Data commingling, in computer science, occurs when different items or kinds of data are stored in such a way that they become commonly accessible when they are supposed to remain separated. In cloud computing, this can occur where different customer data sits on the same server. Data that is commingled can present a security vulnerability. Data commingling can also occur due to high speed data transmission mixing. In this situation, data of one security level can inadvertently or purposely be mixed with data of a lower or higher security level on the same transmission portal. Portal vehicles can be wire, fiber optics, microwave or various radio frequency transmission portals. This commingling can cause breaches of security and become a source of legal issues to any entity, corporation or individual. Data commingling can also occur when personal computers and personal software programs are used for business, security, government, etc. uses. In the early formulation stages of entities, non-profit or profit corporations, LLC's, LLP's, etc., the creation and use of stand-alone computers and stand-alone networks, "absolutely unconnected" to involved individuals, is the easiest, and safest way to prevent Data Commingling.
Biopython
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext
Model Context Protocol
The Model Context Protocol (MCP) is an open standard and open-source framework introduced by Anthropic in November 2024 to standardize the way artificial intelligence (AI) systems like large language models (LLMs) integrate and share data with external tools, systems, and data sources. MCP provides a standardized interface for reading files, executing functions, and handling contextual prompts. Following its announcement, the protocol was adopted by major AI providers, including OpenAI and Google DeepMind. == Background == MCP was announced by Anthropic in November 2024 as an open standard for connecting AI assistants to data systems such as content repositories, business management tools, and development environments. The protocol was created at Anthropic by engineers David Soria Parra and Justin Spahr-Summers. It aims to address the challenge of information silos and legacy systems. Before MCP, developers often had to build custom connectors for each data source or tool, resulting in what Anthropic described as an "N×M" data integration problem. Earlier stop-gap approaches—such as OpenAI's 2023 "function-calling" API and the ChatGPT plug-in framework—solved similar problems but required vendor-specific connectors. MCP re-uses the message-flow ideas of the Language Server Protocol (LSP) and is transported over JSON-RPC 2.0. In December 2025, Anthropic donated the MCP to the Agentic AI Foundation (AAIF), a directed fund under the Linux Foundation, co-founded by Anthropic, Block and OpenAI, with support from other companies. == Features == The protocol was released with software development kits (SDKs) in programming languages including Python, TypeScript, C# and Java. Anthropic maintains an open-source repository of reference MCP server implementations and SDKs. MCP defines a standardized framework for integrating AI systems with external data sources and tools. It includes specifications for data ingestion and transformation, contextual metadata tagging, and AI interoperability across different platforms. The protocol also supports bidirectional connections between data sources and AI tools. MCP enables applications such as querying structured databases with plain language in the field of natural language data access. The protocol is used in AI-assisted software development tools. Integrated development environments (IDEs), coding platforms such as Replit, and code intelligence tools like Sourcegraph have adopted MCP to grant AI coding assistants real-time access to project context. MCP Apps is an official extension to the Model Context Protocol built on mcp-ui. While the base MCP specification is restricted to text and structured data, MCP Apps standardizes the delivery of interactive user interfaces—such as dashboards, forms, and data visualizations—from MCP servers to host applications like Claude and ChatGPT. == Adoption == In March 2025, OpenAI officially adopted the MCP, after having integrated the standard across its products, including the ChatGPT desktop app. In September 2025, OpenAI added support for MCP to ChatGPT apps. This allows for third-party access inside ChatGPT. MCP can be integrated with Microsoft Semantic Kernel, and Azure OpenAI. MCP servers can be deployed to Cloudflare. In April 2026, the AAIF held the MCP Dev Summit North America in New York City, drawing approximately 1,200 attendees. == Reception == The Verge reported that MCP addresses a growing demand for AI agents that are contextually aware and capable of pulling from diverse sources. In April 2025, security researchers released an analysis that concluded there are multiple outstanding security issues with MCP, including prompt injection, tool permissions that allow for combining tools to exfiltrate data, and lookalike tools that can silently replace trusted ones. MCP has been likened to OpenAPI, a similar specification that aims to describe APIs.
Argüman
Argüman is a free and open source software for collective structured argumentation and argument analysis via argumentation graphs or argument maps in which the type of connections can be specified. It allows users to create collaborative "semantic maps" of arguments in well structured tree formats and share them with an audience and potential participants. Arguman.org was an open structured social debate platform that implemented the software. It is down as of 2023. There also is a mobile version of the tool. The project was started, in 2014, and largely built by developers in Turkey. Some studies used or investigated excerpts of argumentations on the platform. Unlike the larger and functional alternative Kialo, which is structured using only 'Pro' and 'Con' relations, argüman arguments are structured by three types of premises – 'because', 'but', and 'however'. As of the latest version, debates are presented in their entirety as a large tree which may be harder to navigate than other formats – for instance, trees "can become extremely dense, and the interface does not make it obvious which arguments the user should pay attention to". Users can also flag arguments for fallacies. Arguman.org also had a Turkish-language subdomain. A researcher suggested the concept of the Semantic Web-interoperability could be useful for argumentative structures on the Web, going beyond the conventional flat structures of discussions and lack of characterizations of their components as implemented in argüman. There is research into how to automatically use these collaborative argumentation graphs, which is a "very active" topic in Artificial Intelligence. There also is research into applying conclusion-making methods to the debates or their data, such as bipolar weighted argumentation frameworks – this could be a way to find out what the current conclusion of debates like "Computer Science is not actually a science" is. A study suggests it could be useful for the development of critical thinking skills.
