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

Ideonomy

Ideonomy is a combinatorial "science of ideas" developed by American independent scholar Patrick M. Gunkel (1947–2017). Specifically, Ideonomy is concerned with the systematic organization of ideas and the discovery of the rules behind how ideas combine, diverge, and transform. Gunkel defined ideonomy as "the science of the laws of ideas and of the application of such laws to the generation of all possible ideas in connection with any subject, idea, or thing." In his 1992 book A History of Knowledge, Charles Van Doren compared ideonomy to a "mining operation" that excavates meanings and thought to discover treasures hidden deep within language. Sources from the 1980s and 1990s demonstrate that ideonomy was useful to academic researchers in fields including biology, toxicology, and nursing/patient care. Beginning in the 2010s, academics in a wide range of fields including machine learning, marketing, computational modeling, and cybersecurity have relied on materials generated for ideonomy to provide methodological support for their research. == Etymology and definition == The word "ideonomy" combines the Greek roots ideo- (from idea, meaning pattern or form) and -nomy (from nomos, meaning law or custom). The suffix -nomy suggests the laws concerning or the totality of knowledge about a given subject, as in astronomy or taxonomy. In a note posted on the MIT ideonomy website, Gunkel states that the word was supposedly first coined by the French Encyclopedists to refer to a science of ideas. No evidence is provided for this statement, however. The concept bears some relationship to Antoine Destutt de Tracy's "ideology" (1796), which originally meant a systematic science of ideas before acquiring its modern political connotations. Gunkel provided several metaphorical descriptions of ideonomy: An "idea bank": a computer network enabling systematic exploration of infinite possible ideas A "kaleidoscope" that can exhibit all possible combinations and transformations of ideas A "prism" capable of diffracting any idea into its cognitive components A "gigantic microscope for magnifying the ideocosm" == History and development == In 1984, Gunkel received a five-year unsolicited grant from the Richard Lounsbery Foundation of New York to develop ideonomy. A June 1, 1987 article on the front page of The Wall Street Journal brought Gunkel and ideonomy to wider public attention. Some academics were interested in using ideonomy's techniques, including biologist Betsey Dyer, who published several contemporaneous peer-reviewed studies citing ideonomy. Academic researchers in the field of toxicology and nursing/patient care also used ideonomy. However, ideonomy's broadest contribution to date came beginning in the 2010s, as a list of personality traits generated for combinatorial matching was used by researchers in artificial intelligence to code human emotions for machine-learning tasks, develop computational models related to personality, develop a measurement framework for influencer-brand recommender systems, and aid information awareness/cybersecurity assessment. == Methodology == The foundational empirical method of ideonomy involves the systematic creation of extensive lists. Gunkel's apartment reportedly contained thousands of lists on every conceivable topic. Gunkel termed each list an "organon," which he described as expanding through "combination, permutation, transformation, generalization, specialization, intersection, interaction, reapplication, recursive use, etc. of existing organons." The ideonomic process follows a progressive structure. The ideonomist begins with a simple list of examples of a particular idea, concept, or thing. The list need not be exhaustive. By studying this list, the ideonomist isolates and identifies types. This categorical analysis then reveals missing items, allowing the primary list to be improved and refined. Gunkel emphasized that list items must not only cover genuine categories of nature but also be formulated in ways that yield the largest possible number of syntactically coherent possibilities when combined. The core technique of ideonomy is "ideocombinatorics"—the systematic intersection and combination of items from different lists to generate novel composite concepts. Gunkel developed computer programs to automate this process. For example, combining a list of 230 Universal Elementary Shapes (pits, pyramids, trenches, hemispheres, needles) with a list of 74 Types of Order (recurrence, identity, likeness of parts) yields 17,020 possible "shapes of order." These combinations, when phrased as questions ("Can there be pits of recurrence?"), could suggest new categories of phenomena worthy of investigation. The computer-generated output is typically repetitive and often meaningless. However, with sufficient frequency, the combinations yield results that are unexpectedly interesting and fruitful. In one documented case, Gunkel's programs generated 45,540 questions about toxins for microbiologist David Bermudes. One question—"Can hierarchies of cell process be used as a basis for classifying toxic action?"