Subject indexing is the act of describing or classifying a document by index terms, keywords, or other symbols in order to indicate what different documents are about, to summarize their contents or to increase findability. In other words, the objective is to identify and describe the subject of documents. Indexes are constructed, separately, on three distinct levels: terms in a document, such as a book; objects in a collection, such as a library; and documents (such as books and articles) within a field of knowledge. Subject indexing is used in information retrieval especially to create bibliographic indexes to retrieve documents on a particular subject. Examples of academic indexing services are Zentralblatt MATH, Chemical Abstracts, and PubMed. The index terms were mostly assigned by experts but author keywords are also common. The process of indexing begins with any analysis of the subject of the document. The indexer must then identify terms that appropriately identify the subject, either by extracting words directly from the document or assigning words from a controlled vocabulary. The terms in the index are then presented in a systematic order. Indexers must decide how many terms to include and how specific the terms should be. Together this gives a depth of indexing. == Subject analysis == The first step in indexing is to decide on the subject matter of the document. In manual indexing, the indexer would consider the subject matter in terms of answer to a set of questions such as "Does the document deal with a specific product, condition or phenomenon?". As the analysis is influenced by the knowledge and experience of the indexer, it follows that two indexers may analyze the content differently and so come up with different index terms. This will impact on the success of retrieval. === Automatic vs. manual subject analysis === Automatic indexing follows set processes of analyzing frequencies of word patterns and comparing results to other documents in order to assign to subject categories. This requires no understanding of the material being indexed. This leads to more uniform indexing but at the expense of the true meaning being interpreted. A computer program will not understand the meaning of statements and may therefore fail to assign some relevant terms or assign incorrectly. Human indexers focus their attention on certain parts of the document such as the title, abstract, summary and conclusions, as analyzing the full text in depth is costly and time-consuming. An automated system takes away the time limit and allows the entire document to be analyzed, but also has the option to be directed to particular parts of the document. == Term selection == The second stage of indexing involves the translation of the subject analysis into a set of index terms. This can involve extracting from the document or assigning from a controlled vocabulary. With the ability to conduct a full text search widely available, many people have come to rely on their own expertise in conducting information searches and full text search has become very popular. Subject indexing and its experts, professional indexers, catalogers, and librarians, remains crucial to information organization and retrieval. These experts understand controlled vocabularies and are able to find information that cannot be located by full text search. The cost of expert analysis to create subject indexing is not easily compared to the cost of hardware, software and labor to manufacture a comparable set of full-text, fully searchable materials. With new web applications that allow every user to annotate documents, social tagging has gained popularity especially in the Web. One application of indexing, the book index, remains relatively unchanged despite the information revolution. === Extraction/Derived indexing === Extraction indexing involves taking words directly from the document. It uses natural language and lends itself well to automated techniques where word frequencies are calculated and those with a frequency over a pre-determined threshold are used as index terms. A stop-list containing common words (such as "the", "and") would be referred to and such stop words would be excluded as index terms. Automated extraction indexing may lead to loss of meaning of terms by indexing single words as opposed to phrases. Although it is possible to extract commonly occurring phrases, it becomes more difficult if key concepts are inconsistently worded in phrases. Automated extraction indexing also has the problem that, even with use of a stop-list to remove common words, some frequent words may not be useful for allowing discrimination between documents. For example, the term glucose is likely to occur frequently in any document related to diabetes. Therefore, use of this term would likely return most or all the documents in the database. Post-coordinated indexing where terms are combined at the time of searching would reduce this effect but the onus would be on the searcher