Tip and cue
Tip and cue, sometimes referred to as tip and que, tipping and cueing, or tipping and queing, is a method for satellite imagery and reconnaissance satellites to automatically coordinate tracking of objects across different satellites in real or near real-time. This technique ensures continuous tracking of targets as they move across different regions by handing them off between satellites, sharing satellite imagery and collateral across discrete satellites. The coordination between various satellites and their complementary sensors allows for more accurate and efficient data collection. This system is particularly useful in scenarios requiring real-time monitoring and rapid response; the method significantly improves situational awareness and operational effectiveness. Tip and cue techniques involve integrating various sensor systems, each playing a specific role in the tracking process. As a target moves, it is handed off from one satellite to another, ensuring continuous monitoring. This coordination optimizes data collection and analysis, enhancing overall tracking accuracy. The real-time information gathered by these satellites is critical for decision-making in various applications, including defense and surveillance. By leveraging multiple satellites and their sensors, it provides broader coverage and more reliable tracking, and the continuous handoff between satellites ensures there are no gaps in monitoring, essential for high-stakes applications. The real-time data provided by this system allows for timely and informed decisions, improving response times and outcomes. Tip and cue methodologies are a part of geospatial intelligence, or GEOINT. Robert Cardillo, a former director of the National Geospatial-Intelligence Agency, highlighted the importance of tip and cue methods to their data collection efforts in 2015. == Historical Development == The concept of tip and cue in satellite monitoring has its origins in early military applications designed to enhance missile detection and tracking systems. During the Cold War, advancements in infrared sensing technologies laid the groundwork for more sophisticated tip and cue techniques. The integration of different sensor types, such as radar and optical sensors, in the 1990s expanded the capabilities of tip and cue systems beyond military applications. These advancements have made tip and cue techniques essential for various civilian uses, including disaster monitoring and environmental surveillance. Significant progress was made with the advent of high-speed data processing and communication technologies in the early 2000s, further refining the method. Advanced algorithms and data fusion techniques have been introduced to better integrate information from multiple sensors. Machine learning technologies now play a crucial role in improving detection and prediction capabilities, allowing for more adaptive and efficient tracking. Richmond and Brennan of Lockheed Martin, presenting to the annual technical conference of the Maui Space Surveillance Complex (formerly the Air Force Maui Optical Station (AMOS)), discussed the algorithms needed for 'tip and cue', to facilitate "multi-phenomenology data fusion." The Space Surveillance Telescope (SST) at Naval Communication Station Harold E. Holt in Australia, operated by the United States Space Force and designed by the Massachusetts Institute of Technology Lincoln Laboratory, was reported by the Defense Advanced Research Projects Agency (DARPA) to be a leader in creating and improving tip and cue techniques, from a large library of orbital object data. == Technical overview == Tip and cue systems utilize a network of at least two satellites equipped with complementary sensor technologies to track moving objects in real-time. The method involves detecting a target with a primary sensor, such as an infrared or photographic sensor, which then cues secondary sensors on the same or other satellites for more detailed monitoring. This handoff process between discrete systems ensures continuous tracking as the target moves across different areas, leveraging each systems strengths. Data collected by these systems and sensors are rapidly processed and shared among the network, enhancing situational awareness. This coordination optimizes resource usage and improves the accuracy of tracking moving objects over large areas. The primary sensors detect initial targets based on specific signatures, such as heat or movement, and then cue secondary sensors to gather more precise data. This ensures that each sensor operates within its optimal range, maintaining high tracking accuracy and reliability. The integration of various sensor types, including optical, radar, and infrared, allows the system to function effectively under different conditions and environments. Real-time data processing and communication between satellites and ground stations are crucial for timely and accurate target tracking. Satellites using tip and cue processes may use either passive or active scanning methodoloigies. These systems may also leverage both orbital and ground-based ELINT (electronic signals intelligence). == Known use cases == Tip and cue systems have been extensively utilized in military applications, particularly for missile detection and defense. These systems enable early detection of missile launches using infrared sensors, which then cue other sensors to track the missile's trajectory more accurately. In environmental monitoring, tip and cue techniques help track natural disasters such as wildfires and hurricanes by coordinating various satellite sensors for comprehensive data collection and analysis. Surveillance and reconnaissance operations also benefit from tip and cue systems, which provide continuous and precise tracking of moving objects, enhancing situational awareness. Additionally, these systems are used in maritime surveillance to monitor ship movements and detect illegal activities such as smuggling and piracy. Tip and cue systems are used in disaster management. For instance, during wildfires, infrared sensors can detect heat signatures, prompting other sensors to gather detailed imagery and data on fire spread and intensity. This coordinated approach allows for real-time monitoring and rapid response, crucial for mitigating damage and saving lives. Similarly, in hurricane tracking, satellites equipped with various sensors can monitor storm development and progression, providing timely information for emergency management agencies. The integration of multiple sensor types ensures accurate and comprehensive coverage of these dynamic and fast-changing events. In maritime surveillance, or maritime domain awareness (MDA), tip and cue systems enhance the detection and monitoring of vessel movements, contributing to maritime security. By coordinating satellite sensors, these systems can track ships over vast ocean areas, identifying potential threats or illegal activities such as smuggling, piracy, and illegal fishing. The ability to maintain continuous surveillance and share data in real-time with maritime authorities improves response times and enforcement capabilities. This application of tip and cue systems not only aids in law enforcement but also supports environmental conservation efforts by monitoring protected marine areas. Automatic Identification System (AIS) is one of the most important sources of data for the MDA agencies. AIS is used in order for ships to know each other's whereabouts, they transmit a signal from ship to ship and to shore. Lately, the system has been developed into satellite system, so called satellite AIS, which makes the system more effective. All ocean-going vessels above 300 tons, are supposed to use and transmit via AIS according to the International Maritime Organization. The satellite constellations help facilitate this with tip and cue methodologies.
