| |
| 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! | | | |
| re3data - Registry of Research Data Repositories | | | |
| SciCrunch - Science resource sharing and searching | | | |
| SciCrunch Resource Identification Portal - Searches and indexes Research Resource Identifiers (RRIDs) in literature | | | |
| |
| https://www.force11.org/group/resource-identification-initiative | | | For more information: |
| |
| Why Open Research? | | | |
Open Science Resources / Bibliography Management Software |
| Mendeley | | | |
| Papers | | | |
| Zotero | | | |
Open Science Resources / Indexing of Publications and Search |
| Europe PMC - Similar to PubMed Central below | | | |
| Google Scholar | | | |
| MyScienceWork | | | |
| PeerLibrary | | | |
| PubMed - NIH NCBI hosted index of biomedical literature | | | |
| PubMed Central (PMC) - The collection of free full-text publications on PubMed | | | |
| Sci-Hub | | | |
| ScienceOpen | | | |
| Semantic Scholar | | | |
| Spharrho | | | |
Open Science Resources / Open Code |
| Awesome Pipeline - List of pipeline, HPC, and scientific software | 6,227 | 11 months ago | |
| Bonsai - Experimental pipeline control, includes video analysis and control of experimental setups | | | |
| Full-stack Science | | | |
| Funding research software development | | | |
| GitHub for Science | | | |
| SciUnit - Formally validating scientific models against data | 48 | almost 2 years ago | |
| 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 | | | |
| Google DataLab | | | |
| 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 | | | |
| Choose a License.com | | | |
| A Quick Guide to Software Licensing for the Scientist-Programmer | | | |
| The Whys and Hows of Licensing Scientific Code | | | |
Open Science Resources / Open Data Repositories and Services |
| academictorrents | | | |
| Broad Institute Data, Software, and Tools | | | |
| COPO - Collaborative Open Plant -Omics | | | |
| DataCite | | | |
| 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 | | | |
Open Science Resources / Open Data Repositories and Services / Nature Recommended Data Repositories |
| https://figshare.com/articles/Scientific_Data_recommended_repositories_June_2015/1434640 | | | Also here: |
Open Science Resources / Open Data Repositories and Services |
| NCBI databases - National Center for Biotechnology Information database list, VERY comprehensive! | | | |
| 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 - Neuroscience Information Framework, massive search engine for neuroscience data, tools, etc. | | | |
| |
| NIF DISCO - Extensible Web DISCOvery tool | | | |
Open Science Resources / Open Data Repositories and Services |
| NIH RePORT - Research Portfolio Open Reporting Tools, repository of grants, data, etc. | | | |
| NITRC - NeuroImaging Tools and Resources Collaboratory | | | |
| OASIS - Cancer genomics portal | | | |
| OBO Foundry - Open Biological and Biomedical Ontology database | | | |
| Open Data Inception - List of open data portals | | | |
| Pathway Commons - Database of public pathway and interaction databases | | | |
| PhysioNet - Database of physiological signal datasets (PhysioBank) and related tools (PhysioToolkit) | | | |
| PLoS Recommended Data Reopositories | | | |
| UniProt - Repository of protein sequence and functional information databases | | | |
| Wikipedia List of Neuroscience Databases | | | |
| Dataverse - Open source research data repository software | | | |
| Datazar - Cloud-based data collaboration platform | | | |
| Dryad Digital Repository | | | |
| Figshare - Online repository for sharing figures, data, and more | | | |
| List of Open Grant Proposals | | | |
| OSF - Open Science Framework | | | |
| re3data - Registry of Research Data Repositories | | | |
| Zenodo - Research data repository | | | |
| GigaDB - Citable datasets that have been assigned DOIs and are available for public download and use | | | |
| 3D Brain Atlas Reconstructor | | | |
| ABIDE - Autism Brain Imaging Data Exchange | | | |
| Allen Brain Atlas Data Portal | | | |
Open Science Resources / Open Data Repositories and Services / Allen Brain Atlas Data Portal |
| More detail here | | | |