to link appropriate terms as opposed to the information professional. In addition terms that occur infrequently may be highly significant for example a new drug may be mentioned infrequently but the novelty of the subject makes any reference significant. One method for allowing rarer terms to be included and common words to be excluded by automated techniques would be a relative frequency approach where frequency of a word in a document is compared to frequency in the database as a whole. Therefore, a term that occurs more often in a document than might be expected based on the rest of the database could then be used as an index term, and terms that occur equally frequently throughout will be excluded. Another problem with automated extraction is that it does not recognize when a concept is discussed but is not identified in the text by an indexable keyword. Since this process is based on simple string matching and involves no intellectual analysis, the resulting product is more appropriately known as a concordance than an index. === Assignment indexing === An alternative is assignment indexing where index terms are taken from a controlled vocabulary. This has the advantage of controlling for synonyms as the preferred term is indexed and synonyms or related terms direct the user to the preferred term. This means the user can find articles regardless of the specific term used by the author and saves the user from having to know and check all possible synonyms. It also removes any confusion caused by homographs by inclusion of a qualifying term. A third advantage is that it allows the linking of related terms whether they are linked by hierarchy or association, e.g. an index entry for an oral medication may list other oral medications as related terms on the same level of the hierarchy but would also link to broader terms such as treatment. Assignment indexing is used in manual indexing to improve inter-indexer consistency as different indexers will have a controlled set of terms to choose from. Controlled vocabularies do not completely remove inconsistencies as two indexers may still interpret the subject differently. == Index presentation == The final phase of indexing is to present the entries in a systematic order. This may involve linking entries. In a pre-coordinated index the indexer determines the order in which terms are linked in an entry by considering how a user may formulate their search. In a post-coordinated index, the entries are presented singly and the user can link the entries through searches, most commonly carried out by computer software. Post-coordination results in a loss of precision in comparison to pre-coordination. == Depth of indexing == Indexers must make decisions about what entries should be included and how many entries an index should incorporate. The depth of indexing describes the thoroughness of the indexing process with reference to exhaustivity and specificity. === Exhaustivity === An exhaustive index is one which lists all possible index terms. Greater exhaustivity gives a higher recall, or more likelihood of all the relevant articles being retrieved, however, this occurs at the expense of precision. This means that the user may retrieve a larger number of irrelevant documents or documents which only deal with the subject in little depth. In a manual system a greater level of exhaustivity brings with it a greater cost as more man-hours are required. The additional time taken in an automated system would be much less significant. At the other end of the scale, in a selective index only the most important aspects are covered. Recall is reduced in a selective index as if an indexer does not include enough terms, a highly relevant article may be overlooked. Therefore, indexers should strive for a balance and consider what the document may be used. They may also have to consider the implications of time and expense. === Specificity === The specificity describes how closel
Spectral shape analysis
Spectral shape analysis relies on the spectrum (eigenvalues and/or eigenfunctions) of the Laplace–Beltrami operator to compare and analyze geometric shapes. Since the spectrum of the Laplace–Beltrami operator is invariant under isometries, it is well suited for the analysis or retrieval of non-rigid shapes, i.e. bendable objects such as humans, animals, plants, etc. == Laplace == The Laplace–Beltrami operator is involved in many important differential equations, such as the heat equation and the wave equation. It can be defined on a Riemannian manifold as the divergence of the gradient of a real-valued function f: Δ f := div grad f . {\displaystyle \Delta f:=\operatorname {div} \operatorname {grad} f.} Its spectral components can be computed by solving the Helmholtz equation (or Laplacian eigenvalue problem): Δ φ i + λ i φ i = 0. {\displaystyle \Delta \varphi _{i}+\lambda _{i}\varphi _{i}=0.