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analysis

Data extraction

  1. Morph.io: automated web-scraping
  2. Google NGram Viewer: chart frequencies of words/short sentences in Google Books
  3. Bellingcat: collaborative space for journalist led and citizen participating fact-checking
  4. Tabula: extract data from pdf tables
  5. WebPlotDigitizer: Extract data from plots, graphs, maps etc
  6. ScraperWiki: extract/scrape tables from PDFs
  7. PDF Miner: Extracting information from PDF documents
  8. TAGS: Google Sheet template which lets you setup and run automated collection of search results from Twitter
  9. Import.io: Turning web into data (scraping, parsing etc.); not restricted to scholarly use

Equipment & research samples

  1. 1degreebio: find reagents & lab products
  2. Selectscience: independent, online review resource for lab equipment and techniques
  3. Biocompare: lab equipment reviews
  4. StrainControl: lab inventory tool
  5. Sample of Science: Marketplace for (physical) sample sharing. Samples get published and receive DOI
  6. Addgene: plasmid sharing platform
  7. Resource Identification Portal: providing, discovering and citing research resources (organisms, antibodies, tools) based on RRIDs
  8. GeoSamples (SESAR): search and register geosamples and get GEOsample ID (IGSN)
  9. BioMedUSA: sharing and licensing of biological research materials and related technologies

Experiment

  1. DISK: Automated discovery of scientific knowledge (automate the hypothesize-test-evaluate discovery cycle) [login required]
  2. GenomeCompiler: Genetic design platform (manipulate and design everything from single genes to entire genomes)
  3. Tatool: Run computer based experiments (web and download) 
  4. Wings: semantic workflow system that assists scientists with the design of computational experiments
  5. Emerald Cloud Lab: web-based life sciences lab -run experiments in a central lab from anywhere in the world

Online surveys

  1. eSurveys Pro: online surveys
  2. FluidSurveys: online surveys
  3. Free online Surveys: online surveys
  4. Google Forms: online surveys
  5. Limesurvey: Online survey creating and running
  6. ProProfs Form maker: Online forms creating and hosting
  7. Qualtrics: web surveying tool
  8. SmartSurvey Academic: survey tool 
  9. Socialsci: data collection platform: design surveys and recruit from participant pool
  10. Survey Gizmo: online surveys
  11. SurveyMonkey: online surveys
  12. TypeForm: create surveys
  13. OpenDataKit: simple mobile data collection in field, with form, cloud storage and visualisation

Lab notebook

  1. Findings App: electronic lab notebook (with some protocol sharing)
  2. HiveBench: electronic lab notebook with some Open protocols
  3. LabArchives: electronic lab notebook (commercial provider); possibility to publish data publicly
  4. LabFolder: electronic lab notebook
  5. LabGuru: electronic lab notebook
  6. Laboratory Logbook: document and manage lab data and metadata
  7. Open Notebook Science: open (lab)notebook
  8. OpenWetWare: lab notebooks and community
  9. Sumatra: automated electronic lab notebook for computational projects - aims to aid reproducibility

Lab management

  1. AssayDepot: pharmaceutical marketplace for life science research services (from commercial suppliers)
  2. Docollab: Research project management and publication of experiments
  3. ELabInventory: Web-based laboratory inventory
  4. ELIXIR Tools and Data Services Registry: provide information about analytical tools and data services for bioinformatics
  5. LabCritics: lab equipment reviews and comparisons
  6. LabSuit: laboratory inventory management, share with other labs
  7. Plasmid.io: Manage plasmids
  8. Quartzy: automation of lab workflow (inventory, orders, protocols, equipment scheduling)

Experiment, collaborative or outsourced

  1. Crowdtruth: framework for crowdsourcing annotation data on text, images and videos
  2. CurateScience: online platform to facilitate replication by aggregating data/syntax files and enabling curation
  3. Experimonths: citizen science; month-long challenges to collect data 
  4. Eyewire: a game to map the brain (citizen science)
  5. Leukippos: collaborative in silico synthetic biology research in the cloud
  6. Notes from Nature: Citizen Science project (Zooniverse) for transcription of with specimens from natural history museums 
  7. OpenML: open science machine learning platform (share and collaborate on data, tasks, workflows, results)
  8. ScienceExchange: outsourcing experiments
  9. Transcriptic: remote, on-demand robotic life science research lab

