Data extraction
- Morph.io: automated web-scraping
- Google NGram Viewer: chart frequencies of words/short sentences in Google Books
- Bellingcat: collaborative space for journalist led and citizen participating fact-checking
- Tabula: extract data from pdf tables
- WebPlotDigitizer: Extract data from plots, graphs, maps etc
- ScraperWiki: extract/scrape tables from PDFs
- PDF Miner: Extracting information from PDF documents
- TAGS: Google Sheet template which lets you setup and run automated collection of search results from Twitter
- Import.io: Turning web into data (scraping, parsing etc.); not restricted to scholarly use
Equipment & research samples
- 1degreebio: find reagents & lab products
- Selectscience: independent, online review resource for lab equipment and techniques
- Biocompare: lab equipment reviews
- StrainControl: lab inventory tool
- Sample of Science: Marketplace for (physical) sample sharing. Samples get published and receive DOI
- Addgene: plasmid sharing platform
- Resource Identification Portal: providing, discovering and citing research resources (organisms, antibodies, tools) based on RRIDs
- GeoSamples (SESAR): search and register geosamples and get GEOsample ID (IGSN)
- BioMedUSA: sharing and licensing of biological research materials and related technologies
Experiment
- DISK: Automated discovery of scientific knowledge (automate the hypothesize-test-evaluate discovery cycle) [login required]
- GenomeCompiler: Genetic design platform (manipulate and design everything from single genes to entire genomes)
- Tatool: Run computer based experiments (web and download)
- Wings: semantic workflow system that assists scientists with the design of computational experiments
- Emerald Cloud Lab: web-based life sciences lab -run experiments in a central lab from anywhere in the world
Online surveys
- eSurveys Pro: online surveys
- FluidSurveys: online surveys
- Free online Surveys: online surveys
- Google Forms: online surveys
- Limesurvey: Online survey creating and running
- ProProfs Form maker: Online forms creating and hosting
- Qualtrics: web surveying tool
- SmartSurvey Academic: survey tool
- Socialsci: data collection platform: design surveys and recruit from participant pool
- Survey Gizmo: online surveys
- SurveyMonkey: online surveys
- TypeForm: create surveys
- OpenDataKit: simple mobile data collection in field, with form, cloud storage and visualisation
Lab notebook
- Findings App: electronic lab notebook (with some protocol sharing)
- HiveBench: electronic lab notebook with some Open protocols
- LabArchives: electronic lab notebook (commercial provider); possibility to publish data publicly
- LabFolder: electronic lab notebook
- LabGuru: electronic lab notebook
- Laboratory Logbook: document and manage lab data and metadata
- Open Notebook Science: open (lab)notebook
- OpenWetWare: lab notebooks and community
- Sumatra: automated electronic lab notebook for computational projects - aims to aid reproducibility
Lab management
- AssayDepot: pharmaceutical marketplace for life science research services (from commercial suppliers)
- Docollab: Research project management and publication of experiments
- ELabInventory: Web-based laboratory inventory
- ELIXIR Tools and Data Services Registry: provide information about analytical tools and data services for bioinformatics
- LabCritics: lab equipment reviews and comparisons
- LabSuit: laboratory inventory management, share with other labs
- Plasmid.io: Manage plasmids
- Quartzy: automation of lab workflow (inventory, orders, protocols, equipment scheduling)
Experiment, collaborative or outsourced
- Crowdtruth: framework for crowdsourcing annotation data on text, images and videos
- CurateScience: online platform to facilitate replication by aggregating data/syntax files and enabling curation
- Experimonths: citizen science; month-long challenges to collect data
- Eyewire: a game to map the brain (citizen science)
- Leukippos: collaborative in silico synthetic biology research in the cloud
- Notes from Nature: Citizen Science project (Zooniverse) for transcription of with specimens from natural history museums
- OpenML: open science machine learning platform (share and collaborate on data, tasks, workflows, results)
- ScienceExchange: outsourcing experiments
- Transcriptic: remote, on-demand robotic life science research lab
Crowdsourced/collaborative analysis
- Crowdcrafting: online tool for making crowdsourcing projects
- Crowdfindings: Crowdsourced social science analysis
- Foldit: citizen science project in protein folding
- Galaxy Zoo (part of Zooniverse): crowdsourced science
- GCAT: share and compare results of different analysis tools on same datasets
- ManyLabs: tools and documentation for citizen science
- Polymath: massively collaborative online mathematical projects
- Project Noah: citizen science (studying wildlife)
- SciStarter: database of citizen science projects
- SETI@home: crowdsourced computer power for analysis (citizen science); finding intelligent life outside earth
- Snapzen: collaboratively discuss / analyze screen captures
- Socientize: citizen science network for infrastructure providers and researchers to recruit participants
- Synapse (Sage): platform for "open collaborative data analysis"
- Zooniverse: crowdsourced analysis (citizen science)
Analysis platform/code
- Appsoma: developing, running and publishing code for science applications
- Arvados: Virtual environment enabling reproducibility of data analysis with versioned scripts and tools
- DHbox: cloud-based digital humanities lab, pre-equipped w/ IPython, RStudio, Omeka, and NLTK.
