ABCDEFGHIJKLMNOPQRSTUVWXY
1
Repository nameRepository abbreviationHome page URLDiscipline specific? (Y/N)DisciplineSoftware 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 CenterARCTIChttps://arcticdata.ioNNatural and Social Sciences, EngineeringNNY
DOI, UUID, ARK, others
YYAuthors submit entries for either pure software packages or Research Objects that are mixes of software and data
https://arcticdata.io/submit/
Y201663606360Count 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 LibraryASCLascl.netYastrophysics, astronomy, planetary scienceYNYASCL IDYYSubmitted by software authors or users
Added by editors
https://ascl.net/home/getwp/1354Y199923812381
4
bio.toolsbio.toolshttps://bio.toolsYBioinformaticsYNNbio.tools IDsNYBy authors, curators, specific communities, and literature miningY20161700020341Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences.
5
BioImage Information Index
BIIIwww.biii.euYes
Bio imaging analysis
NoNoNo
doi and unique url for now for the sofwtare page description
NoYesmanually
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
20131388
6
BioGrids Academic Software PlatformBioGridsbiogrids.orgYBiomedicineYNYDOIYYSuggested by consortium members, curators and software developersY2015378378Academic 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 RepositoryCaltechDATAdata.caltech.eduNNNYDOIYOther - Not manually (we're doing automated metadata improvements)Submitted by authors/developershttps://www.library.caltech.edu/caltechdata/faqY2017321321 software, 1657 all
8
Computational Infrastructure for GeodynamicsCIGhttps://geodynamics.org/cig/software/YgeodynamicsYYYDOINYSubmitted by authors/developers; reviewed by governing body. Must meet donation standards.https://geodynamics.org/cig/software/about/, https://geodynamics.org/cig/dev/code-donation/Y20043333Curating model data in addition to software is an active discussion topic for the community.
We use zenodo for DOIs
9
CoMSES Net Computational Model LibraryCoMSES CMLhttps://comses.net/codebases/Ysocial - ecological systems | coupled human natural systemsYNYDOIYYSubmitted by authors/developershttps://www.comses.net/about/faq/#model-libraryY2007979979 publicOffers peer review https://www.comses.net/reviews/ and mint DOIs for peer reviewed models
10
DDMoRe repositoryhttp://repository.ddmore.foundation//Ydrug developmentYNYDDMore model IDNN but validation checksSubmitted by authors/developersN2015133133
11
Debian-Medhttps://blends.debian.org/med/tasks/Ylife sciences and medicineYYY
DOI, ASCL-Id, CPE, bio.tools, SciCrunch, OMICtools, bii
NYesProject 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/UltimateDebianDatabase200212671267The 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 DataDBDhttps://deepblue.lib.umich.edu/dataNNNYDOIYYesSubmitted by authors or proxies2016637637Deep 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 CODEhttps://www.osti.gov/doecode/NU.S. Dept. of Energy fundedYYYDOI and DOE CODE IDYYSubmitted by software developers or other usershttps://www.osti.gov/doecode/policyY201730153015DOE CODE was launched in 2017, but replaced a historical search tool/software repository ESTSC
14
Environmental Data InitiativeEDI/IMCRhttps://environmentaldatainitiative.org/YecologyYNNNNSubmitted by authorsN20181212
15
Hyper Article online HALhttps://hal.archives-ouvertes.fr/NNNYHAL IDNY
Submitted by authors/developers
https://doc.archives-ouvertes.fr/en/legal-aspects/
Y20186502 625 999 for all deposits 650 software depositshttps://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 RepositoryKNBhttps://knb.ecoinformatics.orgNEarth, Environmental, and Social SciencesNNY
DOI, UUID, ARK, others
YYAuthors submit entries for either pure software packages or Research Objects that ar emixes of software and data
https://knb.ecoinformatics.org/about
Y19992797027970Count 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 ProjectMAPhttps://www.phase-trans.msm.cam.ac.uk/map/mapmain.htmlYMaterials scienceYYYNYOne person does the workRequires a minimum standard of documentation, details on site1993lotsI am happy for anyone to take the entire repository and include it anywhere. Opensource. Some data are also archived.
