GeneRIF

A GeneRIF or Gene Reference Into Function is a short (255 characters or fewer) statement about the function of a gene. GeneRIFs provide a simple mechanism for allowing scientists to add to the functional annotation of genes described in the Entrez Gene database. In practice, function is constructed quite broadly. For example, there are GeneRIFs that discuss the role of a gene in a disease, GeneRIFs that point the viewer towards a review article about the gene, and GeneRIFs that discuss the structure of a gene. However, the stated intent is for GeneRIFs to be about gene function. Currently over half a million geneRIFs have been created for genes from almost 1000 different species. GeneRIFs are always associated with specific entries in the Entrez Gene database. Each GeneRIF has a pointer to the PubMed ID (a type of document identifier) of a scientific publication that provides evidence for the statement made by the GeneRIF. GeneRIFs are often extracted directly from the document that is identified by the PubMed ID, very frequently from its title or from its final sentence. GeneRIFs are usually produced by NCBI indexers, but anyone may submit a GeneRIF. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY. Once the Gene ID is identified, only three types of information are required to complete a submission: a concise phrase describing a function or functions (less than 255 characters in length, preferably more than a restatement of the title of the paper); a published paper describing that function, implemented by supplying the PubMed ID of a citation in PubMed; a valid e-mail address (which will remain confidential). == Example == Here are some GeneRIFs taken from Entrez Gene for GeneID 7157, the human gene TP53. The PubMed document identifiers have been omitted from the examples. Note the wide variability with respect to the presence or absence of punctuation and of sentence-initial capital letters. p53 and c-erbB-2 may have independent role in carcinogenesis of gall bladder cancer Degradation of endogenous HIPK2 depends on the presence of a functional p53 protein. p53 codon 72 alleles influence the response to anticancer drugs in cells from aged people by regulating the cell cycle inhibitor p21WAF1 Logistic regression analysis showed p53 and COX-2 as dependent predictors in pancreatic carcinogenesis, and a reciprocal relationship to neoplastic progression between p53 and COX-2. GeneRIFs are an unusual type of textual genre, and they have recently been the subject of a number of articles from the natural language processing community.

