StoredIQ was a company founded for information lifecycle management (ILM) of unstructured data. Founded in 2001 as Deepfile in Austin, Texas by Jeff Erramouspe, Jeff Bone, Russell Turpin, Rudy Rouhana, Laura Arbilla and Brett Funderburg, the company changed its name in 2005 to StoredIQ. It continued to operate successfully for over a decade until it was acquired in 2012 by IBM. It now serves as a platform for IBM's information life cycle governance, big data governance and enterprise content management technologies. StoredIQ was awarded five patents by the USPTO. The first, originally filed in 2003, enabled unstructured data in file systems to be manipulated in a similar way to information stored in databases. Subsequent patents built upon the patented actionable file system with further enhancements specific to Enterprise Policy Management and expanding the reach of StoredIQ's management capability all the way to individual desktops. In 2008 StoredIQ was recognized as "Best in Compliance" by Network Products Guide. At the same time, StoredIQ was being recognized as a "Top 5 Provider" by the prestigious Socha-Gelbmann eDiscovery survey. There were takeover negotiations with EMC Corporation, initially a strategic investor in StoredIQ, however, the company rejected the approach, leaving EMC to acquire a competitor. The company published a whitepaper titled The Truth About Big Data. This promotion combined with StoredIQ's patented technology led to IBM selecting StoredIQ as the basis for some products.
Spatial embedding
Spatial embedding is one of feature learning techniques used in spatial analysis where points, lines, polygons or other spatial data types. representing geographic locations are mapped to vectors of real numbers. Conceptually it involves a mathematical embedding from a space with many dimensions per geographic object to a continuous vector space with a much lower dimension. Such embedding methods allow complex spatial data to be used in neural networks and have been shown to improve performance in spatial analysis tasks == Embedded data types == Geographic data can take many forms: text, images, graphs, trajectories, polygons. Depending on the task, there may be a need to combine multimodal data from different sources. The next section describes examples of different types of data and their uses. === Text === Geolocated posts on social media can be used to acquire a library of documents bound to a given place that can be later transformed to embedded vectors using word embedding techniques. === Image === Satellites and aircraft collect digital spatial data acquired from remotely sensed images which can be used in machine learning. They are sometimes hard to analyse using basic image analysis methods and convolutional neural networks can be used to acquire an embedding of images bound to a given geographical object or a region. === Point === A single point of interest (POI) can be assigned multiple features that can be used in machine learning. These could be demographic, transportation, meteorological, or economic data, for example. When embedding single points, it is common to consider the entire set of available points as nodes in a graph. === Line / multiline === Among other things, motion trajectories are represented as lines (multilines). Individual trajectories are embedded taking into account travel time, distances and also features of points visited along the way. Embedding of trajectories allows to improve performance of such tasks as clustering and also categorization. === Polygon === The geographic areas analyzed in machine learning are defined by both administrative boundaries and top-down division into grids of regular shapes such as rectangles, for example. Both types are represented as polygons and, like points, can be assigned different demographic, transportation, or economic features. A polygon can also have features related to the size of the area or shape it represents. === Graph === An example domain where graph representation is used is the street layout in a city, where vertices can be intersections and edges can be roads. The vertices can also be destination points like public transport stops or important points in the city, and the edges represent the flow between them. Embedding graphs or single vertices allows to improve accuracy of analysis methods in which the treated geographical domain can be represented as a network. == Usage == POI recommendation - generating personalized point of interest recommendations based on user preferences. Next/future location prediction - prediction of the next location a person will go to based on their historical trajectory. Zone functions classification - based on different mobility of people or POI distribution a function of a given area in a city can be predicted. Crime prediction - estimation of crime rate in different regions of a city. Local event detection - studying spatio-temporal changes in embeddings can provide valuable information in detection of local event occurring in specific location. Regional mobility popularity prediction - analysis of mobility can show patterns in popularity of different regions in a city. Shape matching - finding a similar shape of given polygon, for example finding building with the same shape as input building. Travel time estimation - predicting estimated travel time given current traffic conditions and special occurring events. Time estimation for on-demand food delivery - estimation of delivery time when placing an order through the website. == Temporal aspect == Some of the data analyzed has a timestamp associated with it. In some cases of data analysis this information is omitted and in others it is used to divide the set into groups. The most common division is the separation of weekdays from weekends or division into hours of the day. This is particularly important in the analysis of mobility data, because the characteristics of mobility during the week and at different times of the day are very different from each other. Another area in which time division into, for example, individual months can be used is in the analysis of tourism of a given region. In order to take such a split into account, embedding methods treat the time stamp specifically or separate versions of the model are developed for different subgroups of the analyzed set.