} The solutions are the eigenfunctions φ i {\displaystyle \varphi _{i}} (modes) and corresponding eigenvalues λ i {\displaystyle \lambda _{i}} , representing a diverging sequence of positive real numbers. The first eigenvalue is zero for closed domains or when using the Neumann boundary condition. For some shapes, the spectrum can be computed analytically (e.g. rectangle, flat torus, cylinder, disk or sphere). For the sphere, for example, the eigenfunctions are the spherical harmonics. The most important properties of the eigenvalues and eigenfunctions are that they are isometry invariants. In other words, if the shape is not stretched (e.g. a sheet of paper bent into the third dimension), the spectral values will not change. Bendable objects, like animals, plants and humans, can move into different body postures with only minimal stretching at the joints. The resulting shapes are called near-isometric and can be compared using spectral shape analysis. == Discretizations == Geometric shapes are often represented as 2D curved surfaces, 2D surface meshes (usually triangle meshes) or 3D solid objects (e.g. using voxels or tetrahedra meshes). The Helmholtz equation can be solved for all these cases. If a boundary exists, e.g. a square, or the volume of any 3D geometric shape, boundary conditions need to be specified. Several discretizations of the Laplace operator exist (see Discrete Laplace operator) for the different types of geometry representations. Many of these operators do not approximate well the underlying continuous operator. == Spectral shape descriptors == === ShapeDNA and its variants === The ShapeDNA is one of the first spectral shape descriptors. It is the normalized beginning sequence of the eigenvalues of the Laplace–Beltrami operator. Its main advantages are the simple representation (a vector of numbers) and comparison, scale invariance, and in spite of its simplicity a very good performance for shape retrieval of non-rigid shapes. Competitors of shapeDNA include singular values of Geodesic Distance Matrix (SD-GDM) and Reduced BiHarmonic Distance Matrix (R-BiHDM). However, the eigenvalues are global descriptors, therefore the shapeDNA and other global spectral descriptors cannot be used for local or partial shape analysis. === Global point signature (GPS) === The global point signature at a point x {\displaystyle x} is a vector of scaled eigenfunctions of the Laplace–Beltrami operator computed at x {\displaystyle x} (i.e. the spectral embedding of the shape). The GPS is a global feature in the sense that it cannot be used for partial shape matching. === Heat kernel signature (HKS) === The heat kernel signature makes use of the eigen-decomposition of the heat kernel: h t ( x , y ) = ∑ i = 0 ∞ exp ( − λ i t ) φ i ( x ) φ i ( y ) . {\displaystyle h_{t}(x,y)=\sum _{i=0}^{\infty }\exp(-\lambda _{i}t)\varphi _{i}(x)\varphi _{i}(y).} For each point on the surface the diagonal of the heat kernel h t ( x , x ) {\displaystyle h_{t}(x,x)} is sampled at specific time values t j {\displaystyle t_{j}} and yields a local signature that can also be used for partial matching or symmetry detection. === Wave kernel signature (WKS) === The WKS follows a similar idea to the HKS, replacing the heat equation with the Schrödinger wave equation. === Improved wave kernel signature (IWKS) === The IWKS improves the WKS for non-rigid shape retrieval by introducing a new scaling function to the eigenvalues and aggregating a new curvature term. === Spectral graph wavelet signature (SGWS) === SGWS is a local descriptor that is not only isometric invariant, but also compact, easy to compute and combines the advantages of both band-pass and low-pass filters. An important facet of SGWS is the ability to combine the advantages of WKS and HKS into a single signature, while allowing a multiresolution representation of shapes. == Spectral Matching == The spectral decomposition of the graph Laplacian associated with complex shapes (see Discrete Laplace operator) provides eigenfunctions (modes) which are invariant to isometries. Each vertex on the shape could be uniquely represented with a combinations of the eigenmodal values at each point, sometimes called spectral coordinates: s ( x ) = ( φ 1 ( x ) , φ 2 ( x ) , … , φ N ( x ) ) for vertex x . {\displaystyle s(x)=(\varphi _{1}(x),\varphi _{2}(x),\ldots ,\varphi _{N}(x)){\text{ for vertex }}x.} Spectral matching consists of establishing the point correspondences by pairing vertices on different shapes that have the most similar spectral coordinates. Early work focused on sparse correspondences for stereoscopy. Computational efficiency now enables dense correspondences on full meshes, for instance between cortical surfaces. Spectral matching could also be used for complex non-rigid image registration, which is notably difficult when images have very large deformations. Such image registration methods based on spectral eigenmodal values indeed capture global shape characteristics, and contrast with conventional non-rigid image registration methods which are often based on local shape characteristics (e.g., image gradients).