Data-centric AI
Data-centric AI is an approach within artificial intelligence that emphasizes on improving the quality, consistency and representativeness of the data used to train machine learning models, rather than focusing primarily on optimizing model architectures or algorithms. This idea has gained traction as researchers and practitioners have come to believe that many performance limitations of machine learning systems stem from issues such as noisy labels, biased datasets, and lack of coverage in the data. Data-centric AI involves disciplined approach to data cleaning, augmentation, labeling, and governance that improves model performance and reliability in applications such as computer vision, natural language processing, and further.
The Fractal Prince
The Fractal Prince is the second science fiction novel by Hannu Rajaniemi and the second novel to feature the post-human gentleman thief Jean le Flambeur. It was published in Britain by Gollancz in September 2012, and by Tor in the same year in the US. The novel is the second in the trilogy, following The Quantum Thief (2010) and preceding The Causal Angel (2014). == Plot summary == After the events of The Quantum Thief, Jean le Flambeur and Mieli are on their way to Earth. Jean is trying to open the Schrödinger's Box he retrieved from the memory palace on the Oubliette. After making little progress, he is prodded by the ship Perhonen to talk to Mieli, who turns out to be possessed by the pellegrini again. This time, Jean identifies Mieli's employer as a Sobornost Founder, Joséphine Pellegrini, and gets her to reveal how he got captured, thereby picking up the clues to make plans for his next heist. No sooner is that done than an attack comes from the Hunter. The ship and crew barely survived that, and Jean realizes that he has to find a better way to open the Box - fast. Mieli has been very quiet after they left Mars. She has given up almost everything to the pellegrini, even her identity, as she has promised to let the pellegrini make gogols of her in exchange for rescuing the thief. Yet, having to work with the thief is testing her, especially when the thief eventually does something even more unforgivable than stealing Sydän's jewel from her. In the city of Sirr, on an Earth ravaged by wildcode, Tawaddud and Dunyazad are sisters and members of the powerful Gomelez family. Tawaddud is the black sheep of the family, having run away from her husband and consorted with a notorious jinn, a disembodied intelligence from the wildcode desert. Now Cassar Gomelez, her father, hopes to get her to curry favor with a gogol merchant, Abu Nuwas, so that he has enough votes in the Council for the upcoming decision to renegotiate the Cry of Wrath Accords with the Sobornost. Soon, Tawaddud is embroiled in an investigation with a Sobornost envoy into the murder that triggered the need for her father to forge a new alliance in the first place, and forced to confront old secrets that will change Sirr forever. Somewhere else, in a bookshop and on a beach, a young boy is at play. His mother has told him not to talk to strangers, but there has never been anyone here before. Until now. Should he talk to them? == Influences == In the acknowledgments, Rajaniemi cites the influence of "Andy Clark, Douglas Hofstadter, Maurice Leblanc, Jan Potocki and [...] The Arabian Nights." === Self-loops === In the novel, the idea that the mind is a self-loop may have been influenced by the theories of the Professor of Philosophy, Andy Clark, and the book I Am a Strange Loop by Douglas Hofstadter. === Frame stories === The novel uses frame stories rather extensively, a feature also of The Arabian Nights and Jan Potocki's The Manuscript Found in Saragossa. Several characters in Sirr are the namesakes of characters in these two earlier works as well. The events in The Quantum Thief are also retold at least once by Jean le Flambeur in the course of the events in this novel. == Reception == The novel has received generally positive reviews. However, criticisms of the novel still revolve around Rajaniemi's uncompromising "show, don't tell" style. For example, Amy Goldschlager, writing for the Los Angeles Review of Books, suggested that "[a] bit more explication of the physics involved (“surfing the deficit angle”?) would really be helpful, more helpful than the description of the Schrödinger’s Cat problem given earlier in the book".