A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | |
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1 | Repository name | Repository abbreviation | Home page URL | Discipline specific? (Y/N) | Discipline | Software only? (Y/N) | Require software deposit? (Y/N) | Accept software deposit? (Y/N) | Unique identifier(s) type(s) | Can mint DOIs? (Y/N) | Actively curated? (Y/N/Other) | How are entries added? | If your resource has a public scope/editorial policy, please provide a link to it. | Is your resource currently used to cite software? | Year started (only numbers) | Number of records (only numbers) | Number of records (WAS: as of Feb, 2019) Please update | Notes/comments/additional information | |||||||
2 | Arctic Data Center | ARCTIC | https://arcticdata.io | N | Natural and Social Sciences, Engineering | N | N | Y | DOI, UUID, ARK, others | Y | Y | Authors submit entries for either pure software packages or Research Objects that are mixes of software and data | https://arcticdata.io/submit/ | Y | 2016 | 6360 | 6360 | Count is for all research objects in the system. We only occasionally get pure software deposits, but software and data together in a package is the common model. Software typically represents analysis and modeling code. | |||||||
3 | Astrophysics Source Code Library | ASCL | ascl.net | Y | astrophysics, astronomy, planetary science | Y | N | Y | ASCL ID | Y | Y | Submitted by software authors or users Added by editors | https://ascl.net/home/getwp/1354 | Y | 1999 | 2381 | 2381 | ||||||||
4 | bio.tools | bio.tools | https://bio.tools | Y | Bioinformatics | Y | N | N | bio.tools IDs | N | Y | By authors, curators, specific communities, and literature mining | Y | 2016 | 17000 | 20341 | Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences. | ||||||||
5 | BioImage Information Index | BIII | www.biii.eu | Yes | Bio imaging analysis | No | No | No | doi and unique url for now for the sofwtare page description | No | Yes | manually | https://biii.eu/about | not done for this (discovering tool rather) but some usage seen in the litterature where people where giving the url to the software page in biii to descripbe a soft | 2013 | 1388 | |||||||||
6 | BioGrids Academic Software Platform | BioGrids | biogrids.org | Y | Biomedicine | Y | N | Y | DOI | Y | Y | Suggested by consortium members, curators and software developers | Y | 2015 | 378 | 378 | Academic Software Platform (ASP) BioGrids integrates a collection of ~400 scientific applications (https://biogrids.org/software/), which are ready for execution on research computing clusters. Multiple versions of applications are maintained, and users can also easily install the same stack of software on laptops, research workstations or cloud resources, under Linux or Mac OS X operating systems. Access to ASP is offered to all research groups at Harvard and affiliated institutions, and can be expanded to other academic institutions. | ||||||||
7 | Caltech Research Data Repository | CaltechDATA | data.caltech.edu | N | N | N | Y | DOI | Y | Other - Not manually (we're doing automated metadata improvements) | Submitted by authors/developers | https://www.library.caltech.edu/caltechdata/faq | Y | 2017 | 321 | 321 software, 1657 all | |||||||||
8 | Computational Infrastructure for Geodynamics | CIG | https://geodynamics.org/cig/software/ | Y | geodynamics | Y | Y | Y | DOI | N | Y | Submitted by authors/developers; reviewed by governing body. Must meet donation standards. | https://geodynamics.org/cig/software/about/, https://geodynamics.org/cig/dev/code-donation/ | Y | 2004 | 33 | 33 | Curating model data in addition to software is an active discussion topic for the community. We use zenodo for DOIs | |||||||
9 | CoMSES Net Computational Model Library | CoMSES CML | https://comses.net/codebases/ | Y | social - ecological systems | coupled human natural systems | Y | N | Y | DOI | Y | Y | Submitted by authors/developers | https://www.comses.net/about/faq/#model-library | Y | 2007 | 979 | 979 public | Offers peer review https://www.comses.net/reviews/ and mint DOIs for peer reviewed models | |||||||
10 | DDMoRe repository | http://repository.ddmore.foundation// | Y | drug development | Y | N | Y | DDMore model ID | N | N but validation checks | Submitted by authors/developers | N | 2015 | 133 | 133 | ||||||||||