List of Fortran software and tools
This is a list of Fortran software and tools, including IDEs, compilers, libraries, debugging tools, numerical and scientific computing tools, and related projects. == Fortran compilers == Absoft Pro Fortran — Absoft Pro Fortran is discontinued and ran on Linux and macOS AOCC — from AMD Classic Flang — part of the LLVM Project LLVM Flang — part of the LLVM Project Fortran 77 — Fortran 77 was developed by Digital Equipment Corporation, it is discontinued. G95 – portable open-source Fortran 95 compiler GCC (GNU Fortran) PGI compilers – NVIDIA developed compilers after acquiring The Portland Group IBM XL Fortran — IBM XL Fortran is current and runs on Linux (Power/AIX) and integrates with Eclipse Intel Fortran Compiler – part of Intel OneAPI HPC toolkit LFortran — LFortran is current, cross-platform, and has IDE support. MinGW – cross compiler and forked into Mingw-w64 nAG Fortran Compiler - from nAG Open64 — Open64 is an open-source compiler that has been terminated and ran on Linux Open Watcom — Open Watcom is current, runs on MS-DOS and OS/2, and has IDE support. Oracle Fortran — Oracle Fortran is discontinued, ran on Linux and Solaris. ROSE — source-to-source compiler framework developed at Lawrence Livermore National Laboratory Silverfrost FTN95 — FTN95 from Silverfrost is current, runs on Windows, and has IDE support. == Integrated development environments (IDEs) and editors == Code::Blocks — supports Fortran with plugins Eclipse IDE — with Fortran support via Photran Emacs — extensible text editor with built-in Fortran modes and support for modern tooling via language servers Geany — lightweight cross-platform IDE based on GTK IntelliJ IDEA — cross-platform IDE by JetBrains with Fortran pluggin KDevelop — KDE-based IDE NetBeans — Apache software foundation IDE with Fortran configuration OpenWatcom — IDE and compiler suite for C, C++, and Fortran Simply Fortran — standalone Fortran IDE for Windows, Linux, and macOS Vim — modal text editor with native Fortran syntax support and extensive plugin-based development features Visual Studio — with Intel Fortran integration Visual Studio Code — supports Fortran via extensions == Mathematical libraries == == Scientific libraries == ABINIT — software suite to calculate optical, mechanical, vibrational, and other observable properties of materials Cantera — chemical kinetics, thermodynamics, and transport tool suite CERN Program Library — collection of Fortran libraries for physics applications from CERN CP2K — quantum chemistry and solid-state physics software package for atomistic simulations Dalton — molecular electronic structure program FFTPACK — subroutines for the fast Fourier transform Kinetic PreProcessor – open-source software tool used in atmospheric chemistry MESA — Modules for Experiments in Stellar Astrophysics Nek5000 — MPI parallel higher-order spectral element CFD solver NWChem — open-source high-performance computational chemistry software Octopus — real-space Time-Dependent Density Functional Theory code MODTRAN – model atmospheric propagation of electromagnetic radiation MOLCAS — quantum chemistry software package for multiconfigurational electronic structure calculations NOVAS – software library for astrometry-related numerical computations Physics Analysis Workstation – data analysis and graphical presentation in high-energy physics Quantum ESPRESSO — integrated suite for electronic-structure calculations and materials modeling SIESTA — first-principles materials simulation code using density functional theory Tinker — software tools for molecular design == Debugging and performance tools == GDB — GNU Debugger with Fortran support Valgrind — memory debugging and profiling tool VTune Profiler — performance analysis tool Allinea Forge — debugger and profiler for HPC applications == Build and package management == Autotools — build system supporting Fortran projects CMake — cross-platform build system supporting Fortran Make — build automation tool Spack — package manager for HPC software including Fortran libraries == Machine learning and AI libraries == Athena Fiats (Functional Inference And Training for Surrogates) FNN (Fortran Neural Network) FortNN Fortran-TF-lib (Fortran interface to TensorFlow) FTorch (Fortran interface to PyTorch) MlFortran RoseNNa == Parallel and high-performance computing tools == MPI Fortran bindings — standard interface for distributed-memory parallelism OpenMP — shared-memory parallel programming support through compiler directives Coarray Fortran — parallel programming model introduced in Fortran 2008 ScaLAPACK — parallel linear algebra package built on top of LAPACK == Testing frameworks == FUnit — open-source unit testing framework developed at NASA’s Langley Research Center, for Fortran 90, 95, and 2003. pFUnit — unit testing framework for Fortran, modeled after JUnit == Documentation and code analysis tools == FORD — automatic documentation generator for modern Fortran projects SQuORE — software quality and management platform with code analysis support Understand — static analysis and code comprehension tool for large Fortran projects
Springpad