—prompted Bermudes to develop a novel approach to classifying biological toxins by the type of molecule they attack, rather than by chemical structure or physiological system affected. According to one contemporaneous account of ideonomy, "Gunkel takes for his field all fields and all ideas about anything. He uses a computer to generate lists of words and phrases and by juxtaposition reviews the resultant patterns for novel ideas. The computer is ideal for this task because the mind would rebel at the formidable processing task ideonomy involves. What we have here is computer generated originality." == Applications == Gunkel and his supporters identified several practical applications for ideonomic methods: Scientific research: Biologist Betsey Dyer of Wheaton College published research crediting ideonomy for helping to generate ideas. Medical science: When Austin pathologist Michael T. O'Brien was presented with the ideonomically-generated question "Can arteries have rashes?", he initially dismissed it as nonsense. Upon reflection, he realized that large arteries are supplied with blood by tiny vessels that might become inflamed and dilated, analogous to skin vessels in a rash—a phenomenon potentially worth researching. Analogical thinking: Harvard law professor Robert Clark used ideonomic analogies to write a research paper comparing plant structure with human hierarchies. Artificial intelligence: Douglas Lenat, a researcher at Microelectronics and Computer Technology Corporation (MCC) in Austin, suggested that Gunkel's lists enumerating types of human mistakes could help design AI systems capable of recognizing and correcting their own errors. == Reception and criticism == Ideonomy received mixed reactions from the academic and scientific communities. Prominent supporters included: Edward Fredkin, former director of MIT's computer science laboratory, who praised Gunkel's "provocative ideas on artificial intelligence." Marvin Minsky, AI scientist and MIT professor, who described ideonomy as "perhaps the most extensive study of ways to generate ideas." Frederick Seitz, president emeritus of Rockefeller University, who noted Gunkel's "encyclopedic scope" Robert C. Clark, Harvard law professor, who called Gunkel "the most intelligent person I ever met" However, skeptics questioned whether ideonomy constituted a genuine science. Fredkin himself noted that Gunkel "pours out about 60 ideas a minute, and 59 of them are bad," though he added that "even with one good idea out of 60, it's still an amazing accomplishment." Douglas Lenat observed that brainstorming with Gunkel was "a bit like being hit over the head by the muse with a sledgehammer" and that "he puts people off." Gunkel himself acknowledged that ideonomy was in its infancy and might seem "absurdly utopian." His planned magnum opus on ideonomy remained incomplete, and was posted on an MIT website thanks to faculty advisor Whitman Richards. Gunkel wrote: "Pioneering in a completely new field, yes in a new science, is almost unreal. It is heartbreaking, it is pitiable, it is almost inhuman. Honestly, it is a hell. There is nothing heroic about it." == Related concepts == Gunkel identified several historical precedents for ideonomic thinking: Gottfried Wilhelm Leibniz (1646–1716): The philosopher's work on a universal characteristic (characteristica universalis) and calculus of reasoning Peter Mark Roget (1779–1869): Creator of Roget's Thesaurus, which organized concepts into a systematic taxonomy Dmitri Mendeleev (1834–1907): Developer of the periodic table, demonstrating how combining lists of element families could reveal previously unseen connections Fritz Zwicky (1898–1974): The Caltech astrophysicist whom Gunkel called the "grandfather of ideonomy" for his development of "morphological research"—systematic exploration of all possible solutions t

