Zenodo org что это
Zenodo, как и для чего?
Чем полезен Zenodo?
Обмен и связь исследований: Zenodo предоставляет богатый интерфейс, который позволяет связывать результаты исследований с наборами данных и информацией о финансировании.
Надежный и безопасный: данные хранятся в CERN, который обладает значительными знаниями и опытом работы с крупномасштабными цифровыми хранилищами. Файлы данных и метаданные хранятся в нескольких онлайн и автономных копиях.
Включает информацию о финансировании и упрощает отчетность: Zenodo позволяет связывать загрузки с грантами от более чем 11 спонсоров, таких как Европейская комиссия, Национальный научный фонд и Wellcome Trust. Zenodo далее интегрируется в линии отчетности для исследований, финансируемых Европейской комиссией через OpenAIRE.
Гибкое лицензирование: Zenodo рекомендует Вам делиться своими исследованиями, как можно более открыто, чтобы максимально использовать и повторно использовать результаты своих исследований. Есть возможность загрузки под различными лицензиями и уровнями доступа.
Размещение Ваших исследований на Zenodo даст Вам возможность показать Ваше исследования большему кругу читателей
О том как зарегистрироваться на сайте и добавить статью мы подробно расскажем в нашем видео на YouTube канале «Технологический центр»
About Zenodo
Passionate about Open Science!
Built and developed by researchers, to ensure that everyone can join in Open Science.
The OpenAIRE project, in the vanguard of the open access and open data movements in Europe was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. CERN, an OpenAIRE partner and pioneer in open source, open access and open data, provided this capability and Zenodo was launched in May 2013.
In support of its research programme CERN has developed tools for Big Data management and extended Digital Library capabilities for Open Data. Through Zenodo these Big Science tools could be effectively shared with the long-tail of research.
Open Science knows no borders!
The need for a catch-all is not restricted to one funder, or one nation, so the concept caught on, and Zenodo rapidly started welcoming research from all over the world, and from every discipline.
The digital revolution has necessitated a retooling of the scholarly processes to handle data and software, but this is proceeding at varying speeds across different communities, disciplines, and nations. To ensure no one is left behind through lack of access to the necessary tools and resources, Zenodo makes the sharing, curation and publication of data and software a reality for all researchers.
Every last detail
To fully understand and reproduce research performed by others, it is necessary to have all the details. In the digital age, that means all the digital artefacts, which are all welcomed in Zenodo.
To be an effective catch-all, that eliminates barriers to adopting data sharing practices, Zenodo does not impose any requirements on format, size, access restrictions or licence. Quite literally we wish there to be no reason for researchers not to share!
Data, software and other artefacts in support of publications may be the core, but equally welcome are the materials associated with the conferences, projects or the institutions themselves, all of which are necessary to understand the scholarly process.
Don’t wait until the publication date!
Publication may happen months or years after completion of the research, so collecting together all the research artefacts at that stage to publish openly is often challenging. Zenodo therefore offers the possibility to house closed and restricted content, so that artefacts can be captured and stored safely whilst the research is ongoing, such that nothing is missing when they are openly shared later in the research workflow.
Additionally, to help publishing, research materials for the review process can be safely uploaded to Zenodo in restricted records and then protected links can be shared with the reviewers. Content can also be embargoed and automatically opened when the associated paper is published.
To support all these use cases, the simple web interface is supplemented by a rich API which allows third party tools and services to use Zenodo as a backend in their workflow
Open Science Services
Zenodo helps researchers receive credit by making the research results citable and through OpenAIRE integrates them into existing reporting lines to funding agencies like the European Commission. Citation information is also passed to DataCite and onto the scholarly aggregators.
For future generations
The scholarly communication landscape is undergoing change, there are debates about the ideal services, the ideal business models, the ideal custodians, amidst which Zenodo aims to offer a viable and concrete alternative to commercial services from a memory institution for particle physics, CERN!
The name
Zenodo is derived from Zenodotus, the first librarian of the Ancient Library of Alexandria and father of the first recorded use of metadata, a landmark in library history.
Open in every sense
Zenodo code is itself open source, and is built on the foundation of the Invenio digital library which is also open source. The work-in-progress, open issues, and roadmap are shared openly in GitHub, and contributions to any aspect are welcomed from anyone.
All meta data is openly available under CC0 licence, and all open content is openly accessible through open APIs.
Open to all suggestions for new features, via GitHub, and especially open to all contributions of code via pull requests!