Springpad was a free online application and web service that allowed its registered users to save, organize and share collected ideas and information. As users added content to their Springpad accounts, the application automatically identified and categorized it, then generated additional snippets based on the types of objects added—for example, listing price comparisons for products and showtimes for movies. Springpad was also available as apps on the iPad, iPhone and Android that synchronized with the Web interface. Springpad was bundled on new Toshiba notebook computers through a Web application subscription service. On May 23, 2014, Springpad announced that it would cease operations on June 25, 2014. The company then allowed users to export their data (as JSON and read-only HTML formats), or to automatically migrate it to Evernote accounts before the expiration date. == Features == Springpad users could use the main site interface which uses HTML5 from most browsers or use the smartphone app to capture notes, tasks, or lists which were then added to the user's "My Stuff", the user's personal database or collection. Additionally Springpad let users look up items of interest which were then automatically categorized based on type or manually categorized by the user. Category types included recipes, movies, products, restaurants and wine. Events could also be added to Springpad, and if the user used Google Calendar, they could opt to sync the event to it. In addition to the smartphone app and site, Springpad could be used via browser extension for Google Chrome, or the Springpad Clipper, a bookmarklet to analyze webpages and clip relevant information from them—for example, the ingredients needed for a recipe—or to add the site as a normal bookmark. Another way users could add content to their Springpad "My Stuff" was by emailing entries to an email address specified on Springpad registration. Springpad's smartphone apps could be used to scan barcodes to identify products, save them to the user's "My Stuff", and automatically generate additional product information and links. The mobile app could also save images taken with the phone's camera, and locate nearby businesses. With most of the content added to a user's "My Stuff", relevant news, useful links and other helpful information could be viewed. Users could also attach additional notes and images to content they had already saved, and could add reminders and alerts which could be emailed to the user or texted to their phone. Springpad also added alerts to its own Alerts section for relevant news, deals or coupons for specific products users added. For additional organization, anything added to Springpad could also be tagged. Users could also add entries to "Notebooks" to separate content by projects, or any other way they wished. Each Notebook included a section called a "Board", which acted as a pin board where users could "pin" content they'd added to the Notebook, allowing them to visually lay out items. If the user added a map to the Board and had entries that included an address, Springpad could automatically point out entries on the map. By default, everything added to Springpad was private. However users could change the privacy settings for each of the types of items added, decide to make specific items public and shareable on Facebook and Twitter, add them to their public page, or keep them private but links to them with specific people.
Stride (software)
Stride was a cloud-based team business communication and collaboration tool, launched by Atlassian on 7 September 2017 to replace the cloud-based version of HipChat. Stride software was available to download onto computers running Windows, Mac or Linux, as well as Android, iOS smartphones, and tablets. Stride was bought by Atlassian's competitor Slack Technologies and was discontinued on February 15, 2019. The features of Stride include chat rooms, one-on-one messaging, file sharing, 5 GB of file storage, group voice and video calling, built-in collaboration tools, and up to 25,000 of searchable message history. Premium features include unlimited file storage, users, group chat rooms, file sharing and storage, apps, and history retention. The premium version, priced at $3/user/month, also includes advanced meeting functionality like group screen sharing, remote desktop control, and dial-in/dial-out capabilities. Stride offered integrations with Atlassian's other products as well as other third-party applications listed in the Atlassian Marketplace, such as GitHub, Giphy, Stand-Bot and Google Calendar. Stride offered additional features beyond messaging to improve efficiency and productivity. It aimed to reduce collaboration noise by introducing a "focus" mode, and eliminates the divisions between text chat, voice meetings, and videoconferencing, by simplifying transitioning between these modes in the same channel. On July 26, 2018, Atlassian announced that HipChat and Stride would be discontinued February 15, 2019, and that it had reached a deal to sell their intellectual property to Slack. Slack paid an undisclosed amount over three years to assume the user bases of the services, while Atlassian took a minority investment in Slack. The companies also announced a commitment to work on integration of Slack with Atlassian services.
