Open Science Resources Save
A publicly-editable collection of open science resources, including tools, datasets, meta-resources, etc.
Project README
Open Science Resources
Scientific data and tools should, as much as possible, be free as in beer and free as in freedom. The vast majority of science today is paid for by taxpayer-funded grants; at the same time, the incredible successes of science are strong evidence for the benefit of collaboration in knowledgable pursuits. Within the scientific academy, sharing of expertise, data, tools, etc. is prolific, but only recently with the rise of the Open Access movement has this sharing come to embrace the public. Even though most research data is never shared, both the public and even scientists in their own fields are often unaware of just much data, tools, and other resources are made freely available for analysis! This list is a small attempt at bringing light to data repositories and computational science tools that are often siloed according to each scientific discipline, in the hopes of spurring along both public and professional contributions to science. These categories are very non-exclusive, as many resources could fit multiple categories. If you're interested in computational neuroscience specifically, I've made a similar repo-list of open computational neuroscience resources here.
Contributions are VERY welcome!
- Contents:
Meta-resources
- 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!
- 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
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SciCrunch Resource Identification Portal - Searches and indexes Research Resource Identifiers (RRIDs) in literature
- For more information: https://www.force11.org/group/resource-identification-initiative
- Why Open Research?
Bibliography Management Software
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 Code
- Awesome Pipeline - List of pipeline, HPC, and scientific software
- 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
- SNM - Scientific Software Network Map, tool for analyzing what software is being used in science
Analysis Tools
- 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
Cloud Computing and Containerization
- bioboxes - Bioinformatics software containers
- Neuroscience Gateway - Free cloud computation of neural models
- OpenStack
- Singularity - Containers for science, especially high-performance computing
Code Licensing Guides
- Choose a License.com
- A Quick Guide to Software Licensing for the Scientist-Programmer
- The Whys and Hows of Licensing Scientific Code
Open Data Repositories and Services
Meta-resources for open data repositories
- 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
- 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.
- 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
Non-specific
- 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
Specific to field
- 3D Brain Atlas Reconstructor
- ABIDE - Autism Brain Imaging Data Exchange
- Allen Brain Atlas Data Portal
- 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 Senselab
- 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
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Senselab hosts several other databases, but ModelDB is the most popular:
- 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
- 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 DIY Hardware
- Autopatcher - DIY hardware for builting a cell autopatching system for electrophysiology
- FinchSchope - 3D printed miniature microscope and accompanying VideoCapture software
- Open Ephys - Open-source electrophysiology
- Open Hardware Repository - run by CERN
- Open Optogenetics Hardware
- UCLA Miniscope
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
- 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
Specific to field
- 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
Policy
Project Management
- Clowder - Open source data management for research
- OSF - Open Science Framework built by Center for Open Science
- Synapse built by Sage Bionetworks
- Liquid
Publishing
Journals for Open Science and Open Access
- 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
- 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
Manuscript Collaboration
Manuscript Licensing
Open Source Agenda is not affiliated with "Open Science Resources" Project. README Source: asoplata/open-science-resources
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1 year ago
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