ActivityPub

ActivityPub is a protocol and open standard for decentralized social networking. It provides a client-to-server (C2S) API for creating and modifying content, as well as a federated server-to-server (S2S) protocol for delivering notifications and content to other servers. ActivityPub is the defining standard of the Fediverse, a decentralised social network of various social interaction models, and content types, which consists of independently managed instances of software such as Mastodon, Pixelfed and PeerTube, among others. ActivityPub is considered to be an update to the ActivityPump protocol used in pump.io, and the official W3C repository for ActivityPub is identified as a fork of ActivityPump. The creation of a new standard for decentralized social networking was prompted by the complexity of OStatus, the most commonly used protocol at the time. OStatus was built using a multitude of technologies (such as Atom, Salmon, WebSub and WebFinger), a product of the infrastructure used in GNU social (the originator and largest user of the OStatus protocol), which made it difficult to implement the protocol into new software. OStatus was also only designed to work with microblogging services, with little flexibility to the types of data that it could hold. The standard was first published by the World Wide Web Consortium (W3C) as a W3C Recommendation in January 2018 by the Social Web Working Group (SocialWG), a working group chartered to build the protocols and vocabularies needed to create a standard for social functionality. Shortly after, further development was moved to the Social Web Community Group (SocialCG), the successor to the SocialWG. == Design == ActivityPub uses the ActivityStreams 2.0 format for building its content, which itself uses JSON-LD. The three main data types used in ActivityPub are Objects, Activities and Actors. Objects are the most common data type, and can be images, videos, or more abstract items such as locations or events. Activities are actions that create and modify objects, for example a Create activity creates an object. Actors are representative of an individual, a group, an application or a service, and are the owners of objects. Every actor type contains an inbox and outbox stream, which sends and receives activities for a user. In order to publish data (for example liking an article), a user creates an activity that declares that they liked an Article object and publishes it to their outbox, where it is then delivered by the ActivityPub server via a POST request to the inboxes listed in the activity's to, bto, cc and bcc fields. The receiving servers then account for the newly received activity and update the article by adding the like action to it. === Example data === An example actor object that represents a user account: An example activity that likes an article object: An example article object: == Project status == The SocialCG previously organized a yearly free conference called ActivityPub Conf about the future of ActivityPub. Triages are held regularly to review issues pertaining to the ActivityPub and ActivityStreams 2.0 specifications as part of the SocialCG. In 2023, Germany's Sovereign Tech Fund donated €152,000 to socialweb.coop with the goal of building a new suite for testing various ActivityPub implementations and their compliance with the specification. === Adoption === The initial wave of adoption for ActivityPub (circa 2016–2018) came from software that was already using OStatus as their federation protocol, such as Mastodon, GNU social and Pleroma. Following the acquisition of Twitter by Elon Musk in 2022, many groups of users that were critical of the acquisition migrated to Mastodon, bringing new attention to the ActivityPub protocol with it. Various major social media platforms and corporations have since pledged to implement ActivityPub support, including Tumblr, Flipboard and Meta Platforms' Threads. Threads introduced crossposting to ActivityPub in 2024 for users outside of the European Economic Area, however full 2-way compatibility remains incomplete as of 2025. == Criticism == === Accidental denial-of-service attacks === Poorly optimized ActivityPub implementations can cause unintentional distributed denial-of-service (DDOS) attacks on other websites and servers, due to the decentralized nature of the network. An example would be Mastodon's implementation of OpenGraph link previews, wherein every instance that receives a post that contains a link with OpenGraph metadata will download the associated data, such as a thumbnail, in a very short timeframe, which can slow down or crash servers as a result of the sudden burst of requests. === Account migration === ActivityPub has been criticized for not natively supporting moving accounts from one server to another, forcing implementations to build their own solutions. While there has been work on building a standardized system for migrating accounts using the Move activity via the Fediverse Enhancement Proposal organization, the current proposal only allows for basic follower migration, with all other data remaining linked to the original account. === Missing content and data === ActivityPub implementations have been criticized for missing replies and parts of reply threads from remote posts, and presenting outdated statistics (e.g. likes and reposts) about remote posts. However, this isn't a problem with the ActivityPub protocol itself, but with implementations not refreshing their content for updated data when needed. == Software using ActivityPub == === Future implementations === Flarum, an internet forum software Forgejo, a Git forge and development platform === Uncertain future implementations === GitLab, a Git forge and development platform which had previously had an open issue discussing the topic, but was later closed due to the development team moving focus to other areas. Tumblr, a microblogging platform. Despite previous statements from Automattic CEO Matt Mullenweg, ActivityPub integration has been delayed indefinitely. The integration would have been implemented with its WordPress migration, as the first-party plugin for interoperability would have been used for federation. Flickr, an image and video hosting site.