Open Science Resources / Open Data Repositories and Services |
| BEI Resource Repository - Catalog of pathogens, disease agents, etc. | | | |
| BGAgenomicsDB - Genomics database for cyanobacterial genomes | | | |
| BioLINCC - Biologic Specimen and Data Repository Information Coordinating Center | | | |
| BioGRID - Biological General Repository for Interaction Datasets | | | |
| BrainSlices - Repository of brain tissue images | | | |
| C-BIG - Biological Imaging and Genetic repository | | | |
| CCF - Connectome Coordination Facility, includes Human Connectome Projects | | | |
| 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 | | | |
| COMBINE - Computational modeling in biology network | | | |
| CRCNS - Collaborative Research in Computational Neuroscience | | | |
| CVRG - CardioVascular Research Grid | | | |
| Databrary - Video data library for behavioral scientists | | | |
| DataLad - Data package management system, easing the use of accessing open data sets | | | |
| 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) | | | |
| GEO - Gene Ontology Consortium | | | |
| GeneNetwork (formerly WebQTL) | | | |
| GIN - Modern Research Data Management for Neuroscience | | | |
| Gramene - Ata resource for comparative functional genomics in crops and model plant species | | | |
| 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) | | | |
| Intermine - Open-source collection of life science data repositories, and software for hosting your own | | | |
| IRD - Influenza Research Database | | | |
| 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 | | | |
| ModelDB - Repository of computational neuroscience models for simulation | | | , built by |
| MPD - Mouse Phenome Database | | | |
| MIMIC-II - Multiparameter Intelligent Monitoring in Intensive Care II, a critical care database | | | |
| Nanomaterial Registry | | | |
| NAHDAP - National Addiction and HIV Data Archive Program | | | |
| NACDA - National Archive of Computerized Data on Aging | | | |
| National Sleep Research Resource | | | |
| NCBO BioPortal - National Center for Biomedical Ontology repository | | | |
| 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 | | | |
| NeuroVault - Public repository of MRI and PET statistical maps,
parcellations, and atlases | | | |
| 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) | | | |
| OpenWorm - Popular platform for simulation and analysis of nematode neuroscience models! | | | |
| 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 | | | |
| PhenoExplorer - Search engine for phenotype identification in dbGaP database | | | |
| PsychFileDrawer - Repository of psychology replication reports | | | |
| PubChem chemical database | | | |
| RCSB PDB - Research Collaboration for Structural Bioinformatics Protein Data Bank | | | |
| RGD - Rat Genome Database | | | |
| Reactome - Pathway, protein, and reaction database | | | |
| RxNorm - Database of normalized drug names | | | |
| Senselab | | | hosts several other databases, but is the most popular: |
Open Science Resources / Open Data Repositories and Services / 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." | | | |
| NeuronDB - "Provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances." | | | |
| 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." | | | |
| 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 | | | |
Open Science Resources / Open Data Repositories and Services |
| SNPedia - Single Nucleotide Polymorphism wiki | | | |
| TCIA - The Cancer Imaging Archive | | | |
| 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 | | | |
| WikiPathways - Database of biological pathways | | | |
| Whole Brain Catalog - Virtual catalog of a mouse brain | | | |
| WormBase - Database of nematode information | | | |
| Xenbase - Database of xenopus (frog) information | | | |
| ZFIN - Zebrafish Model Organism Database | | | |
Open Science Resources / Open DIY Hardware |
| Autopatcher - DIY hardware for builting a cell autopatching system for electrophysiology | | | |
| FinchSchope - 3D printed miniature microscope | 35 | almost 2 years ago | and accompanying |
| Open Ephys - Open-source electrophysiology | | | |
| Open Hardware Repository - run by CERN | | | |
| Open Optogenetics Hardware | | | |
