cell data, including barcode handling, UMI counting, and selected immune-receptor analyses.
single-cell sequencing10x Genomics
View entry BInfrastructure
BCFtools
An open-source command-line suite for manipulating, querying, filtering, summarizing, and calling variants in VCF, BCF, and gVCF data.
variant filesgenomics
View entry EInfrastructure
Ensembl VEP
An open-source Ensembl tool that annotates the potential consequences of genomic variants on transcripts, proteins, and regulatory regions.
variant annotationfunctional consequences
View entry IInfrastructure
IGV
An open-source genome viewer for interactively examining sequencing, variation, annotation, and other data positioned on reference genomes.
genome browservisualization
View entry IInfrastructure
ImageJ
Extensible open-source desktop software for displaying, processing, measuring, and analyzing scientific images.
scientific imagesimage analysis
View entry MInfrastructure
Micro-Manager
Open-source software for controlling automated microscope hardware and running time-lapse, multichannel, and z-stack acquisitions.
microscope controlimage acquisition
View entry SInfrastructure
Squidpy
An open-source Python tool for spatial molecular data analysis, including neighborhood graphs, spatial statistics, and tissue-image integration.
spatial omicssingle cell
View entry SInfrastructure
SpatialData
An open-source data framework, schema, and serialization format for representing, transforming, and querying uni- and multimodal spatial omics data.
spatial omicsdata framework
View entry TInfrastructure
TorchDrug
An open-source PyTorch toolbox for graph representation learning in drug discovery, with components for molecules, proteins, reactions, and knowledge graphs.
drug discoverygraph neural networks
View entry DInfrastructure
DeepPurpose
An open-source deep-learning toolkit for drug-target interaction, molecular-property, and related biomedical prediction tasks.
drug-target interactiondeep learning
View entry GInfrastructure
GROMACS
Open-source high-performance software for molecular-dynamics simulation, energy minimization, and trajectory analysis.
molecular dynamicssimulation
View entry SInfrastructure
SwissDock
A free research service for submitting protein-small-molecule docking jobs through a web interface and examining candidate poses.
molecular dockingweb service
View entry SInfrastructure
SwissADME
A free web tool that calculates molecular descriptors and predicts selected ADME, pharmacokinetic, and drug-likeness properties.
ADMEpharmacokinetics
View entry MInfrastructure
MatGL
An open-source Python library for graph deep learning, property prediction, and machine-learning potential development in materials science and chemistry.
materials graph learningmachine-learning potentials
View entry DInfrastructure
DScribe
An open-source Python package that converts atomic structures into fixed-size numerical descriptors such as SOAP and MBTR.
atomic descriptorsmaterials ML
View entry PInfrastructure
phonopy
Open-source software for phonon spectra, density-of-states, and thermal-property calculations within harmonic and quasi-harmonic approximations.
phononslattice dynamics
View entry GInfrastructure
GPAW
Open-source Python software for density-functional-theory calculations using the projector-augmented-wave method and the Atomic Simulation Environment.
DFTelectronic structure
View entry CInfrastructure
CP2K
Open-source high-performance software for quantum chemistry and atomistic simulation of solids, liquids, molecules, and biological systems.
quantum chemistryatomistic simulation
View entry VInfrastructure
VASP
Proprietary research software for first-principles electronic-structure, materials-property, and quantum molecular-dynamics calculations.
first principleselectronic structure
View entry AInfrastructure
ABINIT
An open-source suite for DFT, perturbation-theory, and many-body electronic-structure calculations on materials and molecules.
DFTmany-body methods
View entry SInfrastructure
SIESTA
Open-source software that uses strictly localized atomic orbitals for electronic-structure and first-principles molecular-dynamics calculations on molecules and solids.
DFTlocalized orbitals
View entry OInfrastructure
OpenMX
Open-source software using pseudo-atomic localized basis functions for electronic-structure, molecular-dynamics, and transport calculations in nanoscale materials.
DFTnanomaterials
View entry VInfrastructure
Vega-Lite
An open-source high-level grammar and toolchain for defining interactive statistical graphics with concise declarative JSON specifications.
declarative visualizationinteractive charts
View entry VInfrastructure
Vega-Altair
An open-source Python library that builds declarative statistical visualizations on the Vega-Lite specification.
statistical visualizationPython
View entry BInfrastructure
Bokeh
An open-source Python library for interactive browser graphics, data applications, and linked visual exploration.
interactive visualizationPython
View entry PInfrastructure
PyVista
An open-source Python library for three-dimensional visualization and mesh analysis, with a NumPy-oriented interface over VTK.