Galaksija BASIC

Galaksija BASIC was the BASIC interpreter of the Galaksija build-it-yourself home computer from Yugoslavia. While being partially based on code taken from TRS-80 Level 1 BASIC, which the creator believed to have been a Microsoft BASIC, the extensive modifications of Galaksija BASIC—such as to include rudimentary array support, video generation code (as the CPU itself did it in absence of dedicated video circuitry) and generally improvements to the programming language—is said to have left not much more than flow-control and floating point code remaining from the original. The core implementation of the interpreter was fully contained in the 4 KiB ROM "A" or "1". The computer's original mainboard had a reserved slot for an extension ROM "B" or "2" that added more commands and features such as a built-in Zilog Z80 assembler. == ROM "A"/"1" symbols and keywords == The core implementation, in ROM "A" or "1", contained 3 special symbols and 32 keywords: ! begins a comment (equivalent of standard BASIC REM command) # Equivalent of standard BASIC DATA statement & prefix for hex numbers ARR$(n) Allocates an array of strings, like DIM, but can allocate only array with name A$ BYTE serves as PEEK when used as a function (e.g. PRINT BYTE(11123)) and POKE when used as a command (e.g. BYTE 11123,123). CALL n Calls BASIC subroutine as GOSUB in most other BASICs (e.g. CALL 100+4X) CHR$(n) converts an ASCII numeric code into a corresponding character (string) DOT x, y draws (command) or inspects (function) a pixel at given coordinates (0<=x<=63, 0<=y<=47). DOT displays the clock or time controlled by content of Y$ variable. Not in standard ROM EDIT n causes specified program line to be edited ELSE standard part of IF-ELSE construct (Galaksija did not use THEN) EQ compare alphanumeric values X$ and Y$ FOR standard FOR loop GOTO standard GOTO command HOME equivalent of standard BASIC CLS command - clears the screen HOME n protects n characters from the top of the screen from being scrolled away IF standard part of IF-ELSE construct (Galaksija did not use THEN) INPUT user entry of variable INT(n) a function that returns the greatest integer value equal to or lesser than n KEY(n) test whether a particular keyboard key is pressed LIST lists the program. Optional numeric argument specifies the first line number to begin listing with. MEM returns memory consumption data (need details here) NEW clears the current BASIC program NEW n clears BASIC program and moves beginning of BASIC area NEXT standard terminator of FOR loop OLD loads a program from tape OLD n loads program to different address PTR Returns address of the variable PRINT Printing numeric or string expression. RETURN Return from BASIC subroutine RND function (takes no arguments) that returns a random number between 0 and 1. RUN runs (executes) BASIC program. Optional numeric argument specifies the line number to begin execution with. SAVE saves a program to tape. Optional two arguments specify memory range to be saved (need details here). STEP standard part of FOR loop STOP stops execution of BASIC program TAKE replacement for READ and RESTORE. If the parameter is variable name, acts as READ, if it is number, acts as RESTORE UNDOT x, y "undraws" (resets) at specified coordinates (see DOT) UNDOT Stops the clock, not part of ROM USR Calls machine code subroutine WORD Double byte PEEK and POKE == ROM "B"/"2" additional symbols and keywords == The extended BASIC features, in ROM "B" or "2", contained one extra reserved symbol and 22 extra keywords: % /LABEL ABS(x) ARCTG(x) COS(x) COSD(x) DEL DUMP EXP(x) INP(x) LDUMP LLIST LN(x) LPRINT OUT PI POW(x,y) REN SIN(x), SIND(x) SQR(x) TG(x) TGD(x)