Ampere Computing
Ampere Computing LLC is an American fabless semiconductor company that designs ARM-based central processing units (CPUs) with high core counts for use in cloud computing and data center environments. Founded in 2017 by former Intel president Renée James, the company is headquartered in Santa Clara, California, and operates as an independent subsidiary of SoftBank Group since November 2025. == History == Ampere Computing was founded in fall 2017 by Renée James, ex-President of Intel, with funding from The Carlyle Group. James acquired a team from MACOM Technology Solutions (formerly AppliedMicro) in addition to several industry hires to start the company. Ampere Computing is an ARM architecture licensee and develops its own server microprocessors. Ampere fabricates its products at TSMC. In April 2019, Ampere announced its second major investment round, including investment from Arm Holdings and Oracle Corporation. In June 2019, Nvidia announced a partnership with Ampere to bring support for Compute Unified Device Architecture (CUDA). In November 2019, Nvidia announced a reference design platform for graphics processing unit (GPU)-accelerated ARM-based servers including Ampere. In the first half of 2020, Ampere announced Ampere Altra, an 80-core processor, and Ampere Altra Max, a 128-core processor, without the use of simultaneous multithreading. In March 2020, the company announced a partnership with Oracle. In September 2020, Oracle said it would launch bare-metal and virtual machine instances in early 2021 based on Ampere Altra. In November 2020, Ampere was named one of the top 10 hottest semiconductor startups by CRN. In May 2021, the company announced a partnership with Microsoft. In April 2022, Ampere said that it had filed a confidential prospectus with the U.S. Securities and Exchange Commission, signaling its intent to go public. In June 2022, HPE announced their Gen11 ProLiant system would use Ampere Altra and Ampere Altra Max Cloud Native Processors. In July 2022, Google announced T2A instances using Ampere Altra in the Google cloud and in August 2022 Microsoft announced their instances of Ampere running in Azure. On March 19, 2025, investment holding company SoftBank Group announced it will acquire Ampere Computing for $6.5 billion. The deal finalized in November 2025, with Ampere remaining as an independent subsidiary with its headquarters in Santa Clara, California. == Products == Ampere develops ARM-based computer processors and CPU cores under their Altra brands. These are used in databases, media encoding, web services, network acceleration, mobile gaming, AI inference processing, and other applications and programs that need to scale. On February 5, 2018, Ampere announced the eMAG 8180 featuring 32x Skylark cores fabricated on TSMC's 16FF+ process. It supports a turbo of up to 3.3 GHz with a TDP of 125 W, 8ch 64-bit DDR4, up to 1 TB DDR4 per socket, and 42x PCIe 3.0 Lanes. The Skylark cores were based on AppliedMicro's X-Gene 3. Packet offers servers with the eMAG 8180 and 128 GB DRAM, 480 GB SSD, and 2x 10 Gbit/s networking. On September 19, 2018, Ampere announced the availability of a version featuring 16x Skylark cores. === 2020 === On March 3, 2020, Ampere announced the Ampere Altra featuring 80 cores fabricated on TSMC's N7 process for hyperscale computing. It was the first server-grade processor to include 80 cores and the Q80-30 conserves power by running at 161 W in use. The cores are semi-custom Arm Neoverse N1 cores with Ampere modifications. It supports a frequency of up to 3.3 GHz with TDP of 250 W, 8ch 72-bit DDR4, up to 4 TB DDR4-3200 per socket, 128x PCIe 4.0 Lanes, 1 MB L2 per core and 32 MB SLC. Ampere also announced their roadmap with Ampere Altra Max (2021) in development and AmpereOne (2022) defined. === 2021 === The 128-core Altra Max was released in 2021 and targeted hyperscale cloud providers. It uses the same server socket and platforms as Ampere Altra, and both products have one thread per core. The Altra Max CPUs provide 128 Arm v8.2+ cores per chip and run up to 3.0 GHz. They also support eight channels of DDR4-3200 memory and 128 lanes of PCIe Gen4. Also in 2021, Oracle launched its Oracle Cloud Infrastructure (OCI) using Ampere Altra processors. === 2022 === In February 2022, Ampere and Rigetti Computing announced a strategic partnership to create hybrid quantum-classical computers. The companies will combine Ampere's Altra Max CPUs with Rigetti's Quantum Processing Units (QPU) in cloud-based High-Performance Computing (HPC) environments. In April, Microsoft previewed its Azure Virtual Machines running on the Ampere Altra. The VMs run scale-out workloads, web servers, application servers, open source databases, cloud native .NET applications, Java applications, gaming servers, media servers, and other processes. In May, Ampere announced the sampling of AmpereOne CPUs, 5 nanometer chips based on its in-house Ampere-developed core. AmpereOne will add support for DDR5 main memory and PCIe Gen5 peripherals. On June 28, 2022, HPE became first tier-one server provider to offer compute with optimized cloud-native silicon for service providers and enterprises embracing