3D visualizationmesh analysis
View entry OInfrastructure
OVITO
Scientific software for visualizing and analyzing atomistic, molecular, and particle-simulation data, available as open-source Basic tools and a proprietary Pro edition.
particle simulation3D analysis
View entry VInfrastructure
VisIt
An open-source application for interactive and parallel visualization and quantitative analysis of mesh-based scientific data.
scientific visualizationparallel analysis
View entry CInfrastructure
Cytoscape
An open-source desktop platform for visualizing, analyzing, and extending complex networks, with broad use in molecular and biological network research.
network analysisbiological networks
View entry GInfrastructure
Gephi
Open-source software for interactively exploring, laying out, filtering, and presenting complex networks on desktop or in a browser.
network visualizationgraph analysis
View entry RInfrastructure
RStudio IDE
An integrated development environment for R and selected Python workflows, available in open-source desktop and server editions and commercial variants.
Rintegrated development environment
View entry QInfrastructure
Quarto
An open-source scientific publishing system that renders Markdown, notebooks, and executable code into articles, reports, presentations, websites, and books.
reproducible publishingtechnical writing
View entry DInfrastructure
DVC
An open-source data version control tool that records large datasets, models, and machine-learning pipelines alongside Git-managed code.
data version controlreproducible workflows
View entry MInfrastructure
MLflow
An open-source platform for recording machine-learning experiments, managing models and artifacts, and supporting self-hosted collaboration.
experiment trackingmodel management
View entry WInfrastructure
Weights & Biases
A hosted platform and client tools for recording, comparing, and collaboratively managing machine-learning experiments, models, and data artifacts.
experiment trackingML collaboration
View entry IInfrastructure
Imaris
Proprietary modular software for visualizing, segmenting, tracking, and quantitatively measuring two- to four-dimensional microscopy images.
microscopy imaging3D analysis
View entry DInfrastructure
DOCK 6
An open-source command-line suite for small-molecule docking, virtual screening, and scoring candidate receptor-ligand poses.
molecular dockingvirtual screening
View entry AInfrastructure
Amber
A molecular-dynamics software suite for biomolecular simulation. AmberTools is free and mostly open source, while Amber26 has a separate license and fee structure.
molecular dynamicsbiomolecular simulation
View entry SInfrastructure
Schrödinger Platform
A proprietary integrated platform for molecular modeling, simulation, informatics, and computational research in drug discovery and materials science.
molecular modelingcomputational drug discovery
View entry MInfrastructure
MOE
Molecular Operating Environment is a proprietary integrated platform for molecular modeling, drug design, cheminformatics, and simulation.
molecular modelingdrug design
View entry MInfrastructure
Mayavi
An open-source Python library and interactive application for two- and three-dimensional scientific-data visualization built on VTK.
3D visualizationPython
View entry FInfrastructure
FastQC
Open-source software for checking raw high-throughput sequencing data and producing modular plots, tables, and HTML reports.
sequencing QCFASTQ
View entry AInfrastructure
AiiDA
Open-source Python infrastructure for running computational-science workflows and recording the provenance of their data and processes.
workflow automationdata provenance
View entry NInfrastructure
NumPy
The foundational open-source Python library for multidimensional arrays, vectorized numerical operations, linear algebra, and related numerical routines.
numerical computingarrays
View entry PInfrastructure
pandas
An open-source Python library for reading, cleaning, transforming, joining, and summarizing tabular and time-series data.
tabular datadata processing
View entry SInfrastructure
SciPy
An open-source scientific-computing library built on NumPy, with maintained algorithms for optimization, integration, signals, sparse computation, statistics, and more.
scientific computingnumerical methods
View entry SInfrastructure
scikit-learn
An open-source Python machine-learning library covering supervised and unsupervised estimators, preprocessing, pipelines, model selection, and evaluation.
machine learningmodel evaluation
View entry PInfrastructure
PyMC
An open-source probabilistic-programming library for specifying Bayesian models in Python and fitting them with MCMC or variational inference.
Bayesian modelingprobabilistic programming
View entry SInfrastructure
Stan
An open-source probabilistic-programming language and cross-language toolkit for Bayesian statistical modeling and posterior inference.