Cygwin

Cygwin ( SIG-win) is a free and open-source Unix-like environment and command-line interface (CLI) for Microsoft Windows. The project also provides a software repository containing open-source packages. Cygwin allows source code for Unix-like operating systems to be compiled and run on Windows. Cygwin provides native integration of Windows-based applications. The terminal emulator mintty is the default command-line interface provided to interact with the environment. The Cygwin installation directory layout mimics the root file system of Unix-like systems, with directories such as /bin, /home, /etc, /usr, and /var. Cygwin is released under the GNU Lesser General Public License version 3. It was originally developed by Cygnus Solutions, which was later acquired by Red Hat (now part of IBM), to port the GNU toolchain to Win32, including the GNU Compiler Suite. Rather than rewrite the tools to use the Win32 runtime environment, Cygwin implemented a POSIX-compatible environment in the form of a DLL. The brand motto is "Get that Linux feeling – on Windows", although Cygwin doesn't have Linux in it. == History == Cygwin began in 1995 as a project of Steve Chamberlain, a Cygnus engineer who observed that Windows NT and 95 used COFF as their object file format, and that GNU already included support for x86 and COFF, and the C library newlib. He thought that it would be possible to retarget GCC and produce a cross compiler generating executables that could run on Windows. A prototype was later developed. Chamberlain bootstrapped the compiler on a Windows system, to emulate Unix to let the GNU configure shell script run. Initially, Cygwin was called Cygwin32. When Microsoft registered the trademark Win32, the "32" was dropped to simply become Cygwin. In 1999, Cygnus offered Cygwin 1.0 as a commercial product. Subsequent versions have not been released, instead relying on continued open source releases. Geoffrey Noer was the project lead from 1996 to 1999. Christopher Faylor was lead from 1999 to 2004; he left Red Hat and became co-lead with Corinna Vinschen. Corinna Vinschen has been the project lead from mid-2014 to date (as of September, 2024). From June 23, 2016, the Cygwin library version 2.5.2 was licensed under the GNU Lesser General Public License (LGPL) version 3. == Description == Cygwin is provided in two versions: the full 64-bit version and a stripped-down 32-bit version, whose final version was released in 2022. Cygwin consists of a library that implements the POSIX system call API in terms of Windows system calls to enable the running of a large number of application programs equivalent to those on Unix systems, and a GNU development toolchain (including GCC and GDB). Programmers have ported the X Window System, K Desktop Environment 3, GNOME, Apache, and TeX. Cygwin permits installing inetd, syslogd, sshd, Apache, and other daemons as standard Windows services. Cygwin programs have full access to the Windows API and other Windows libraries. Cygwin programs are installed by running Cygwin's "setup" program, which downloads them from repositories on the Internet. The Cygwin API library is licensed under the GNU Lesser General Public License version 3 (or later), with an exception to allow linking to any free and open-source software whose license conforms to the Open Source Definition. Cygwin consists of two parts: A dynamic-link library in the form of a C standard library that acts as a compatibility layer for the POSIX API and A collection of software tools and applications that provide a Unix-like look and feel. Cygwin supports POSIX symbolic links, representing them as plain-text files with the system attribute set. Cygwin 1.5 represented them as Windows Explorer shortcuts, but this was changed for reasons of performance and POSIX correctness. Cygwin also recognises NTFS junction points and symbolic links and treats them as POSIX symbolic links, but it does not create them. The POSIX API for handling access control lists (ACLs) is supported. === Technical details === A Cygwin-specific version of the Unix mount command allows mounting Windows paths as "filesystems" in the Unix file space. Initial mount points can be configured in /etc/fstab, which has a format very similar to Unix systems, except that Windows paths appear in place of devices. Filesystems can be mounted in binary mode (by default), or in text mode, which enables automatic conversion between LF and CRLF endings (which only affects programs that open files without explicitly specifying text or binary mode). Cygwin 1.7 introduced comprehensive support for POSIX locales, and the UTF-8 Unicode encoding became the default. The fork system call for duplicating a process is fully implemented, but the copy-on-write optimization strategy could not be used. Cygwin's default user interface is the bash shell running in the mintty terminal emulator. The DLL also implements pseudo terminal (pty) devices, and Cygwin ships with a number of terminal emulators that are based on them, including rxvt/urxvt and xterm. The version of GCC that comes with Cygwin has various extensions for creating Windows DLLs, such as specifying whether a program is a windowing or console-mode program. Support for compiling programs that do not require the POSIX compatibility layer provided by the Cygwin DLL used to be included in the default GCC, but as of 2014, it is provided by cross-compilers contributed by the MinGW-w64 project. == Software packages == Cygwin's base package selection is approximately 100MB, containing the bash (interactive user) and dash (installation) shells and the core file and text manipulation utilities. Additional packages are available as optional installs from within the Cygwin "setup" program and package manager ("setup-x86_64.exe" – 64 bit). The Cygwin Ports project provided additional packages that were not available in the Cygwin distribution itself. Examples included GNOME, K Desktop Environment 3, MySQL database, and the PHP scripting language. Most ports have been adopted by volunteer maintainers as Cygwin packages, and Cygwin Ports are no longer maintained. Cygwin ships with GTK+ and Qt. The Cygwin/X project allows graphical Unix programs to display their user interfaces on the Windows desktop for both local and remote programs.

Mastodon (social network)

