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