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Zenodo Advocacy
Happy with Zenodo? Every little effort helps reach a global audience and spread the word about Open Science and how Zenodo makes it possible.
Material
Feel free to use the following material to help present Zenodo. All material is licensed CC-BY.
In the press
Check out our Zotero group for articles mentioning or talking about Zenodo.
Know of an article not on the list? Contact us, so we can add it.
Citing Zenodo
To cite Zenodo, you can use the following BibTeX:
Infrastructure
Organisational
Host institution
Zenodo is hosted by CERN which has existed since 1954 and currently has an experimental programme defined for the next 20+ years. CERN is a memory institution for High Energy Physics and renowned for its pioneering work in Open Access. Organisationally Zenodo is embedded in the IT Department, Collaboration Devices and Applications Group, Digital Repositories Section (IT-CDA-DR).
Zenodo is offered by CERN as part of its mission to make available the results of its work (CERN Convention, Article II, §1).
Legal status
CERN is an intergovernmental organisation and has legal personality in the metropolitan territories of all CERN Member States (CERN Convention, Article IX) and enjoys the corresponding legal capacity under public international law.
As an intergovernmental organization CERN enjoys certain privileges and immunities, including e.g. immunity from jurisdiction of the national courts to ensure our independence from individual Member States. This does not mean that CERN operate in some kind of legal vacuum as protocols requires that CERN settle its disputes by other means. Read more about CERN’s legal status in the CERN Bulletin.
Funding
Zenodo is funded by:
Zenodo is developed and supported as a marginal activity, and hosted on top of existing infrastructure and services at CERN, in order to reduce operational costs and rely on existing efforts for High Energy Physics. CERN has some of the world’s top experts in running large scale research data infrastructures and digital repositories that we rely on in order to deliver a trusted digital repository.
Staff
Zenodo is operated currently by:
Zenodo is however embedded in a much larger team, headed by Jose Benito Gonzalez Lopez, which runs services such as CERN Document Server, CERN Open Data, CERN Analysis Preservation and we rely heavily on co-developing features via the Invenio digital library framework.
Memberships
CERN is an active member of the following organisations and international bodies (non-exhaustive):
We are partners in multiple European Commission funded projects, amongst others:
Technical
Zenodo is powered by CERN Data Centre and the Invenio digital library framework and is fully run on open source products all the way through.
Physically, Zenodo’s entire technical infrastructure is located on CERN’s premises which is subject to CERN’s legal status (see above).
Server management
Zenodo servers are managed via OpenStack and Puppet configuration management system which ensures that our servers always have the latest security patches applied. Servers are monitored via CERN’s monitoring infrastructure based on Flume, Elasticsearch, Kibana and Hadoop. Application errors are logged and aggregated in a local Sentry instance. Traffic to Zenodo frontend servers is load balanced via a combination of DNS load balancing and HAProxy load balancers.
We are furthermore running two independent systems: one production system and one quality assurance system. This ensures that all changes, whether at infrastructure level or source code level, can be tested and validated on our quality assurance system prior to being applied to our production system.
Frontend servers
Zenodo frontend servers are responsible for running the Invenio repository platform application which is based on Python and the Flask web development framework. The frontend servers are running nginx HTTP server and uwsgi application server in front of the application and nginx is in addition in charge of serving static content.
Data storage
All files uploaded to Zenodo are stored in CERN’s EOS service in an 18 petabytes disk cluster. Each file copy has two replicas located on different disk servers.
For each file we store two independent MD5 checksums. One checksum is stored by Invenio, and used to detect changes to files made from outside of Invenio. The other checksum is stored by EOS, and used for automatic detection and recovery of file corruption on disks.
Zenodo may, depending on access patterns in the future, move the archival and/or the online copy to CERN’s offline long-term tape storage system CASTOR in order to minimize long-term storage costs.
EOS is the primary low latency storage infrastructure for physics data from the Large Hadron Collider (LHC) and CERN currently operates multiple instances totalling 150+ petabytes of data with expected growth rates of 30-50 petabytes per year. CERN’s CASTOR system currently manages 100+ petabytes of LHC data which are regularly checked for data corruption.
Invenio provides an object store like file management layer on top of EOS which is in charge of e.g. version changes to files.
Metadata storage
Metadata and persistent identifiers in Zenodo are stored in a PostgreSQL instance operated on CERN’s Database on Demand infrastructure with 12-hourly backup cycle with one backup sent to tape storage once a week. Metadata is in addition indexed in an Elasticsearch cluster for fast and powerful searching. Metadata is stored in JSON format in PostgreSQL in a structure described by versioned JSONSchemas. All changes to metadata records on Zenodo are versioned, and happening inside database transactions.