18
ModelDBModelDBhttps://senselab.med.yale.edu/modeldb/Ycomputational neuroscienceYNYNYSubmitted by authors/developers or entered by ModelDB team.https://senselab.med.yale.edu/ModelDB/Y199616531653 public model entriesMoving (gradually) to modeldb.science
19
Neuroimaging Informatics Tools and Resources CollaboratoryNITRCNITRC.orgYNeuroimagingNNYDOI and RRIDYYSubmitted by Resouce developershttps://www.nitrc.org/include/about_us.phpY20078891,239 resources, 889 software resources
20
OntoSoftOntoSofthttp://ontosoft.org/NGeosciences and allYNNNYCrowd sourcedN2015940940+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 DynamicsORNL DAAChttps://daac.ornl.govYbiogeochemistry (including ecological models)NNYDOIYYProjects 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.Y199320Total: 1650 (data and SW). SW only: 20We 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
OSSRhttps://purl.org/escape/ossrYes
Astrophysics, Particle and Astroparticle Physics
NoNoYesDOIYesYes
Curated process with onboarding talks and review process.
https://doi.org/10.5281/zenodo.6757112
Yes202052
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.GOVhttps://www.osti.gov/NU.S. Dept. of Energy fundedNYYDOI and OSTI IDYYSubmitted by authors/developershttps://www.osti.gov/faqsY201830232643023264OSTI.GOV was relaunched in 2018, combining the old osti.gov website and the SciTech Connect discovery tool.
24
Physical Oceanography Distributed Active Archive CenterPO.DAAChttps://podaac.jpl.nasa.gov/Yphysical oceanographyNNNDOIYYWe're only a repository for data, that happen to have some recipes. Entries are added by PO.DAACN1991lotsPO.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
RDAhttps://researchdata.ands.org.au/NallNNNDOIYOther - 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) protocolhttps://documentation.ands.org.au/display/DOC/Collection#Collection-SoftwareN2010223223 software records, 143133 data recordsRDA (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/
NoYesNoNo
DOI for software, DOI for related research outputs, ORCID for contributors, ROR for organizations
NoYes
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)
Yes2022307
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 EncyclopediaRSEPediahttps://rseng.github.io/software/NoYesNoYesDOIs (when available) and version control addressesNoYesThe 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)NAThe goal is to direct the visitor to the source of truth - the GitHub / version control repository, which can have that (e.g., CITATION.cff).20201832We have anywhere from 20-50 new records added weekly, and when more sources are added this is expected to increase.
28
SBGrid Academic Software PlatformSBGridsbgrid.orgYStructural BiologyYNYDOIYYSuggested by consortium members, curators and software developersY2001453453Academic 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.orgSBML.orghttp://sbml.orgYsystems biologyynnNYEither submitted by authors or by maintainersN2003290290+Currently in the process of being revised & updated
30
SciCrunchRRIDhttps://scicrunch.org/browse/resourcedashboardNlife science; other experimental sciencesNNNRRIDNYSubmitted by curators, or paper authors, sometimes tool authors or editorshttps://scicrunch.org/page/Curation%20GuidelinesY200620,04420,044Should 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
SimTKSimTKhttps://simtk.orgYBiocomputationNNYDOIYNSubmitted by authors/developersY200512321536 projects (Feb, 2021)
32
Software HeritageSWHhttps://www.softwareheritage.org/NYNYSWHIDNOther- 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 opennessY2016150000000 origins (a.k.a url from where the code was available) 88.3M in Febuary 90.9 October 2019, 150 millions in February 2021SWH guidelines for using Save Code Now: https://annex.softwareheritage.org/public/guidelines/archive-research-software.pdf
33
swMATHswMATHhttps://swmath.orgYMathematicsYNN
swMATH IDs https://www.wikidata.org/wiki/Property:P6830
NYBy domain experts from swMATHN/AY20113442334423
34
ZenodoZenodohttps://zenodo.orgNNNYDOIYN1. 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/
Y2013115,694
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.
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100