cloud-native development with new line of HPE ProLiant RL Gen11 servers, using Ampere® Altra® and Ampere® Altra® Max processors, delivering high performance and power efficiency. === 2023 === During April 2023, Ampere released the Altra developer's kit, an IoT Prototype Kit based on Ampere Altra, aimed at cloud developers, available in 32-core, 64-core, and 80-core formats. === 2024 === In May 2024, Ampere updated its AmpereOne roadmap to 256 cores and announced a joint effort with Qualcomm on CPUs and accelerators. == Customers == Ampere's customers include Microsoft Azure, Tencent Cloud, Oracle, ByteDance, Hewlett Packard Enterprise (HPE), Cloudflare, Equinix, Kingsoft Cloud, Meituan, Scaleway, UCloud, Foxconn Industrial Internet, Gigabyte, Inspur, Cruise, Hetzner, Project Ronin, Wiwynn and Google Cloud Platform Cruise uses an Ampere Altra variant for its autonomous driving unit. The CPU was selected because of its throughput and low power consumption. In 2021, Oracle, Microsoft, Tencent, and ByteDance committed to using Ampere's customized chips, first announced in May. In April 2022, Microsoft previewed Ampere Altra processors in its new Azure D-and E- series virtual machines. The Dpsv5 series is built for Linux enterprise application types, and the Epsv5 series is for memory-intensive Linux workloads. They provide up to 64 vCPUs, include VM sizes with 2GiB, 4GiB, and 8GiB per vCPU memory configurations, up to 40 Gbit/s networking, and high-performance local SSD storage. In 2022, Microsoft's Ampere Altra-based Azure servers became the first cloud solution provider server to be Arm SystemReady SR certified. The Azure VMs, powered by Altra processors, were also the first to be SystemReady Virtual Environment standard certified. SystemReady defines a set of firmware and hardware standards as a baseline for system development for software developers, original equipment vendors, and chipmakers.
Flektor
Flektor was a web application that allowed users the ability to create and "mashup" their own content (photos, videos, music, etc.) and share it via email, on social networking websites MySpace, Facebook, Blogger, Digg, eBay or on personal blogs. The company's website (Flektor.com) launched on April 2, 2007, and over 40,000 people began utilizing its features just one month later. Flektor closed down in January 2009. Flektor offered tools and widgets that included audio, video, photos, text, and approximately 100 effects, transitions and filters to be used with media. Users could create personalized slideshows, polls, postcards, and streaming video projects which the website calls "fleks". Flektor also offered Chat (used as a MySpace addon) and Movie Editor, which provided the ability to edit content and assets together. Users of Flektor could import media from websites like Photobucket and Google's YouTube, and then edit their content with the site's editing tools. Flektor's erstwhile competitors include Slide.com (founded by PayPal co-founder Max Levchin), RockYou!, Yahoo's JumpCut and Brightcove. == History == Flektor was created by Jason Rubin, Andy Gavin and former HBO executive Jason R. Kay. Both Rubin and Gavin spent most of their careers in the video game industry developing games for publishers like Electronic Arts, Universal Interactive Studios and Sony Computer Entertainment America. They founded a successful game development studio called Naughty Dog and were responsible for games such as Crash Bandicoot and Jak and Daxter. After selling Naughty Dog to Sony, Rubin focused on a comic book series called Iron and the Maiden before teaming up again with Gavin to venture into the web industry with Flektor. Jason Kay spent four years at Home Box Office, working as a consultant to the EVP of Business Development. They recruited former employee and then Naughty Dog Lead Programmer Scott Shumaker to lead the technology team along with Gavin. Ryan Evans joined shortly thereafter, spearheading product development. Flektor is based in Culver City, California. In May 2007, the company was sold to Fox Interactive Media, which is a division of News Corp., for more than $20 million. The deal coincided with Fox's acquisition of Photobucket, an image-hosting and sharing website. Fox Interactive Media already holds possession of MySpace, IGN Entertainment, FOXSports.com, AmericanIdol.com and Rotten Tomatoes. After the acquisition, Rubin, Gavin and Kay departed, leaving the studio in the hands of Shumaker and Evans. In the fall of 2007, Flektor partnered with its sister company, MySpace, and MTV to provide instant audience feedback via polls for the interactive MySpace/ MTV Presidential Dialogues series with presidential candidates Senator Barack Obama, Senator John McCain and John Edwards. Use of Flektor's polling system, enabled hosts John McLaughlin and Geoffrey Garin to cater their questions towards subjects of voter-interest. In the fall of 2008, Flektor built the official site for the 2008 Presidential debates, hosted at MyDebates. In January 2009, due to a company directive to focus on the core MySpace property, Fox Interactive announced that Flektor would be shut down, with some of its technology being incorporated into MySpace.