| UCLA Miniscope | | | |
Open Science Resources / Organizations Conferences Communities |
| BD2K - Big Data to Knowledge at NIH | | | |
| Biostars - Bioinformatics Q & A | | | |
| BSSW - Better Scientific SoftWare project | | | |
| Codata - Committee on Data of the International Council for Science | | | |
| Code for Science and Society | | | |
| Code is Science | | | |
| COS - Center for Open Science | | | |
| Data Carpentry - Teaching universal data literacy, sibling of Software Carpentry | | | |
| eLife Innovation | | | |
| experiment - Kickstarter for science | | | |
| F1000Research | | | |
| FORCE11 - Scientific community dedicated to improving knowledge sharing capabilities in scholarly communication | | | |
| FOSTER - Fostering open science | | | |
| Helmholtz Open Science | | | |
| Hypothes.is - Public annotation of scientific publications | | | |
| IODC - International Open Data Conference | | | |
| LinkedScience.org | | | |
| Mozilla Science Lab - Very exciting work focused on open science coding and communication | | | |
| NDS - National Data Service | | | |
Open Science Resources / Organizations Conferences Communities / NDS - National Data Service |
| NDS Labs code | 8 | almost 2 years ago | |
Open Science Resources / Organizations Conferences Communities |
| Neurostars - Neuroscience Q and A | | | |
| NumFocus - Open Code = Better Science | | | |
| OBF - Open Bioinformatics Foundation, geared towards open science code development | | | |
| OCSD - Open and Collaborative Science in Development Network | | | |
| ODI - Open Data Institute | | | |
| OpenAIRE - Open science in Europe | | | |
| OpenCon conference | | | |
| OpenData StackExchange | | | |
| OpenScienceASAP | | | |
| ORCID - Universal identifiers for researchers | | | |
| OSC - Open Science Commons | | | |
| RDA - Research Data Alliance | | | |
| ResBaz - Research Bazaar | | | |
| SHARE - Open data about research lifecycles | | | |
| Software Carpentry - Teaching basic lab skills for research computing | | | |
| SPARC - Scholarly Publishing and Academic Resources Coalition | | | |
| SSI - Software Sustainability Institute, focused on enhancing scientific coding | | | |
| TailorDev - "Best practices and software for an Open Science" | | | |
| Zooniverse - Large community of open citizen science projects | | | |
| OpenPlant - Synthetic Biology Research Center | | | |
| Organization for Human Brain Mapping | | | |
| NEON - Open access data and infrastructure for ecology | | | |
| Public Lab - Inexpensive DIY environmental science | | | |
| songbird-code - Community for software related to song bird research | | | |
Open Science Resources / Policy |
| European Commission Open Science Policy Platform | | | |
| NIH Software Discovery Index report | | | |
Open Science Resources / Project Management |
| Clowder - Open source data management for research | | | |
| OSF - Open Science Framework | | | built by |
| Synapse | | | built by |
| Liquid | | | |
Open Science Resources / Publishing |
| arXiv - Famous preprint server for physics, computer science, etc. | | | |
| biorXiv - Preprint server for biology | | | |
| Cofactor - Open access journal selector | | | |
| DOAJ - Directory of Open Access Journals | | | |
| eLife - High-quality journal that's open access | | | |
| F1000Research | | | |
| Funding for open access article publication | 4 | over 6 years ago | |
| gitXiv - Preprint server for computer science | | | |
| OAD - Open Access Directory | | | |
| PeerJ | | | |
| psyArXiv - Preprint server for psychology | | | |
| ReScience Journal - Journal focused on reproducible computational research
and replication | | | |
| Authorea | | | |
| eLife Libero - Open publishing platform | | | |
| Overleaf | | | |
| ShareLatex | | | |
| Curvenote | | | |
| Creative Commons - Choose a License | | | |
| "Why the CC-BY License?" - Open Access Scholarly Publishers Association | | | |
open-science-resources 
0ex/more-awesome
ptdz/sorted
openwdl/wdl
kirillseva/ruigi
argoproj/argo-workflows
scipipe/scipipe
jackbackes/happycommit
stadiamaps/pmtiles-rs
keikoproj/active-monitor
argoproj-labs/hera
minerva-ml/steppy
duecredit/duecredit
aiidateam/aiida-core
broadinstitute/cromwell