open-science-resources
A publicly-editable collection of open science resources, including tools, datasets, meta-resources, etc.
https://github.com/asoplata/open-science-resources
Last synced: 6 days ago
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Uncategorized
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Uncategorized
- Connected Researchers - Digital tools for researchers
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Creative Commons - Choose a License
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- IODC - International Open Data Conference
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- PsychFileDrawer - Repository of psychology replication reports
- Nature Recommended Data Repositories
- Connected Researchers - Digital tools for researchers
- Glossary of Open Research Terms
- GRID - Global Research Identifier Database
- NCBI databases - National Center for Biotechnology Information database list, VERY comprehensive!
- Entrez Direct - Command-line tools for interacting with these databases
- NIF - Neuroscience Infomation Framework - Search for EVERY kind of neuroscience data, atlas, software, everything!
- SciCrunch - Science resource sharing and searching
- SciCrunch Resource Identification Portal - Searches and indexes Research Resource Identifiers (RRIDs) in literature
- Why Open Research?
- Mendeley
- Zotero
- MyScienceWork
- PeerLibrary
- Sci-Hub
- ScienceOpen
- Semantic Scholar
- Spharrho
- Bonsai - Experimental pipeline control, includes video analysis and control of experimental setups
- Full-stack Science
- GitHub for Science
- SNM - Scientific Software Network Map, tool for analyzing what software is being used in science
- Bioconductor - R software suite for analyzing high-throughput genomic data
- pandas - Data analysis in Python
- rOpenSci - Infrastructure for R software tools for scientific data analysis
- bioboxes - Bioinformatics software containers
- Neuroscience Gateway - Free cloud computation of neural models
- OpenStack
- Singularity - Containers for science, especially high-performance computing
- A Quick Guide to Software Licensing for the Scientist-Programmer
- The Whys and Hows of Licensing Scientific Code
- Broad Institute Data, Software, and Tools
- COPO - Collaborative Open Plant -Omics
- ELIXIR Core Data Resources
- EMBL-EBI - European Bioinformatics Institute database of molecular data repositories
- ExPASy - Swiss Institute of Bioinformatics (SIB) Resource Portal
- GitHub public datasets (not comprehensive)
- Google spreadsheet
- INDI - International Neuroimaging Data-Sharing Initiative
- Nature Recommended Data Repositories
- NCIP - National Cancer Informatics Program data repository
- NDA - National Institute of Mental Health (NIMH) Data Archive
- NDCT - National Database for Clinical Trials Related to Mental Illness (by the NIMH)
- NIDA Data Share - National Institute on Drug Abuse data repository
- NIDDK (National Institute of Diabetes and Digestive and Kidney Diseases) Central Repository
- NIF DISCO - Extensible Web DISCOvery tool
- NIH RePORT - Research Portfolio Open Reporting Tools, repository of grants, data, etc.
- NITRC - NeuroImaging Tools and Resources Collaboratory
- OASIS - Cancer genomics portal
- Open Data Inception - List of open data portals
- PLoS Recommended Data Reopositories
- Wikipedia List of Neuroscience Databases
- Pathway Commons - Database of public pathway and interaction databases
- PhysioNet - Database of physiological signal datasets (PhysioBank) and related tools (PhysioToolkit)
- Dataverse - Open source research data repository software
- Datazar - Cloud-based data collaboration platform
- Figshare - Online repository for sharing figures, data, and more
- List of Open Grant Proposals
- Zenodo - Research data repository
- ABIDE - Autism Brain Imaging Data Exchange
- BEI Resource Repository - Catalog of pathogens, disease agents, etc.
- BGAgenomicsDB - Genomics database for cyanobacterial genomes
- BioLINCC - Biologic Specimen and Data Repository Information Coordinating Center
- BrainSlices - Repository of brain tissue images
- C-BIG - Biological Imaging and Genetic repository
- CEBS - Chemical Effects in Biological Systems
- CERN Open Data
- Channelpedia - Wiki of neuron ion channels, hosted by the Blue Brain Project
- ClinEpiDB - Clinical Epidemiology Resources
- ClinicalTrials.gov - Probably the premier database of clinical studies
- CVRG - CardioVascular Research Grid
- Databrary - Video data library for behavioral scientists
- DIP - Database of Interacting Proteins
- EMERGE - Electronic medical records and genomics network of tools and databases
- ENSANUT - (in Spanish) Health and Nutrition National Survey of Mexico
- Ensembl - Vertebrate genome browser including BLAST, BLAT, BioMart, and VEP
- EuPathDB - Eukaryotic Pathogen Database Resources
- EumicrobeDB - Microbe and transcriptomics database
- FaceBase - Craniofacial data resource
- FITBIR - Federal Interagency Traumatic Brain Injury Research Informatics System
- FlyBase - A Drosophila Genomic and Genetic Database
- G2Aging - Gateway to Global Aging Data
- GDC - National Cancer Institute (NCI) Genomic Data Commons (formerly Cancer Genome Atlas)
- H-CUP - Healthcare Cost and Utilization Project
- Healthdata.gov - US federal government health database
- IDA LONI - Image and Data Archive for neuroscience by Laboratory of Neuro Imaging
- ICPSR - Inter-university Consortium for Political and Social Research
- iDASH - Integrating Data for Analysis, Anonymization, and Sharing
- iEEG.org - National Institutes of Neurological Disorders and Stroke (NINDS) EEG data repository for epilepsy research
- IHEC - International Human Epigenome Consortium Data Portal
- ImmPort - Immunology Database and Analysis Portal
- InterLex - Lexicon of biomedical terms (formerly NeuroLex)
- GeneNetwork (formerly WebQTL)
- Gramene - Ata resource for comparative functional genomics in crops and model plant species
- Intermine - Open-source collection of life science data repositories, and software for hosting your own