Windows Live OneCare Safety Scanner
Windows Live OneCare Safety Scanner (formerly Windows Live Safety Center and codenamed Vegas) was an online scanning, PC cleanup, and diagnosis service to help remove of viruses, spyware/adware, and other malware. It was a free web service that was part of Windows Live. On November 18, 2008, Microsoft announced the discontinuation of Windows Live OneCare, offering users a new free anti-malware suite Microsoft Security Essentials, which had been available since the second half of 2009. However, Windows Live OneCare Safety Scanner, under the same branding as Windows Live OneCare, was not discontinued during that time. The service was officially discontinued on April 15, 2011 and replaced with Microsoft Safety Scanner. == Overview == Windows Live OneCare Safety Scanner offered a free online scanning and protection from threats. The Windows Live OneCare Safety Scanner must be downloaded and installed to your computer to scan your computer. The "Full Service Scan" looks for common PC health issues such as viruses, temporary files, and open network ports. It searches and removes viruses, improves a computer's performance, and removes unnecessary clutter on the PC's hard disk. The user can choose between a "Full Scan" (which can be customized) or a "Quick Scan". The "Full Scan" scans for viruses (comprehensive scan or quick scan), hard disk performance (Disk fragmentation scan and/or Desk cleanup scan) and network safety (open port scan). The "Quick Scan" only scans for viruses, only on specific areas on the computer. The quick scan is faster than the full scan, hence that appellation. The service also provides a virus database, information about online threats, and general computer security documentation and tools. == Limits == The virus scanner on the Windows Live OneCare Safety Scanner site runs a scan of the user's computer only when the site is visited. It does not run periodic scans of the system, and does not provide features to prevent viruses from infecting the computer at the time, or thereafter. It simply resolves detected infections. Many users who have posted on the Product Feedback forum report script errors relating to Internet Explorer 7 (besides IE being the only browser supported by this service). The OneCare safety scanner team have been actively solving these problems, many of them registry-related.
Software agent
In computer science, a software agent is a computer program that acts for a user or another program in a relationship of agency. The term agent is derived from the Latin agere (to do): an agreement to act on one's behalf. Such "action on behalf of" implies the authority to decide which, if any, action is appropriate. Some agents are colloquially known as bots, from robot. They may be embodied, as when execution is paired with a robot body, or as software such as a chatbot executing on a computer, such as a mobile device, e.g. Siri. Software agents may be autonomous or work together with other agents or people. Software agents interacting with people (e.g. chatbots, human-robot interaction environments) may possess human-like qualities such as natural language understanding and speech, personality or embody humanoid form (see Asimo). Related and derived concepts include intelligent agents (in particular exhibiting some aspects of artificial intelligence, such as reasoning), autonomous agents (capable of modifying the methods of achieving their objectives), distributed agents (being executed on physically distinct computers), multi-agent systems (distributed agents that work together to achieve an objective that could not be accomplished by a single agent acting alone), and mobile agents (agents that can relocate their execution onto different processors). == Concepts == The basic attributes of an autonomous software agent are that agents: are not strictly invoked for a task, but activate themselves, may reside in wait status on a host, perceiving context, may get to run status on a host upon starting conditions, do not require interaction of user, may invoke other tasks including communication. The concept of an agent provides a method of describing a complex software entity that is capable of acting with a certain degree of autonomy in order to accomplish tasks on behalf of its host. But unlike objects, which are defined in terms of methods and attributes, an agent is defined in terms of its behavior. Various authors have proposed different definitions of agents, these commonly include concepts such as: persistence: code is not executed on demand but runs continuously and decides for itself when it should perform some activity; autonomy: agents have capabilities of task selection, prioritization, goal-directed behavior, decision-making without human intervention; social ability: agents are able to engage other components through some sort of communication and coordination, they may collaborate on a task; reactivity: agents perceive the context in which they operate and react to it appropriately. === Distinguishing agents from programs === All agents are programs, but not all programs are agents. Contrasting the term with related concepts may help clarify its meaning. Franklin & Graesser (1997) discuss four key notions that distinguish agents from arbitrary programs: reaction to the environment, autonomy, goal-orientation and persistence. === Intuitive distinguishing agents from objects === Agents are more autonomous than objects. Agents have flexible behavior: reactive, proactive, social. Agents have at least one thread of control but may have more. === Distinguishing agents from expert systems === Expert systems are not coupled to their environment. Expert systems