Mastodon is a free and open-source software platform for decentralized social networking with microblogging features similar to Twitter. It operates as a federated network of independently managed servers that communicate using the ActivityPub protocol, allowing users to connect across different instances within the Fediverse. Each Mastodon instance establishes its own moderation policies and content guidelines, distinguishing it from centrally controlled social media platforms. First released in 2016 by Eugen Rochko, Mastodon has positioned itself as an alternative to mainstream social media, particularly for users seeking decentralized, community-driven spaces. The platform has experienced multiple surges in adoption, most notably following the Twitter acquisition by Elon Musk in 2022, as users sought alternatives to Twitter. It is part of a broader shift toward decentralized social networks, including Bluesky and Lemmy. Mastodon emphasizes user privacy and moderation flexibility, offering features such as granular post visibility controls, content warning options, and local community-driven moderation. The software is written in Ruby on Rails and Node.js, with a web interface built using React and Redux. It is interoperable with other ActivityPub-based platforms, such as Threads, and supports various third-party applications on desktop and mobile devices. == Functionality == Users post short-form status messages, historically known as "toots", for others to see and interact with. On a standard Mastodon instance, these messages can include up to 500 text-based characters, greater than Twitter's 280-character limit. Some instances support even longer messages. Images, audio files, videos or polls can also be added to a message. Users join a specific Mastodon server, rather than a single centralized website or application. The servers are connected as nodes in a network, and each server can administer its own rules, account privileges, and whether to share messages to and from other servers. Users can communicate and follow each other across connected Mastodon servers with usernames similar in format to full email addresses. Since version 2.9.0, Mastodon's web user interface has offered a single-column mode for new users by default. In advanced mode, the interface approximates the microblogging interface of TweetDeck. === Privacy === Mastodon includes a number of specific privacy features. Each message has a variety of privacy options available, and users can choose whether the message is public or private. Messages can display public on a global feed, known as a timeline, or can be shared only to the user's followers. Messages can also be marked as unlisted from timelines or direct between users. Users can also mark their accounts as completely private. In the timeline, messages can display with an optional content warning feature, which requires readers to click on the hidden main body of the message to reveal it. Mastodon servers have used this feature to hide spoilers, trigger warnings, and not safe for work (NSFW) content, though some accounts use the feature to hide links and thoughts others might not want to read. Mastodon aggregates messages in local and federated timelines in real time. The local timeline shows messages from users on a singular server, while the federated timeline shows messages across all participating Mastodon servers. === Content moderation === In early 2017, journalists like Sarah Jeong distinguished Mastodon from Twitter for its approach to combating harassment. Mastodon uses community-based moderation, in which each server can limit or filter out undesirable types of content, while Twitter uses a single, global policy on content moderation. Servers can choose to limit or filter out messages with disparaging content. The founder of Mastodon, Eugen Rochko, believes that small, closely related communities deal with unwanted behavior more effectively than a large company's small safety team. In Move Slowly and Build Bridges, Robert W. Gehl argues that predominantly white participation has shaped Mastodon in ways that affect how reports of racism are received and limit its ability to replicate Black Twitter on Twitter. Users can also block and report others to administrators, much like on Twitter. Instance administrators can block other instances from interacting with their own, an action called defederation. By posting toots hashtagged with #fediblock, some instance administrators and users alert others of issues requiring moderation. === Searching === Mastodon by default allows searching for hashtags and mentioned accounts in the Fediverse. Server administrators can optionally enable Elasticsearch to search the full-text of public posts that have opted in to being indexed. == Versions == In September 2018, with the release of version 2.5 with redesigned public profile pages, Mastodon marked its 100th release. Mastodon 2.6 was released in October 2018, introducing the possibilities of verified profiles and live, in-stream link previews for images and videos. Version 2.7, in January 2019, made it possible to search for multiple hashtags at once, instead of searching for just a single hashtag, with more robust moderation capabilities for server administrators and moderators, while accessibility, such as contrast for users with sight issues, was improved. The ability for users to create and vote in polls, as well as a new invitation system to manage registrations was integrated in April 2019. Mastodon 2.8.1, released in May 2019, made images with content warnings blurred instead of completely hidden. In version 2.9 in June 2019, an optional single-column view was added. This view became the default displayed to new users, with a user "preferences" option to switch to a multiple-column-based view. In August 2020, Mastodon 3.2 was released. It included a redesigned audio player with custom thumbnails and the ability to add personal notes to one's profile. In July 2021, an official client for iOS devices was released. According to the project's then CEO, Eugen Rochko, the release was part of an effort to attract new users. Mastodon 4.0 was released in November 2022, including language support for translating posts, editing posts and following hashtags. Mastodon 4.5 was released in November 2025. Among other features it introduced quote posts, which were previously rejected from being implemented due to concerns about toxicity and harassment. To mitigate these issues Mastodon's quote post feature has been designed in a way that lets users decide if and by whom their posts can be quoted. == Software == Mastodon is published as free and open-source software under the Affero GPL license, allowing anyone to use the software or modify it as they wish. Servers can be run by any individual or organization, and users can join these servers as they wish. The server software itself is powered by Ruby on Rails and Node.js, with its web client being written in React.js and Redux. The only database software supported is PostgreSQL, with Redis being used for job processing and various actions that Mastodon needs to process. The service is interoperable with the fediverse, a collection of social networking services which use the ActivityPub protocol for communication between each other, with previous versions containing support for OStatus. Client apps for interacting with the Mastodon API are available for desktop computer operating systems, including Windows, macOS and the Linux family of operating systems, as well as mobile phones running iOS and Android. The API is open for anyone to utilize, allowing clients to be built for any operating system that can connect to the internet. === Integration with Fediverse === Mastodon uses the ActivityPub protocol for federation; this allows users to communicate between independent Mastodon instances and other ActivityPub compatible services. Thus, Mastodon is generally considered to be a part of the Fediverse. Services utilizing the ActivityPub protocol exist which allow for searching all posts on all instances as long as users opt-in. For similar reasons, only hashtags can appear in a Mastodon instance's trending topics, not arbitrary popular words. Trending topics vary between instances, since individual instances are aware of different subsets of posts from the whole fediverse. === Security concerns === While Mastodon's decentralized structure is one of its most distinctive features, it also poses additional security challenges. Since many Mastodon instances are run by volunteers, some security experts are concerned about data security and responsiveness to new threats and vulnerabilities across the network, considering the difficulty of configuring and maintaining an instance as well as uneven skill levels among administrators. Administrators of an instance also have access to the private information of any users that are either registered with that instance or have federated