Bayesian inferenceprobabilistic programming
View entry VInfrastructure
VTK
An open-source toolkit for processing and visualizing scientific data, with capabilities spanning 2D plots, image processing, volume rendering, and 3D graphics.
scientific visualization3D rendering
View entry HInfrastructure
HoloViews
An open-source Python library that uses declarative objects to connect data semantics with static or interactive visualizations.
Pythondeclarative visualization
View entry DInfrastructure
Datashader
An open-source Python rasterization pipeline that projects, aggregates, transforms, and shades large datasets into viewable representations.
large-scale datarasterization
View entry PInfrastructure
plotnine
An open-source Python visualization package based on a grammar of graphics, using layers and aesthetic mappings to compose statistical plots.
Pythongrammar of graphics
View entry VInfrastructure
VisPy
An open-source Python library that uses GPU and OpenGL acceleration for interactive two- and three-dimensional data visualization.
GPUinteractive visualization
View entry MInfrastructure
Mol*
An open-source web technology stack for visualizing and analyzing large macromolecular structures and associated experimental data.
molecular visualizationstructural biology
View entry FInfrastructure
fastp
An open-source command-line tool for quality control and preprocessing of short-read FASTQ data, including filtering, trimming, and HTML or JSON reporting.
FASTQ preprocessingshort-read sequencing
View entry CInfrastructure
Cutadapt
An open-source tool that finds and removes specified adapters, primers, poly-A tails, and other unwanted sequences from high-throughput sequencing reads.
adapter trimmingFASTQ
View entry SInfrastructure
SeqKit
A cross-platform open-source command-line toolkit for querying, transforming, summarizing, sampling, and indexing FASTA and FASTQ files.
sequence filesFASTA/FASTQ
View entry MInfrastructure
minimap2
An open-source aligner for mapping DNA or mRNA sequences to a reference, with modes for long reads, short reads, spliced transcripts, and assembly comparison.
sequence alignmentlong reads
View entry BInfrastructure
Bowtie 2
An open-source FM-index aligner for mapping sequencing reads to long reference sequences in local, end-to-end, gapped, and paired-end modes.
short-read alignmentreference genome
View entry BInfrastructure
BEDTools
An open-source command-line suite for intersecting, merging, comparing, covering, and otherwise analyzing genomic intervals.
genomic intervalsset operations
View entry SInfrastructure
statsmodels
An open-source Python package for statistical modeling and econometrics, with model estimation, statistical tests, diagnostics, and structured result summaries.
statistical modelingeconometrics
View entry PInfrastructure
Polars
An open-source DataFrame query engine written in Rust, with eager and lazy execution, query optimization, and streaming support.
DataFramesquery engine
View entry DInfrastructure
DuckDB
An open-source in-process analytical SQL database for querying local files, object storage, and in-memory data without a separate database server.
analytical databaseSQL
View entry JInfrastructure
JAX
An open-source Python library for high-performance array computing and composable transformations including automatic differentiation, compilation, batching, and parallelization.
automatic differentiationaccelerated computing
View entry OInfrastructure
Optuna
An open-source framework for automated hyperparameter optimization with dynamic search spaces, trial pruning, parallel execution, and study visualization.
hyperparameter optimizationexperiment search
View entry PInfrastructure
PyTorch
An open-source deep-learning library for tensor computation, automatic differentiation, neural networks, and distributed training on CPUs and supported accelerators.
deep learningtensor computation
View entry TInfrastructure
TensorFlow
An open-source framework for building, training, evaluating, and deploying machine-learning models, with related components for servers, browsers, and mobile devices.
machine learningmodel deployment
View entry KInfrastructure
Kedro
An open-source Python framework for organizing modular, maintainable, and reproducible data-science code through pipelines, configuration, and a data catalog.
data pipelinesreproducible computing
View entry DInfrastructure
DataLad
An open-source distributed data-management tool built on Git and git-annex for versioning, retrieving, and sharing research datasets of any size.
data version controlresearch data management
View entry CInfrastructure
CADIMA
A free web application for organizing systematic reviews and systematic maps, including import, deduplication, screening, data extraction, and process documentation.
systematic reviewsevidence maps
View entry RInfrastructure
revtools
An open-source R package for importing and deduplicating bibliographic data and interactively screening titles, abstracts, and topics for evidence synthesis.
evidence synthesisR
View entry JInfrastructure
JabRef
An open-source cross-platform reference manager centered on BibTeX and BibLaTeX libraries, with metadata import, organization, citation, and export tools.
reference managementBibTeX
View entry