11 | Debian-Med | https://blends.debian.org/med/tasks/ | Y | life sciences and medicine | Y | Y | Y | DOI, ASCL-Id, CPE, bio.tools, SciCrunch, OMICtools, bii | N | Yes | Project members package bioinformatic and other scientific software for Debian for their own needs and upon request from the public via the Debian "Intent to Package" and "Request for Package" mechanism: https://www.debian.org/devel/wnpp/ | https://en.wikipedia.org/wiki/Debian_Free_Software_Guidelines | We include the citations from the authors ("upstream" in Debian parlance). Some users may use this information to cite their dependencies.See also the https://wiki.debian.org/UltimateDebianDatabase | 2002 | 1267 | 1267 | The Debian Med team is a group of Debian Developers, Debian Maintainers, and members of the public who package bioinformatic and medical software for the Debian distribution of GNU/Linux. Similar teams following the same pattern exist for other scientific and research domains: https://www.debian.org/blends/ | ||||||||
12 | Deep Blue Data | DBD | https://deepblue.lib.umich.edu/data | N | N | N | Y | DOI | Y | Yes | Submitted by authors or proxies | 2016 | 637 | 637 | Deep Blue Data is an institutional data repository for the University of Michigan, supported by the UM Library. It is open to all UM Faculty and Graduate Students and all of the data is open access. | ||||||||||
13 | DOE CODE | https://www.osti.gov/doecode/ | N | U.S. Dept. of Energy funded | Y | Y | Y | DOI and DOE CODE ID | Y | Y | Submitted by software developers or other users | https://www.osti.gov/doecode/policy | Y | 2017 | 3015 | 3015 | DOE CODE was launched in 2017, but replaced a historical search tool/software repository ESTSC | ||||||||
14 | Environmental Data Initiative | EDI/IMCR | https://environmentaldatainitiative.org/ | Y | ecology | Y | N | N | N | N | Submitted by authors | N | 2018 | 12 | 12 | ||||||||||
15 | Hyper Article online | HAL | https://hal.archives-ouvertes.fr/ | N | N | N | Y | HAL ID | N | Y | Submitted by authors/developers | https://doc.archives-ouvertes.fr/en/legal-aspects/ | Y | 2018 | 650 | 2 625 999 for all deposits 650 software deposits | https://doc.archives-ouvertes.fr/en/homepage/ https://www.ccsd.cnrs.fr/en/open-archives/ https://doc.archives-ouvertes.fr/en/deposit/deposit-software-source-code/ | ||||||||
16 | KNB Data Repository | KNB | https://knb.ecoinformatics.org | N | Earth, Environmental, and Social Sciences | N | N | Y | DOI, UUID, ARK, others | Y | Y | Authors submit entries for either pure software packages or Research Objects that ar emixes of software and data | https://knb.ecoinformatics.org/about | Y | 1999 | 27970 | 27970 | Count is for all research objects in the system. We only occasionally get pure software deposits, but software and data together in a package is the common model. Software typically represents analysis and modeling code. | |||||||
17 | Materials Algorithms Project | MAP | https://www.phase-trans.msm.cam.ac.uk/map/mapmain.html | Y | Materials science | Y | Y | Y | N | Y | One person does the work | Requires a minimum standard of documentation, details on site | 1993 | lots | I am happy for anyone to take the entire repository and include it anywhere. Opensource. Some data are also archived. | ||||||||||
18 | ModelDB | ModelDB | https://senselab.med.yale.edu/modeldb/ | Y | computational neuroscience | Y | N | Y | N | Y | Submitted by authors/developers or entered by ModelDB team. | https://senselab.med.yale.edu/ModelDB/ | Y | 1996 | 1653 | 1653 public model entries | Moving (gradually) to modeldb.science | ||||||||
19 | Neuroimaging Informatics Tools and Resources Collaboratory | NITRC | NITRC.org | Y | Neuroimaging | N | N | Y | DOI and RRID | Y | Y | Submitted by Resouce developers | https://www.nitrc.org/include/about_us.php | Y | 2007 | 889 | 1,239 resources, 889 software resources | ||||||||
20 | OntoSoft | OntoSoft | http://ontosoft.org/ | N | Geosciences and all | Y | N | N | N | Y | Crowd sourced | N | 2015 | 940 | 940+ | OntoSoft is a decentralized software metadata registry. The goal is to enable researchers describe and specify how they want their software to be cited. OntoSoft welcomes users downloading their software descriptions, although it also hosts them online | |||||||||