Lossless join decomposition
In database design, a lossless join decomposition is a decomposition of a relation r {\displaystyle r} into relations r 1 , r 2 {\displaystyle r_{1},r_{2}} such that a natural join of the two smaller relations yields back the original relation. This is central in removing redundancy safely from databases while preserving the original data. Lossless join can also be called non-additive. == Definition == A relation r {\displaystyle r} on schema R {\displaystyle R} decomposes losslessly onto schemas R 1 {\displaystyle R_{1}} and R 2 {\displaystyle R_{2}} if π R 1 ( r ) ⋈ π R 2 ( r ) = r {\displaystyle \pi _{R_{1}}(r)\bowtie \pi _{R_{2}}(r)=r} , that is r {\displaystyle r} is the natural join of its projections onto the smaller schemas. A pair ( R 1 , R 2 ) {\displaystyle (R_{1},R_{2})} is a lossless-join decomposition of R {\displaystyle R} or said to have a lossless join with respect to a set of functional dependencies F {\displaystyle F} if any relation r ( R ) {\displaystyle r(R)} that satisfies F {\displaystyle F} decomposes losslessly onto R 1 {\displaystyle R_{1}} and R 2 {\displaystyle R_{2}} . Decompositions into more than two schemas can be defined in the same way. == Criteria == A decomposition R = R 1 ∪ R 2 {\displaystyle R=R_{1}\cup R_{2}} has a lossless join with respect to F {\displaystyle F} if and only if the closure of R 1 ∩ R 2 {\displaystyle R_{1}\cap R_{2}} includes R 1 ∖ R 2 {\displaystyle R_{1}\setminus R_{2}} or R 2 ∖ R 1 {\displaystyle R_{2}\setminus R_{1}} . In other words, one of the following must hold: ( R 1 ∩ R 2 ) → ( R 1 ∖ R 2 ) ∈ F + {\displaystyle (R_{1}\cap R_{2})\to (R_{1}\setminus R_{2})\in F^{+}} ( R 1 ∩ R 2 ) → ( R 2 ∖ R 1 ) ∈ F + {\displaystyle (R_{1}\cap R_{2})\to (R_{2}\setminus R_{1})\in F^{+}} === Criteria for multiple sub-schemas === Multiple sub-schemas R 1 , R 2 , . . . , R n {\displaystyle R_{1},R_{2},...,R_{n}} have a lossless join if there is some way in which we can repeatedly perform lossless joins until all the schemas have been joined into a single schema. Once we have a new sub-schema made from a lossless join, we are not allowed to use any of its isolated sub-schema to join with any of the other schemas. For example, if we can do a lossless join on a pair of schemas R i , R j {\displaystyle R_{i},R_{j}} to form a new schema R i , j {\displaystyle R_{i,j}} , we use this new schema (rather than R i {\displaystyle R_{i}} or R j {\displaystyle R_{j}} ) to form a lossless join with another schema R k {\displaystyle R_{k}} (which may already be joined (e.g., R k , l {\displaystyle R_{k,l}} )). == Example == Let R = { A , B , C , D } {\displaystyle R=\{A,B,C,D\}} be the relation schema, with attributes A, B, C and D. Let F = { A → B C } {\displaystyle F=\{A\rightarrow BC\}} be the set of functional dependencies. Decomposition into R 1 = { A , B , C } {\displaystyle R_{1}=\{A,B,C\}} and R 2 = { A , D } {\displaystyle R_{2}=\{A,D\}} is lossless under F because R 1 ∩ R 2 = A {\displaystyle R_{1}\cap R_{2}=A} and we have a functional dependency A → B C {\displaystyle A\rightarrow BC} . In other words, we have proven that ( R 1 ∩ R 2 → R 1 ∖ R 2 ) ∈ F + {\displaystyle (R_{1}\cap R_{2}\rightarrow R_{1}\setminus R_{2})\in F^{+}} .