are not designed for reactive, proactive behavior. Expert systems do not consider social ability. === Distinguishing intelligent software agents from intelligent agents in AI === Intelligent agents (also known as rational agents) are not just computer programs: they may also be machines, human beings, communities of human beings (such as firms) or anything that is capable of goal-directed behavior. == Impact of software agents == Software agents may offer various benefits to their end users by automating complex or repetitive tasks. However, there are organizational and cultural impacts of this technology that need to be considered prior to implementing software agents. === Organizational impact === === Work contentment and job satisfaction impact === People like to perform easy tasks providing the sensation of success unless the repetition of the simple tasking is affecting the overall output. In general implementing software agents to perform administrative requirements provides a substantial increase in work contentment, as administering their own work does never please the worker. The effort freed up serves for a higher degree of engagement in the substantial tasks of individual work. Hence, software agents may provide the basics to implement self-controlled work, relieved from hierarchical controls and interference. Such conditions may be secured by application of software agents for required formal support. === Cultural impact === The cultural effects of the implementation of software agents include trust affliction, skills erosion, privacy attrition and social detachment. Some users may not feel entirely comfortable fully delegating important tasks to software applications. Those who start relying solely on intelligent agents may lose important skills, for example, relating to information literacy. In order to act on a user's behalf, a software agent needs to have a complete understanding of a user's profile, including his/her personal preferences. This, in turn, may lead to unpredictable privacy issues. When users start relying on their software agents more, especially for communication activities, they may lose contact with other human users and look at the world with the eyes of their agents. These consequences are what agent researchers and users must consider when dealing with intelligent agent technologies. === History === The concept of an agent can be traced back to Hewitt's Actor Model (Hewitt, 1977) - "A self-contained, interactive and concurrently-executing object, possessing internal state and communication capability." To be more academic, software agent systems are a direct evolution of Multi-Agent Systems (MAS). MAS evolved from Distributed Artificial Intelligence (DAI), Distributed Problem Solving (DPS) and Parallel AI (PAI), thus inheriting all characteristics (good and bad) from DAI and AI. John Sculley's 1987 "Knowledge Navigator" video portrayed an image of a relationship between end-users and agents. Being an ideal first, this field experienced a series of unsuccessful top-down implementations, instead of a piece-by-piece, bottom-up approach. The range of agent types is now (from 1990) broad: WWW, search engines, etc. == Examples of intelligent software agents == === Buyer agents (shopping bots) === Buyer agents travel around a network (e.g. the internet) retrieving information about goods and services. These agents, also known as 'shopping bots', work very efficiently for commodity products such as CDs, books, electronic components, and other one-size-fits-all products. Buyer agents are typically optimized to allow for digital payment services used in e-commerce and traditional businesses. === User agents (personal agents) === User agents, or personal agents, are intelligent agents that take action on your behalf. In this category belong those intelligent agents that already perform, or will shortly perform, the following tasks: Check your e-mail, sort it according to the user's order of preference, and alert you when important emails arrive. Play computer games as your opponent or patrol game areas for you. Assemble customized news reports for you. There are several versions of these, including CNN. Find information for you on the subject of your choice. Fill out forms on the Web automatically for you, storing your information for future reference Scan Web pages looking for and highlighting text that constitutes the "important" part of the information there Discuss topics with you ranging from your deepest fears to sports Facilitate with online job search duties by scanning known job boards and sending the resume to opportunities who meet the desired criteria Profile synchronization across heterogeneous social networks === Monitoring-and-surveillance (predictive) agents === Monitoring and surveillance agents are used to observe and report on equipment, usually computer systems. The agents may keep track of company inventory levels, observe competitors' prices and relay them back to the company, watch stock manipulation by insider trading and rumors, etc. For example, NASA's Jet Propulsion Laboratory has an agent that monitors inventory, planning, schedules equipment orders to keep costs down, and manages food storage facilities. These agents usually monitor complex computer networks that can keep track of the configuration of each computer connected to the network. A special case of monitoring-and-surveillance agents are organizations of agents used to automate decision-making process during tactical operations. The agents monitor the status of assets (ammunition, weapons available, platforms for transport, etc.) and receive goals from hi
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