Patent visualisation

Patent visualisation is an application of information visualisation. The number of patents has been increasing, encouraging companies to consider intellectual property as a part of their strategy. Patent visualisation, like patent mapping, is used to quickly view a patent portfolio. Software dedicated to patent visualisation began to appear in 2000, for example Aureka from Aurigin (now owned by Thomson Reuters). Many patent and portfolio analytics platforms, such as Questel, Patent Forecast, PatSnap, Patentcloud, Relecura, and Patent iNSIGHT Pro, offer options to visualise specific data within patent documents by creating topic maps, priority maps, IP Landscape reports, etc. Software converts patents into infographics or maps, to allow the analyst to "get insight into the data" and draw conclusions. Also called patinformatics, it is the "science of analysing patent information to discover relationships and trends that would be difficult to see when working with patent documents on a one-and-one basis". Patents contain structured data (like publication numbers) and unstructured text (like title, abstract, claims and visual info). Structured data are processed by data-mining and unstructured data are processed with text-mining. == Data mining == The main step in processing structured information is data-mining, which emerged in the late 1980s. Data mining involves statistics, artificial intelligence, and machine learning. Patent data mining extracts information from the structured data of the patent document. These structured data are bibliographic fields such as location, date or status. === Structured fields === === Advantages === Data mining allows study of filing patterns of competitors and locates main patent filers within a specific area of technology. This approach can be helpful to monitor competitors' environments, moves and innovation trends and gives a macro view of a technology status. == Text-mining == === Principle === Text mining is used to search through unstructured text documents. This technique is widely used on the Internet, it has had success in bioinformatics and now in the intellectual property environment. Text mining is based on a statistical analysis of word recurrence in a corpus. An algorithm extracts words and expressions from title, summary and claims and gathers them by declension. "And" and "if" are labeled as non-information bearing words and are stored in the stopword list. Stoplists can be specialised in order to create an accurate analysis. Next, the algorithm ranks the words by weight, according to their frequency in the patent's corpus and the document frequency containing this word. The score for each word is calculated using a formula such as: W e i g h t = T e r m F r e q u e n c y D o c u m e n t F r e q u e n c y = F r e q u e n c y o f t h e w o r d o r e x p r e s s i o n i n t h e T e x t S e a N u m b e r o f d o c u m e n t s c o n t a i n i n g t h e e x p r e s s i o n o r w o r d {\displaystyle Weight={\frac {Term\ Frequency}{Document\ Frequency}}={\frac {Frequency\ of\ the\ word\ or\ expression\ in\ the\ Text\ Sea}{Number\ of\ documents\ containing\ the\ expression\ or\ word}}} A frequently used word in several documents has less weight than a word used frequently in a few patents. Words under a minimum weight are eliminated, leaving a list of pertinent words or descriptors. Each patent is associated to the descriptors found in the selected document. Further, in the process of clusterisation, these descriptors are used as subsets, in which the patent are regrouped or as tags to place the patents in predetermined categories, for example keywords from International Patent Classifications. Four text parts can be processed with text-mining : Title Abstract Claim Patent Full-Text Software offer different combinations but title, abstract and claim are generally the most used, providing a good balance between interferences and relevancy. === Advantages === Text-mining can be used to narrow a search or quickly evaluate a patent corpus. For instance, if a query produces irrelevant documents, a multi-level clustering hierarchy identifies them in order to delete them and refine the search. Text-mining can also be used to create internal taxonomies specific to a corpus for possible mapping. == Visualisations == Allying patent analysis and informatic tools offers an overview of the environment through value-added visualisations. As patents contain structured and unstructured information, visualisations fall in two categories. Structured data can be rendered with data mining in macrothematic maps and statistical analysis. Unstructured information can be shown in like clouds, cluster maps and 2D keyword maps. === Data mining visualisation === === Text mining visualisation === === Visualisation for both data-mining and text-mining === Mapping visualisations can be used for both text-mining and data-mining results. == Uses == What patent visualisation can highlight: Competitors Partners New innovations Technologic environment description Networks Field application: R&D strategy management Competitive intelligence Licensing Strategy