The Cancer Imaging Archive
The Cancer Imaging Archive (TCIA) is an open-access database of medical images for cancer research. The site is funded by the National Cancer Institute's (NCI) Cancer Imaging Program, and the contract is operated by the University of Arkansas for Medical Sciences. Data within the archive is organized into collections which typically share a common cancer type and/or anatomical site. The majority of the data consists of CT, MRI, and nuclear medicine (e.g. PET) images stored in DICOM format, but many other types of supporting data are also provided or linked to, in order to enhance research utility. All data are de-identified in order to comply with the Health Insurance Portability and Accountability Act and National Institutes of Health data sharing policies. TCIA resources are intended to support: Development of computer aided diagnosis methods (quantitative imaging) Evaluation of unbiased science reproducibility by acceptable standard statistical methods Research on correlation of clinical diagnostic medical images with digital microscopic histological images Exploratory biomarker research for which imaging is a key element Collaboration between cross-disciplinary investigators where imaging is crucial to research on tumor heterogeneity, between patients and within the tumor; tissue temporal response tracking - objective measurements of tumor progression; imaging genomics and Big Data linkages and analysis (clinical, histo-pathology, genomics) TCIA is recognized as a recommended repository for the Scientific Data, PLOS One, and F1000Research journals. It is also listed in the Registry of Research Data Repositories. == History == Prior to the creation of TCIA, the NCI funded development of the National Biomedical Imaging Archive. NBIA is an open-source Web application which was designed to allow the storage and query of DICOM images. TCIA was subsequently initiated in December 2010 to expand data sharing activities by funding a service component which would help address the technical and policy challenges associated with medical imaging research. TCIA leverages open-source tools such as NBIA and Clinical Trials Processor in order to provide its services. == Organization of the archive == The site content is organized into five categories: About Us - Provides a general overview of the site the organizations responsible for operating it. Share Your Data - Provides an overview of how to apply to upload data to the archive. Access the Archive - Provides information about the available data, methods for accessing that data and system usage metrics. Research Activities - Provides information about major research initiatives being conducted using TCIA data as well as information about publication guidelines. Help - Provides information about how to get support using the archive as well as documentation and data usage policies. == Methods for accessing data == Most collections on the Cancer Imaging Archive can be accessed without an account, but a few are restricted to specific users and therefore require an account to access them. TCIA has several ways to browse, filter, and download data. They include: Downloading the entire contents of a collection in bulk Leveraging the NBIA application to filter or search within or across collections Utilizing the RESTful Application programming interface to filter or search within or across collections === Browsing, bulk downloading and access to supporting data === The home page includes a list of all available collections. Basic information about the data such as the cancer type, cancer location, modalities, and number of subjects are also provided. Clicking on a collection name presents a page which describes the data including its original research purpose, how the data were generated, and how it might be useful to other TCIA users. For example, doi:10.7937/K9/TCIA.2015.L4FRET6Z describes the NSCLC-Radiomics-Genomics Collection. In the lower section of the page there are links to search or download the images and any available supporting data in the Data Access tab. Additional tabs provide information about data versions and how to cite the data if used in publications. Many collections contain additional data types such as genomics, patient demographics, treatment details, and expert analyses of the images. This data is usually only found by browsing the collection pages as opposed to searching in NBIA or using the API. === Filtering or searching with NBIA === On each Collection page and also in the main menu of the site there are links to "Search TCIA". This will load the NBIA application which allows simple, advanced and free text searches. Search results follow the conventional DICOM hierarchy of patient -> study -> series. TCIA provides comprehensive documentation on the various features of the NBIA software. === RESTful API === A number of search and download commands are also available through the API. New iterations on the API are released as new versions, so that existing applications developed against older versions of the API continue to function. == Research activities == A list of known publications based on TCIA data is maintained as a convenience to researchers who might want to investigate how it has been used previously. In addition to peer-reviewed publications there are also several major research initiatives described in the Research Activities section of the site. === The CIP TCGA Radiology Initiative for Radiogenomics Research === A large number of collections contain subjects which were analyzed as part of the NIH/NHGRI database known as The Cancer Genome Atlas (TCGA). This offers researchers the ability to correlate clinical images using shared unique identifiers each study that has in TCGA extensive genomic analysis, digital pathology slides and bulk download of individual demographic data and clinical data. A multi-institutional network of investigators volunteering their time is using the data to develop methods to determine prognosis or predict the response to therapy. TCGA collections are designated by nomenclature shared by the TCGA Data Portal (e.g.: TCGA-BRCA, TCGA-GBM, etc). They are subject to a special publication policy which is unique from the other public data on TCIA. === Challenge competitions === TCIA also provides specific data sets used for "Challenge" competitions such as international digital image-focused professional societies like MICCAI, SPIE, or ISBI. A directory of previous and upcoming challenges is maintained on the site. === Digital object identifiers === To facilitate data sharing, many publications encourage authors to include data citations to the data that the authors used in creating the results described in their scholarly papers. In addition, new journals are now available for describing data collections outright (e.g., Nature Scientific Data). TCIA assigns digital object identifiers (DOIs) to all collections when they are submitted, and also has the ability to create persistent identifiers linked to subsets of data held within TCIA that authors may use for data citations in their scholarly papers.