Overview of nDEX
NDEx users can easily create accounts or sign in using their Google credentials thanks to the supported open authentication (OAUTH2) method and mint DOIs for their networks to use in publications or include in other resources for long term access.
NDEx, created by members of the same research lab, serves as an Expo for networks—researchers can share networks they have developed and other researchers can search for networks and made them the basis for further incorporation of data or analyses.
NDEx, the Network Data Exchange, is an open-source (Data S1, Open Source) software framework that facilitates the sharing of networks of many types and formats, the publication of networks as data, and the use of networks in modular software.
NDEx client libraries for this API have been created in the Java, Python, and R languages to facilitate easy use by scientists, though NDEx can be accessed via any language capable of Internet communications (Data S1, REST API).
NDEx therefore differs in approach from WikiPathways (Pico et al., 2008), a pioneering collaborative platform for the curation of biological pathways, where all documents are publically edited and use a single format.
NDEx promotes the development of new network analysis algorithms and applications by expanding access to networks as inputs, by facilitating immediate sharing of network results and by providing a path to publication.
NDEx is distinct from other online network repositories which include KEGG and Pathway Commons in that users manage their own networks rather than the networks being managed by the organization that maintains the resource.
NDEx provides accession identifiers for every network, assigning a universal unique identifier (UUID) that distinguishes it from all other networks across all servers.
NDEx lets you specify Licenses and Request DOIs for your networks to include in grant proposals or publications thus enabling papers to link directly to the data.
NDEx 2.0 is a significant step in the evolution of the NDEx data commons, supporting its mission to foster network-centered communities of scientists.
Screen shot of NDEx after search for networks that include per2, cry2, or bmal1, three prominent mammalian circadian genes
The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.One of the goals of the project is to create a home for models that are currently available only as figures, tables, or supplementary information, such as networks produced via systematic mining and integration of large-scale molecular data.The NDEx project does not compete with existing pathway and interaction databases, such as Pathway Commons, KEGG, or Reactome; instead, NDEx provides a novel, common distribution channel for these efforts, preserving their identity and attribution rather than subsuming them.
>> Learn More…Individual users and organizations can make networks public, findable and accessible in NDEx; each public network has its unique, stable URL and can always be downloaded either manually or programmatically, via our REST API.NDEx includes features to support data distribution and access according to FAIR principles and is registered on FAIRsharing.org .Readers can now go from static figures to interactive, actionable data objects in just a few clicks!Vice versa, networks linking out to the papers they support provide you with new opportunities for discovery and citation.NDEx is recommended by Scientific Data, Springer Nature and the PLOS family of journals.
A private NDEx can also be deployed on local servers or on a scientist’s desktop for applications that store very large networks or perform frequent, large transactions.An NDEx server can be installed behind a firewall to handle cases where strong security is required, enabling storage of proprietary networks developed for the health sciences industry or those that incorporate patient information subject to privacy standards (e.g., HIPAA, the Health Insurance Portability and Accountability Act).Applications can simultaneously access both public and private NDEx servers, or users can coordinate private NDEx instances with a public server using NDEx Sync (Data S1, NDEx Sync), a command line utility that can copy and update selected networks between servers.Finally, users can download and deploy the NDEx server software for private uses that would be impractical or unsupported on the shared public server.
What is ndex?
NDEx Python includes a client and a data model.Visit Snyk Advisor to see a
full health score report
for ndex, including popularity, security, maintenance
& community analysis.
Why the N-DEx System?
The N-DEx system complements other well-known FBI systems, such as the National Crime Information Center (NCIC), Interstate Identification Index (III), and Next Generation Identification (NGI) that provide critical information to the criminal justice community.The information that would not be contained in those systems, i.e., incident and case reports, full Department of Justice (DOJ) case files, and corrections data, is available in N-DEx.And the N-DEx system has been endorsed by a number of major criminal justice associations, including the following: International Chiefs of Police, National Sheriffs’ Association, Association of State Correctional Administrators, National Institute of Corrections, American Probation and Parole Administrators, Corrections Technology Association, Major Cities Chiefs Association, and Major County Sheriffs’ Association.