- ITN TrialShare - Immune Tolerance Network clinical trials research portal
- KEGG - Kyoto Encyclopedia of Genes and Genomes
- KLoSA - (in Korean) Korean Longitudinal Study of Ageing
- LINCS - Library of Integrated Network-based Cellular Signatures
- Metabolomics Workbench - NIH metabolomics database and toolset
- MHAS - Mexican Health and Aging Study
- miRBase - microRNA database and registry
- MPD - Mouse Phenome Database
- Nanomaterial Registry
- NAHDAP - National Addiction and HIV Data Archive Program
- National Sleep Research Resource
- NeuroData.io - Open Connectome data
- NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
- NeuroMorpho - Curated repository of digitally reconstructed neuron geometries
- NIDA (National Institute of Drug Abuse) Genetics Repository
- NIH (National Institutes of Health) Human Microbiome Project
- NMC - Neocortical Microcircuit Collaboration, part of Blue Brain
- NURSA - Nuclear Receptor Signaling Atlas
- NWB - Neurodata Without Borders - Database of electrophysiological neuroscience data
- OpenfMRI data repository
- OpenNeuro - Free and open platform for neuroimaging data (succeeds OpenfMRI)
- NACDA - National Archive of Computerized Data on Aging
- OSB - Open Source Brain
- Panther Classification System - for gene ontologies
- PDBP DMR - Parkinson's Disease Biomarkers Program Data Management Resource
- PPMI - Parkinson's Progression Markers Initiative
- PeptideAtlas - Compendium of peptides from proteomics
- ORModelDB - "A resource that is a repository of the results of the efforts of the community is computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding."
- OdorMapDB - Olfactory Bulb Odor Map DataBase
- SNPedia - Single Nucleotide Polymorphism wiki
- TCDB - Transporter Classification Database
- UCSC (University of California Santa Cruz) Genome Browser
- VectorBase - Bioinformatics resource for invertebrate vectors of human pathogens
- Wikidata for research on Wikipedia
- PhenoExplorer - Search engine for phenotype identification in dbGaP database
- RGD - Rat Genome Database
- Senselab
- CellPropDB - "Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells."
- MicrocircuitDB - "Provides an accessible location for storing and efficiently retrieving realistic computational models of brain microcircuits and networks."
- 3DModelDB - "A collection of 3D printable versions of published neuron morphologies, both traced and artificial."
- Whole Brain Catalog - Virtual catalog of a mouse brain
- Xenbase - Database of xenopus (frog) information
- ZFIN - Zebrafish Model Organism Database
- Autopatcher - DIY hardware for builting a cell autopatching system for electrophysiology
- Open Ephys - Open-source electrophysiology
- Open Optogenetics Hardware
- UCLA Miniscope
- BD2K - Big Data to Knowledge at NIH
- Biostars - Bioinformatics Q & A
- BSSW - Better Scientific SoftWare project
- eLife Innovation
- experiment - Kickstarter for science
- F1000Research
- FOSTER - Fostering open science
- Neurostars - Neuroscience Q and A
- Hypothes.is - Public annotation of scientific publications
- LinkedScience.org
- Mozilla Science Lab - Very exciting work focused on open science coding and communication
- NDS - National Data Service
- OCSD - Open and Collaborative Science in Development Network
- ODI - Open Data Institute
- OpenAIRE - Open science in Europe
- OpenData StackExchange
- OpenScienceASAP
- ORCID - Universal identifiers for researchers
- OSC - Open Science Commons
- RDA - Research Data Alliance
- SHARE - Open data about research lifecycles
- Software Carpentry - Teaching basic lab skills for research computing
- SPARC - Scholarly Publishing and Academic Resources Coalition
- Zooniverse - Large community of open citizen science projects
- OpenPlant - Synthetic Biology Research Center
- NEON - Open access data and infrastructure for ecology
- Public Lab - Inexpensive DIY environmental science
- songbird-code - Community for software related to song bird research
- European Commission Open Science Policy Platform
- NIH Software Discovery Index report
- Clowder - Open source data management for research
- OSF - Open Science Framework
- Synapse
- Liquid
- arXiv - Famous preprint server for physics, computer science, etc.
- biorXiv - Preprint server for biology
- DOAJ - Directory of Open Access Journals
- eLife - High-quality journal that's open access
- Funding for open access article publication
- gitXiv - Preprint server for computer science
- PeerJ
- Authorea
- eLife Libero - Open publishing platform
- ShareLatex
- Curvenote
- "Why the CC-BY License?" - Open Access Scholarly Publishers Association
- Nature Recommended Data Repositories
- CERN Open Data
- ModelDB - Repository of computational neuroscience models for simulation
- CellPropDB - "Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells."
- NeuronDB - "Provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances."
- 3DModelDB - "A collection of 3D printable versions of published neuron morphologies, both traced and artificial."
- ORModelDB - "A resource that is a repository of the results of the efforts of the community is computationally elucidating the structure of the olfactory receptor with a view to establishing a mechanistic basis for OR-odorant binding."
- OdorMapDB - Olfactory Bulb Odor Map DataBase
- OdorDB - Odor Molecules DataBase
- ORDB - Olfactory Receptor DataBase
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- OASIS - Cancer genomics portal
- Overleaf
- Open Hardware Repository - run by CERN
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- miRBase - microRNA database and registry
- Nature Recommended Data Repositories
- CVRG - CardioVascular Research Grid
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- psyArXiv - Preprint server for psychology
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Nature Recommended Data Repositories
- Connected Researchers - Digital tools for researchers
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