Crowdsourced/collaborative analysis

  1. Crowdcrafting: online tool for making crowdsourcing projects
  2. Crowdfindings: Crowdsourced social science analysis
  3. Foldit: citizen science project in protein folding
  4. Galaxy Zoo (part of Zooniverse): crowdsourced science
  5. GCAT: share and compare results of different analysis tools on same datasets 
  6. ManyLabs: tools and documentation for citizen science
  7. Polymath: massively collaborative online mathematical projects
  8. Project Noah: citizen science (studying wildlife)
  9. SciStarter: database of citizen science projects
  10. SETI@home: crowdsourced computer power for analysis (citizen science); finding intelligent life outside earth
  11. Snapzen: collaboratively discuss / analyze screen captures
  12. Socientize: citizen science network for infrastructure providers and researchers to recruit participants 
  13. Synapse (Sage): platform for "open collaborative data analysis"
  14. Zooniverse: crowdsourced analysis (citizen science)

Analysis platform/code

  1. Appsoma: developing, running and publishing code for science applications
  2. Arvados: Virtual environment enabling reproducibility of data analysis with versioned scripts and tools
  3. DHbox: cloud-based digital humanities lab, pre-equipped w/ IPython, RStudio, Omeka, and NLTK.
  4. Galaxy: online data manipulation and analysis, for biomedical research but in principle field agnostic
  5. GenePattern: genomic analysis platform that provides access to hundreds of genomics tools.
  6. Google Cloud Datalab: interactive tool/platform for exploring and visualizing data
  7. iPython Notebook (now Jupyter Notebook): editing document format that allows combination of executable code, txt, mathematics, plots and media; parallel computing
  8. Jupyter: Multi-language interactive computing environments - the future home of IPython notebook and related language-agnostic projects
  9. Kaggle Datasets: discover and analyse public datasets [part of Kaggle]
  10. Kepler: create, execute, and share models and analyses; environment for integrating disparate software components
  11. Kitware: software solutions (many open-source) and support services for data-intensive R&D
  12. Opendatafit: open source tools and information to collect, fit (model) and store experimental data (esp. biomedicine) 
  13. OpenRefine (formerly Google Refine): cleaning and transforming data, extending data with other data from web services
  14. Pegasus: workflow management platform that helps workflow-based applications execute
  15. ROpenSci: packages to connect data/literature/metric/visualization etc. repositories/search engines to R using APIs
  16. Statcrunch: web-based data analysis
  17. Voyeur/Voyant tools: web-based text analysis environment
  18. Wakari: web-based python data analysis
  19. Statcheck: check a PDF or HTML file for errors in statistical reporting
  20. TBE Validator service: web-based validator for XML-encoded text
  21. Dedoose: cross-platform app for analyzing qualitative and mixed methods research with text, photos, audio, videos, spreadsheet data and more

Other

  1. Hackuarium: community and lab for biohacking
  2. eagle-i: sharing and discovery tool for biomedical resources
  3. AllTrials: campaign for preregistration of clinical trials
  4. ClinicalTrials.gov: preregistration of clinical trials
  5. Prospero: preregistration of systematic reviews
  6. Riffyn: Process design and analysis software for reproducible research and development 
  7. Prolific Academic: recruit participants for online studies (crowdsourcing)
  8. ResearchforGood: respondent samples for surveys; donates to charities/non-profits for every completed survey
  9. Protocol online: database of research protocols
  10. Benchfly: video protocols and video platform for scientists
  11. Benchling: data management and collaboration platform to create, find, and discuss protocols
  12. Protocols.io: sharing protocols
  13. Scientific Protocols: open source, open access scientific protocols
  14. OpenTrials: locate, match, and share all publicly accessible data and documents on all clinical trials
  15. Crowdlabs: share Vistrails workflows
  16. JoVe: Video Journal for biomedicine
  17. myExperiment: sharing workflows, esp. in bioinformatics
  18. RPubs: web publishing of RMarkdown documents created in RStudio
  19. Argo web based text mining: web based text mining
  20. CWL Reference Runner: Reference Implementation for the CWL Standards that enable portable batch data analysis pipelines
  21. BOINC: open source software for volunteer and grid computing
  22. Folding@home: Distributed computing project which studies protein folding, misfolding, aggregation, and related diseases
  23. Open Science Grid: software to support collaborative computing

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