Peñabot

Peñabot is the nickname for automated social media accounts allegedly used by the Mexican government of Enrique Peña Nieto and the PRI political party to keep unfavorable news from reaching the Mexican public. Peñabot accusations are related to the broader issue of fake news in the 21st century. == History of disinformation in Mexican politics == The PRI political party has been reported to use fake news since before Peña Nieto. The main tactic originally was to spread such propaganda through open radio and television networks. Such tactic was effective in Mexico, because newspaper readership is low and cable TV is largely limited to the middle classes; consequently, the country's two major television networks – Televisa and TV Azteca – exert a significant influence in national politics. Televisa itself, not only owns around two-thirds of the programming on Mexico's TV channels, making it not only Mexico's largest television network, but also is the largest media network in the Spanish-speaking world. == Peñabots == Analysts have given the name Peñabots to a suspected network of automated accounts on social media used by the Mexican government to spread pro-government propaganda and to marginalize dissenting opinions in social media. The bots were first noticed in the 2012 elections when they were used to disseminate opinions in support of Enrique Peña Nieto on social networks such as Twitter and Facebook. According to Aristegui Noticias, their usage went against articles 6 and 134 of the Mexican Constitution. Those used by Peña Nieto's government cost an estimated 80 million pesos monthly, which news outlets argued only helped the government spread fake support towards the president, but did not have a benefit towards Mexican people (with whom EPN was highly unpopular). Facebook held approximately 640,321 Peñabots, while Twitter had less. As of July 2017, Oxford Internet Institute's Computational Propaganda Research Project claimed many western democracies, Mexico included, perform social media manipulation, thus saying the manipulation comes directly from the Mexican government itself. During Peña Nieto's subsequent presidency, analysts noted that Peñabots were used to overpower trending topics that critiqued government, to flood trending government critical hashtags with spam, to create fake trends by pushing alternative hashtags, and to push smear campaigns and threats against government-critical activists and journalists. Peñabots were distinguished as their pattern of activity was distinct from that of ordinary interaction on social networks. === Meadebots === On Twitter it was reported that about 94% of the followers of 2018 presidential candidate from the PRI Jose Antonio Meade were bots. When Antonio Meade presented himself as a candidate for the 2018 presidential election, his social media accounts such as "@MovimientoMEADE" (created by the PRI's official account @PRI_Nacional), obtained a huge quantity of followers in a short span of time. Some users noticed and brought it to attention, and after investigation it was reported 94% of such followers were bots (702,000 out of 747,000), and the account was eliminated from Twitter after 20 hours. The fake accounts used the hashtags #YoConMeade and #Meade18. It was further revealed was that Meade's official account on Twitter, @JoseAMeadeK had 25% bots (216,000 fake followers out of the 981,000). == Manipulation of news media in Mexico, through television == The Mexican government of Peña Nieto has been accused of using various means to keep unfavorable news from reaching the Mexican people. Many Mexicans have protested this practice as it clearly goes against the freedom of speech. The PRI has been reported to use fake news since before Peña Nieto. The main tactic has been to spread such propaganda through radio and television. This tactic is perceived as effective in Mexico, because newspaper readership is low and research on the Internet and cable TV is largely limited to the middle classes; consequently, the country's two major television networks – Televisa and TV Azteca – exert a significant influence in national politics. Televisa itself, owns around two-thirds of the programming on Mexico's TV channels, making it not only Mexico's largest television network, but also is the largest media network in the Spanish-speaking world. In June 2012, before the 2012 Mexican presidential elections, the British newspaper The Guardian published a series of allegations claiming Televisa, sold favorable coverage to top politicians in its news and entertainment shows, this scandal became known as the Televisa controversy. The documents published by 'The Guardian alleged that a secretive circle within Televisa manipulated news coverage to favor PRI presidential candidate Enrique Peña Nieto, who was poised as favorite to win. Televisa's secret circle supposedly commissioned videos to promote Peña Nieto and lash out his political rivals in 2009. The Guardian documents suggest that Televisa's secret team distributed such videos through e-mail, posting them posted them on Facebook and YouTube, some can still be seen there. Another document was a PowerPoint presentation, with a slide explicitly aimed at rival leftist candidate of the Party of the Democratic Revolution (PRD), Andrés Manuel López Obrador. Supposedly given to The Guardian by a Televisa employee. The document's authenticity was never possible to confirm– however dates, names, and events largely coincide. Televisa refused to talk the documents, and denied a relationship with the PRI or its presidential candidate, saying that they had provided equal media coverage to all parties. Televisa published an article supposedly showing discrepancies in The Guardian documents and denying accusations. Mexican citizens complained about the perceived favoritism towards Enrique Peña Nieto and the PRI, protesting through the Yo Soy 132 movement which Televisa covered in detail. However, Televisa's news media coverage is perceived to have been biased, by using a media coverage tactic Mexican citizens call cortinas de humo (smoke screens). These introduce a news scandal giving extensive coverage to distract citizens from a potential conflict-of-interest or controversy that could damage the image of the politician favored by the network. An example of a perceived smoke screen would be the news media coverage of "Caso Michoacán" and "Caso Paolette" distracting all the attention from the parallel "Yo soy 132" movement. A few years later, on the day of September 11, 2016; factual evidence of Televisa's performing media manipulation emerged, when a Televisa news anchor while live-on air reading a teleprompter, mistakenly read out loud that "try that Jaime "Ël Bronco" Rodríguez Calderón (Nuevo Leon's governor) is mentioned as little as possible". Newspaper El Universal caught it on video and published it social media. Televisa didn't mention the story and declined to comment. Lack of news coverage concerning Nuevo León's Governor Jaime Rodriguez, is perceived due to him being the first elected governor to not be part of any political party (Independent Governor), and because unlike the governors from the PRI preceding him, the independent governor "El Bronco" doesn't spend money on publicity at all, preferring to communicate all news by using social media such as Twitter and Facebook. While the incident may have proven Televisa's bias, there wasn't anything to incriminate the PRI political party or Enrique Peña Nieto, though it did further suspicion of Televisa manipulating news media. In contrast, a December 2017 article of The New York Times, reported Enrique Peña Nieto spending about 2000 million dollars on publicity, during his first 5 years as president, the largest publicity budget ever spent by a Mexican President. Additionally, 68 percent of news journalists admitted to not believe to have enough freedom of speech, and award-winning news reporter Carmen Aristegui was controversially fired shortly after revealing the Mexican White House scandals. == Violence and spying towards news journalists and civil rights activists == Far for only being receiving accusations of spreading fake news, the Mexican government of EPN (Enrique Peña Nieto) has also been accused of violence towards news journalists, and of spying on them, and also towards civil right leaders and their families. During his tenure as president, Peña Nieto has been accused of failing to protect news journalists, whose deaths are speculated to be politically triggered, by politicians attempting to prevent them from covering political scandals. The New York Times published a news report on the matter titled, "In Mexico it's easy to kill a journalist", on it mentioning how during EPN's government, Mexico became one of the worst countries on which to be a journalist. The assassination of journalist Javier Valdez on May 23, 2017, received national coverage, with multiple news journalists