BioBIKE

BioBike(nee. BioLingua ) is a cloud-based, through-the-web programmable (Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent biocomputing (that is, the application of Artificial Intelligence to computational biology) accessible to research scientists who are not expert programmers. == Unique capabilities == BioBIKE is an integrated symbolic biocomputing and bioinformatics platform, built from the start as an entirely (what is now called) cloud-based architecture where all computing is done in remote servers, and all user access is accomplished through web browsers. BioBIKE has a built-in frame system in which all objects, data, and knowledge are represented. This enables code written either in the native Lisp, in the visual programming language, or systems of rules expressed in the SNARK theorem prover to access the whole of biological knowledge in an integrated manner. For its time (released in 2002) it was unique in permitting users to create fully functional biocomputing programs that run on the back-end servers entirely through the web browser UI. (In modern terms it was one of the first PaaS (Platform as a Service) systems, predating even Salesforce in this capability.) Initially this programming was carried out in raw Lisp, but Jeff Elhai's team at VCU, with NSF funding, created an entirely graphical programming environment on top of BioBIKE based upon the Boxer-style programming environments. Being a multi-headed, multi-threaded, multi-user, multi-tenancy cloud-based system, BioBIKE users were able to directly work together through their web browsers, remotely sharing the same listener and memory space. This permitted a unique sort of collaboration, discussed in Shrager (2007). A specialized offshoot of BioBIKE called "BioDeducta" includes SRI's SNARK theorem prover, offering unique "deductive biocomputing" capabilities. == Implementation == BioBIKE is open-source software implemented using the Lisp programming language. Continuing development takes place by the BioBIKE team centered at Virginia Commonwealth University . == History == BioBIKE was originally called "BioLingua", and was developed by Jeff Shrager at The Carnegie Inst. of Washington Dept. of Plant Biology, and JP Massar with funding from NASA's Astrobiology Division. Shrager and Massar wanted to create a web-based, multi-user Lisp Machine, specialized for bioinformatics. Other early contributors to the project included Mike Travers, and Jeff Elhai of VCU. Elhai obtained continuing funding from the National Science Foundation for the project, which was renamed BioBIKE. Elhai and colleagues added BioBIKE's unique visual programming language. Shrager, meanwhile, collaborated with Richard Waldinger at SRI to build SRI's (SNARK) theorem prover into BioBIKE, creating a deductive biocomputing system, called BioDeducta. == Instances == There used to be a number of BioBIKE verticals in different biological domains, including viral pathogens, cyanobacteria and other bacteria, Arabidopsis thaliana, and several others described in the references.