- Galaxy: online data manipulation and analysis, for biomedical research but in principle field agnostic
- GenePattern: genomic analysis platform that provides access to hundreds of genomics tools.
- Google Cloud Datalab: interactive tool/platform for exploring and visualizing data
- iPython Notebook (now Jupyter Notebook): editing document format that allows combination of executable code, txt, mathematics, plots and media; parallel computing
- Jupyter: Multi-language interactive computing environments - the future home of IPython notebook and related language-agnostic projects
- Kaggle Datasets: discover and analyse public datasets [part of Kaggle]
- Kepler: create, execute, and share models and analyses; environment for integrating disparate software components
- Kitware: software solutions (many open-source) and support services for data-intensive R&D
- Opendatafit: open source tools and information to collect, fit (model) and store experimental data (esp. biomedicine)
- OpenRefine (formerly Google Refine): cleaning and transforming data, extending data with other data from web services
- Pegasus: workflow management platform that helps workflow-based applications execute
- ROpenSci: packages to connect data/literature/metric/visualization etc. repositories/search engines to R using APIs
- Statcrunch: web-based data analysis
- Voyeur/Voyant tools: web-based text analysis environment
- Wakari: web-based python data analysis
- Statcheck: check a PDF or HTML file for errors in statistical reporting
- TBE Validator service: web-based validator for XML-encoded text
- Dedoose: cross-platform app for analyzing qualitative and mixed methods research with text, photos, audio, videos, spreadsheet data and more
Other
- Hackuarium: community and lab for biohacking
- eagle-i: sharing and discovery tool for biomedical resources
- AllTrials: campaign for preregistration of clinical trials
- ClinicalTrials.gov: preregistration of clinical trials
- Prospero: preregistration of systematic reviews
- Riffyn: Process design and analysis software for reproducible research and development
- Prolific Academic: recruit participants for online studies (crowdsourcing)
- ResearchforGood: respondent samples for surveys; donates to charities/non-profits for every completed survey
- Protocol online: database of research protocols
- Benchfly: video protocols and video platform for scientists
- Benchling: data management and collaboration platform to create, find, and discuss protocols
- Protocols.io: sharing protocols
- Scientific Protocols: open source, open access scientific protocols
- OpenTrials: locate, match, and share all publicly accessible data and documents on all clinical trials
- Crowdlabs: share Vistrails workflows
- JoVe: Video Journal for biomedicine
- myExperiment: sharing workflows, esp. in bioinformatics
- RPubs: web publishing of RMarkdown documents created in RStudio
- Argo web based text mining: web based text mining
- CWL Reference Runner: Reference Implementation for the CWL Standards that enable portable batch data analysis pipelines
- BOINC: open source software for volunteer and grid computing
- Folding@home: Distributed computing project which studies protein folding, misfolding, aggregation, and related diseases
- Open Science Grid: software to support collaborative computing