Convergent encryption

Convergent encryption, also known as content hash keying, is a cryptosystem that produces identical ciphertext from identical plaintext files. This has applications in cloud computing to remove duplicate files from storage without the provider having access to the encryption keys. The combination of deduplication and convergent encryption was described in a backup system patent filed by Stac Electronics in 1995. This combination has been used by Farsite, Permabit, Freenet, MojoNation, GNUnet, flud, and the Tahoe Least-Authority File Store. The system gained additional visibility in 2011 when cloud storage provider Bitcasa announced they were using convergent encryption to enable de-duplication of data in their cloud storage service. == Overview == The system computes a cryptographic hash of the plaintext in question. The system then encrypts the plaintext by using the hash as a key. Finally, the hash itself is stored, encrypted with a key chosen by the user. == Known Attacks == Convergent encryption is open to a "confirmation of a file attack" in which an attacker can effectively confirm whether a target possesses a certain file by encrypting an unencrypted, or plain-text, version and then simply comparing the output with files possessed by the target. This attack poses a problem for a user storing information that is non-unique, i.e. also either publicly available or already held by the adversary - for example: banned books or files that cause copyright infringement. An argument could be made that a confirmation of a file attack is rendered less effective by adding a unique piece of data such as a few random characters to the plain text before encryption; this causes the uploaded file to be unique and therefore results in a unique encrypted file. However, some implementations of convergent encryption where the plain-text is broken down into blocks based on file content, and each block then independently convergently encrypted may inadvertently defeat attempts at making the file unique by adding bytes at the beginning or end. Even more alarming than the confirmation attack is the "learn the remaining information attack" described by Drew Perttula in 2008. This type of attack applies to the encryption of files that are only slight variations of a public document. For example, if the defender encrypts a bank form including a ten digit bank account number, an attacker that is aware of generic bank form format may extract defender's bank account number by producing bank forms for all possible bank account numbers, encrypt them and then by comparing those encryptions with defender's encrypted file deduce the bank account number. Note that this attack can be extended to attack a large number of targets at once (all spelling variations of a target bank customer in the example above, or even all potential bank customers), and the presence of this problem extends to any type of form document: tax returns, financial documents, healthcare forms, employment forms, etc. Also note that there is no known method for decreasing the severity of this attack -- adding a few random bytes to files as they are stored does not help, since those bytes can likewise be attacked with the "learn the remaining information" approach. The only effective approach to mitigating this attack is to encrypt the contents of files with a non-convergent secret before storing (negating any benefit from convergent encryption), or to simply not use convergent encryption in the first place.