In addition to the metadata and data storage, Zenodo relies on Redis for caching and RabbitMQ and python Celery for distributed background jobs.
Security
We take security very serious and do our best to protect your data.
Special note on closed access data
Инструменты публикации кода в научных исследованиях
Алена Беглер, лаб-менеджер небезызвестной «семерки» на факультете психологии СПбГУ, написала для #горячихюныхкогнитивных большой и очень полезный материал по инструментам публикации кода в научных исследованиях. Особенно полезно будет тем, кто участвует в нашем конкурсе экспериментальных программ MARVIN (http://thinkcognitive.org/ru/nerd).
Сейчас существует более семидесяти специализированных хранилищ научного кода (по данным Регистра научных репозиториев), не считая университетских хранилищ и инструментов для совместной работы с кодом, ориентированных на разработчиков. Эти хранилища отличаются по дисциплинам (например, для биохимиков), типам данных (например, только для массивов сырых данных), странам и предназначению (например, для публикации данных определённого проекта). Хранилищ общего назначения для публикации кода научных исследований в открытом доступе есть минимум четыре: figshare (https://figshare.com/), Zenodo (https://zenodo.org/), OSF (https://osf.io/) и GitHub (https://github.com/). Про них дальше и пойдёт речь.
Что это такое?
По сути, это хранилища данных в широком смысле: результатов экспериментов, постеров, исходного кода и так далее. OSF, figshare и Zenodo изначально создавались для научных исследований; GitHub позиционировался как инструмент для совместной работы над кодом и в последние несколько лет добавил функционал, делающий его полностью подходящим для хранения исследовательского кода. У этих четырёх систем много общего (по крайней мере, на уровне пользователя). Все они:
Общие минусы всех проектов такого типа: слабый редактор кода (или его отсутствие) и некоторый порог вхождения — на них нужно как минимум зарегистрироваться в английском интерфейсе, а для некоторых платформ и посмотреть краткий мануал.
Как этим пользоваться?
Если кратко: зарегистрироваться — залить данные/код/итд — добавить метаданные — опубликовать. Два момента, которые важны при выкладке своих материалов в открытый доступ. Первый — упомянутые метаданные. Это, по сути, описание проекта: название, краткая характеристика, информация об авторах и так далее. В большинстве хранилищ наличие минимума метаданных — обязательное условие добавления файлов, но чем они полнее, тем, во-первых, проще другим будет получить информацию о проекте (и вообще найти его), во-вторых, вспомнить детали через пару лет после его завершения. Второй — лицензия. Всё, что выложено в открытый доступ обязательно нужно лицензировать — без этого ваши данные или код будут фактически недоступны для других исследователей, ведь по умолчанию отсутствие лицензии означает, что автор не разрешил использование. Лицензия — это способ его разрешить и заодно проконтролировать то, какие права вы готовы предоставить пользователям. По умолчанию большинство репозиториев предлагает лицензию Creative Commons CC-BY, которая позволяет использовать и изменять материалы как угодно (в том числе и для коммерческого использования) при указании авторства. Больше информации — по ссылкам внизу поста. А теперь немного про сами репозитории.
Principles
Best Effort Principles
Zenodo does not sign SLAs (service-level agreements). This is not a weakness, it is by design and marks a philosophy that we believe is most appropriate for Science. Instead, Zenodo is run by leading practitioners according to best practices.
What Science needs is inherent reliability, or more accurately demonstrated reliability based on open best practices. Furthermore the users should be able to influence these best practices. In the long-term, a service which is trusted is much more valuable than one for which assurances must be bought.
Service failure can never be undone. Enforcing an SLA means being prepared to litigate against the contract, which means compensation, frequently assessed on the basis of loss of revenue… but none of these concepts have any place or relevance in the free exchange of research results!
Living by these principles, Zenodo strives to make available architecture, implementation, practices and statistics. Please see for example the infrastructure page. We are also aiming to have these certified.
FAIR Principles
FAIR Principles definition as referenced from: Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3:160018 doi: 10.1038/sdata.2016.18 (2016).
To be Findable:
To be Accessible:
To be Interoperable:
To be Reusable:
The following is a self-assessment of Zenodo against the Plan S requirements for Open Access Repositories (as published October 2019).
See the Plan S Principles and Implementation (under Part III: Technical Guidance and Requirements / 2. Requirements for Open Access Repositories).