21 | ORNL DAAC for Biogeochemical Dynamics | ORNL DAAC | https://daac.ornl.gov | Y | biogeochemistry (including ecological models) | N | N | Y | DOI | Y | Y | Projects funded by NASA and selected for this repository + specific request process | https://daac.ornl.gov/submit/ Note that this is broad and covers data and software. | Y | 1993 | 20 | Total: 1650 (data and SW). SW only: 20 | We have, at least in the past, archived specific versions of ecological models. We have significant interest from our advisory group in helping to guide the ecology community (especially the NASA-funded ecologists) in where and how to archive their (research) software. | |||||||
22 | Open-source Scientific Software and Service Repository | OSSR | https://purl.org/escape/ossr | Yes | Astrophysics, Particle and Astroparticle Physics | No | No | Yes | DOI | Yes | Yes | Curated process with onboarding talks and review process. | https://doi.org/10.5281/zenodo.6757112 | Yes | 2020 | 52 | OSSR in short: The ESCAPE Open-source Scientific Software and Service Repository (OSSR) is a sustainable open-access repository to share scientific software, services and datasets to the astro-particle-physics-related communities and enable open science. It is built as a curated Zenodo community integrated with several tools to enable a complete software life-cycle. The ESCAPE Zenodo community welcomes entries that support the software and service projects in the OSSR such as user-support documentation, tutorials, presentations and training activities. It also encourages the archival of documents and material that disseminate and support the goals of ESCAPE. | ||||||||
23 | OSTI.GOV | https://www.osti.gov/ | N | U.S. Dept. of Energy funded | N | Y | Y | DOI and OSTI ID | Y | Y | Submitted by authors/developers | https://www.osti.gov/faqs | Y | 2018 | 3023264 | 3023264 | OSTI.GOV was relaunched in 2018, combining the old osti.gov website and the SciTech Connect discovery tool. | ||||||||
24 | Physical Oceanography Distributed Active Archive Center | PO.DAAC | https://podaac.jpl.nasa.gov/ | Y | physical oceanography | N | N | N | DOI | Y | Y | We're only a repository for data, that happen to have some recipes. Entries are added by PO.DAAC | N | 1991 | lots | PO.DAAC is a data repository, not software. However we do develop our own software and interact with software developers regularly and are starting to look into credit and citations, but not storing software | |||||||||
25 | RDA | https://researchdata.ands.org.au/ | N | all | N | N | N | DOI | Y | Other - our repository is an aggregator, curation responsibility resides with software/data owners | Harvested from partners' repository through OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting) protocol | https://documentation.ands.org.au/display/DOC/Collection#Collection-Software | N | 2010 | 223 | 223 software records, 143133 data records | RDA (Research Data Australia) is a metadata repository, harvesting metadata from our partners' repository. RDA schema (RIF-CS) allows to describe data, software, data services, people, organisation and publications; and relationship between these objects. ARDC, who operates RDA services, work with their partners on guidelines of descibing, cititing, and curating data/software. RDA provides a DOI minting service to our partners, DOI points to the record/landing page at partner's repository. | ||||||||
26 | Research Software Directory | RSD | https://research-software-directory.org/ | No | Yes | No | No | DOI for software, DOI for related research outputs, ORCID for contributors, ROR for organizations | No | Yes | Entries are added by users via their accounts. Records are added manually but we automate this process as much as possible, for example by harvesting data from sources such as GitHub, Zenodo, DataCite, ORCID, based on persistent identifiers. | We don't have this (yet) | Yes | 2022 | 307 | The RSD has been in use by the Netherlands eScience Center as a prototype since 2018. The registry was initially only used to showcase the software produced by the eScience Center and collaborating researchers and organizations. After ample outside interest, a team of developers from the eScience Center and the Helmholtz Association has transformed the RSD into a service that can be used by all researchers and research organizations. We launched the Research Software Directory as a service in November 2022. | |||||||||