HashClash

HashClash was a volunteer computing project running on the Berkeley Open Infrastructure for Network Computing (BOINC) software platform to find collisions in the MD5 hash algorithm. It was based at Department of Mathematics and Computer Science at the Eindhoven University of Technology, and Marc Stevens initiated the project as part of his master's degree thesis. The project ended after Stevens defended his M.Sc. thesis in June 2007. However, SHA1 was added later, and the code repository was ported to git in 2017. The project was used to create a rogue certificate authority certificate in 2009.

Continuum robot

A continuum robot is a type of robot that is characterised by infinite degrees of freedom and number of joints. These characteristics allow continuum manipulators to adjust and modify their shape at any point along their length, granting them the possibility to work in confined spaces and complex environments where standard rigid-link robots cannot operate. In particular, we can define a continuum robot as an actuatable structure whose constitutive material forms curves with continuous tangent vectors. This is a fundamental definition that allows to distinguish between continuum robots and snake-arm robots or hyper-redundant manipulators: the presence of rigid links and joints allows them to only approximately perform curves with continuous tangent vectors. The design of continuum robots is bioinspired, as the intent is to resemble biological trunks, snakes and tentacles. Several concepts of continuum robots have been commercialised and can be found in many different domains of application, ranging from the medical field to undersea exploration. == Classification == Continuum robots can be categorised according to two main criteria: structure and actuation. === Structure === The main characteristic of the design of continuum robots is the presence of a continuously curving core structure, named backbone, whose shape can be actuated. The backbone must also be compliant, meaning that the backbone yields smoothly to external loads. According to the design principles chosen for the continuum manipulator, we can distinguish between: single-backbone: these continuum manipulators have one central elastic backbone through which actuation/transmission elements can run. multi-backbone: the structure of these continuum robots has two or more elastic elements (either rods or tubes) parallel to each other and constrained with one another in some way. concentric-tube: the backbone is made of concentric tubes that are free to rotate and translate between each other, depending on the actuation happening at the base of the robot. === Actuation === The actuation strategy of continuum manipulators can be distinguished between extrinsic or intrinsic actuation, depending on where the actuation happens: extrinsic actuation: the actuation happens outside the main structure of the robot and the forces are transmitted via mechanical transmission; among these techniques, there are cable/tendon driven actuators and multi-backbone strategies. intrinsic actuation: the actuation mechanism operates within the structure of the robot; these strategies include pneumatic or hydraulic chambers and the shape memory effect. The Actuated Flexible Manifold (AFM), introduced by Medina, Shapiro, and Shvalb (2016), models flexible grid-based robots that approximate smooth manifolds using discrete segments, each contributing one degree of freedom. Their work provides forward and inverse kinematics for planar and spatial configurations, bridging hyper-redundant and continuum robotics. == Advantages == The particular design of continuum robots offers several advantages with respect to rigid-link robots. First of all, as already said, continuum robots can more easily operate in environments that require a high level of dexterity, adaptability and flexibility. Moreover, the simplicity of their structure makes continuum robots more prone to miniaturisation. The rise of continuum robots has also paved the way for the development of soft continuum manipulators. These continuum manipulators are made of highly compliant materials that are flexible and can adapt and deform according to the surrounding environment. The "softness" of their material grants higher safety in human-robot interactions. == Disadvantages == The particular design of continuum robots also introduces many challenges. To properly and safely use continuum robots, it is crucial to have an accurate force and shape sensing system. Traditionally, this is done using cameras that are not suitable for some of the applications of continuum robots (e.g. minimally invasive surgery), or using electromagnetic sensors that are however disturbed by the presence of magnetic objects in the environment. To solve this issue, in the last years fiber-Bragg-grating sensors have been proposed as a possible alternative and have shown promising results. It is also necessary to notice that while the mechanical properties of rigid-link robots are fully