What can I do with NDEx ? Why should I care to use it? These are very common questions that scientists might ask when presented a new tool they have never used before…
Is ndex popular?
The python package ndex receives a total of
437 weekly downloads.As such,
ndex popularity was classified as
on Snyk Advisor to see the full health analysis.
Is ndex safe to use?
While scanning the latest version of ndex, we found
that a security review is needed.A total of
1 vulnerabilities or license issues were
detected.See the full
security scan results.
History of nDEX
In 2008, the St.
In 1154, the scientist and cartographer al-Idrisi made a map of the world that was better than the world maps Europeans were producing.
In 1961, Yayoi Kusama, then thirty-two years old, displayed a painting that was thirty-three feet long and almost ten feet high at Stephen Radich Gallery in New York.
In 1975, Jack Bogle created the index fund, a practical approach for retail investors to compete with professionals.
In 1988, South-African businessman Johan Rupert founded Compagnie Financiere Richemont SA to serve as a holding company for the luxury goods market.
In 1997, Simovski et al.
In 1998, they published a scientific paper in which they introduced the concept of “PageRank.” This topic was further explored in another paper that Brin and Page contributed to, “PageRank Citation Ranking: Bringing Order to the Web.”
in 2000 from Jadavpur University, India.
In 2001, Thailand’s Corruption Perceptions Index (CPI) score was 3.2 (ranked 61), whilst in 2005, the CPI was 3.8 (ranked 59).
In 2002, Mexico City had a Human Development Index score of 0.915, identical to that of South Korea.
In 2006 alone, approximately 1.3 million peer reviewed scientific articles were published, aided by a large rise in the number of available scientific journals from 16,000 in 2001 to 23,750 by 2006. The increasing scientific articles have fuelled the demand for new journal.
In 2009, Haiphong state budget revenue reached 34,000 billion Vnd.
In 2010 the Dow Jones Indexes subsidiary was sold to the CME Group and the company focused on financial news publications, including its flagship publication The Wall Street Journal and providing financial news and information tools to financial companies.
In 2011, budget revenues in the city reached 47,725 billion, increase 19% compared to 2010. In 2015, total revenues of the city reached 56 288 billion.
In 2011, Constellation was contracted to construct and operate what was then the largest rooftop solar array ever constructed for the Toys-R-Us distribution center in Flanders, NJ.
In 2013, gains for the index were 14.7 percent; in 2014, it was up 10.4 percent and 9.2 percent in 2015.
In 2013, the founding team foresaw the great potential of the blockchain industry to revolutionize the future of the global financial system.
In 2015, Carlyle was the world’s largest private equity firm by capital raised over the previous five years, according to the PEI 300 index, though by 2020 it had slipped into second place.
In 2015, in his best-selling book “Internet + Finance = Crowdfunding Finance”, he is the first scholar to analyse blockchain application in the financial industry.
In 2016 and 2017, the index was up three percent and 7.4 percent, respectively, according to PivotalPath, a hedge fund research and data firm.
In 2016 Ethereum was recognised worldwide and its records were noted worldwide.
In 2016 Google started rolling out mobile-first indexing.
In 2016, just over 18,000 Coloradans were able to benefit from this program.
In 2017, our team successfully pioneered the first tokenized crypto-only index fund, which used the seed funding to buy the underlying crypto assets.
In 2017, the book “Fintech Law: Blockchain Business Practice and Legal Guide” was published which focus on the practice and strategy of blockchain application in enterprise level.
In 2018 Armenia produced 7.8 TW/h electricity, whereas at the same time BitCoin mining electricity consumption was 6 times more in the world.
In 2018, the exemption is $11.18 and this amount will be indexed annually for inflation until 2026, when the exemption amount is scheduled to revert to $5.49 million, with an adjustment for inflation.
In 2019 Google shift to mobile-first which means that Google will now use your website’s mobile version for indexing and ranking in Google search results.
In 2020, despite inflationary fears due to pandemic-related spending, the U.S.
In 2020, despite the impact of the Covid-19 pandemic, bilateral trade reached US$1.6 billion.
In 2020, the average daily trading volume of the entire cryptocurrency market fluctuated in the approximate range of $50-$200 million.
In 2023, the price can go down again to the point of $84.