27 | The Research Software Encyclopedia | RSEPedia | https://rseng.github.io/software/ | No | Yes | No | Yes | DOIs (when available) and version control addresses | No | Yes | The entries are automatically discovered via curated sources from journals (e.g., JoSS) and other software repositories (e.g., ROpenSci, Hal, bio.tools, Research Software NL, and more to be added, current list is at: https://rseng.github.io/rse/getting-started/scrapers/index.html#scrapers) | NA | The goal is to direct the visitor to the source of truth - the GitHub / version control repository, which can have that (e.g., CITATION.cff). | 2020 | 1832 | We have anywhere from 20-50 new records added weekly, and when more sources are added this is expected to increase. | |||||||||
28 | SBGrid Academic Software Platform | SBGrid | sbgrid.org | Y | Structural Biology | Y | N | Y | DOI | Y | Y | Suggested by consortium members, curators and software developers | Y | 2001 | 453 | 453 | Academic Software Platform (ASP), SBGrid stack integrates a collection of ~500 scientific applications (https://sbgrid.org/software/), which are ready for execution on research computing clusters. Multiple versions of applications are maintained, and users can also easily install the same stack of software on laptops, research workstations or cloud resources, under Linux or Mac OS X operating systems. Access to ASP is offered to structural biology groups globally. | ||||||||
29 | SBML.org | SBML.org | http://sbml.org | Y | systems biology | y | n | n | N | Y | Either submitted by authors or by maintainers | N | 2003 | 290 | 290+ | Currently in the process of being revised & updated | |||||||||
30 | SciCrunch | RRID | https://scicrunch.org/browse/resourcedashboard | N | life science; other experimental sciences | N | N | N | RRID | N | Y | Submitted by curators, or paper authors, sometimes tool authors or editors | https://scicrunch.org/page/Curation%20Guidelines | Y | 2006 | 20,044 | 20,044 | Should contact info@scicrunch.org; if you are interested in how many RRIDs are being used please check here (as of 2/2021 it is ~35K papers!) https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=RRID&btnG= | |||||||
31 | SimTK | SimTK | https://simtk.org | Y | Biocomputation | N | N | Y | DOI | Y | N | Submitted by authors/developers | Y | 2005 | 1232 | 1536 projects (Feb, 2021) | |||||||||
32 | Software Heritage | SWH | https://www.softwareheritage.org/ | N | Y | N | Y | SWHID | N | Other- Index metadata with automatic crawlers for intrinsic metadata, codemeta.json files or package manager's files (blog-post: https://www.softwareheritage.org/2019/05/28/mining-software-metadata-for-80-m-projects-and-even-more/) | 1. harvested from forges like GitHub, Gitlab and package managers like NPM and Pypi (full list here: https://archive.softwareheritage.org/) 2. push-based deposit of software artifacts to the archive from specific clients (HAL, Intel, etc..) 3. ingestion of deprecated forges (Google Code, CodePlex) 4. User triggered archival of publicly available software projects (see https://save.softwareheritage.org) | https://www.softwareheritage.org/legal/ for SWH usage ; https://www.softwareheritage.org/mission/approach/ for our firm design decisions in terms of openness | Y | 2016 | 150000000 | origins (a.k.a url from where the code was available) 88.3M in Febuary 90.9 October 2019, 150 millions in February 2021 | SWH guidelines for using Save Code Now: https://annex.softwareheritage.org/public/guidelines/archive-research-software.pdf | ||||||||
33 | swMATH | swMATH | https://swmath.org | Y | Mathematics | Y | N | N | swMATH IDs https://www.wikidata.org/wiki/Property:P6830 | N | Y | By domain experts from swMATH | N/A | Y | 2011 | 34423 | 34423 | ||||||||
34 | Zenodo | Zenodo | https://zenodo.org | N | N | N | Y | DOI | Y | N | 1. Users can manually upload their software 2. REST APIs allow uploads via scripts or as part of CI/CD workflows 3. GitHub integration allows automatic publishing of software releases | Terms of use: https://about.zenodo.org/terms/ General Policies: https://about.zenodo.org/policies/ | Y | 2013 | 115,694 | 1,824,609 (115,694 software records) | Zenodo is based on the Invenio digital repositories framework, which at the moment is developing InvenioRDM, a turn-key solution for setting up research data management platforms with a featureset based on Zenodo. | ||||||||
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