understood, the comprehension of the behaviour and properties of continuum robots is still subject of study and debate. This poses new challenges in developing accurate models and control algorithms for this kind of robots. == Modelling == Creating an accurate model that can predict the shape of a continuum robot allows to properly control the robot's shape. There are three main approaches to model continuum robots: Cosserat rod theory: this approach is an exact solution to the static of a continuum robot, as it is not subject to any assumption. It solves a set of equilibrium equations between position, orientation, internal force and torque of the robot. This method requires to be solved numerically and it is therefore computationally expensive, due to its high complexity. Constant curvature: this technique assumes the backbone to be made of a series of mutually tangent sections that can be approximated as arcs with constant curvature. This approach is also known as piecewise constant-curvature. This assumption can be applied to the entire segment of the backbone or to its subsegments. This model has shown promising results, however it must be taken into account that the segment/subsegments of the backbone may not comply to the constant curvature assumption and therefore the model's behaviour may not entirely reflect the behaviour of the robot. Rigid-link model: this approach is based on the assumption that the continuum robot can be divided in small segments with rigid links. This is a strong assumption, since if the number of segments is too low, the model hardly behaves like the continuum robot, while increasing the number of segments means increasing the number of variables, and thus complexity. Despite this limitation, rigid-link modelling allows the use of the standard control techniques that are well known for rigid-link robots. It has been proven that this model can be coupled with shape and force sensing to mitigate its inaccuracy and can lead to promising results. == Sensing == To develop accurate control algorithms, it is necessary to complement the presented modelling techniques with real time shape sensing. The following options are currently available: Electromagnetic (EM) sensing: shape is reconstructed thanks to the mutual induction between a magnetic field generator and a magnetic field sensor. The most common external EM tracking system is the commercially available NDI Aurora: small sensors can be placed on the robot and their position is tracked in an external generated magnetic field. The validity of this method has been extensively assessed, however its performance is hindered by the limited workspace, whose dimension depends on the magnetic field. Another alternative is to embed the sensors internally in the continuum robot, combining magnetic sensors with Hall effect sensors: the magnetic field is measured at the level of the Hall effect sensors in order to estimate the deflection of the robot. However, it has been noticed that the higher the bending of the manipulator, the higher is the estimation error, due to crosstalk between sensors and magnets. Optical sensing: fiber Bragg grating sensors incorporated in an optical fiber can be embedded into the backbone of the continuum robot to estimate its shape; these sensors can only reflect a small range of the input light spectrum depending on their strain; therefore, by measuring the strain on each sensor it is possible to obtain the shape of the robot. This type of sensor is however expensive and is more prone to breaking in case of excessive strain, and this can happen in robots that can perform high deflections. == Control strategies == The control strategies can be distinguished in static and dynamic; the first one is based on the steady-state assumption, while the latter also considers the dynamic behaviour of the continuum robot. We can also differentiate between model-based controllers, that depend on a model of the robot, and model-free, that learn the robot's behaviour from data. Model-based static controllers: they rely on one of the modelling approaches presented above; once the model is defined, the kinematics must be inverted to obtain the desired actuator or configuration space variables. There are several ways to do this, like differential inverse kinematics, direct inversion or optimization. Model-free static controllers: these approaches learn directly, via machine learning techniques (e.g. regression methods and neural networks), the inverse kinematic or the direct kinematic representation of the con

Philco computers

Philco was one of the pioneers of transistorized computers, also known as second-generation computers. After the company developed the surface-barrier transistor, which was much faster than previous point-contact types, it was awarded contracts for military and government computers. Commercialized derivatives of some of these designs became successful business and scientific computers. The TRANSAC (Transistor Automatic Computer) Model S-1000 was released as a scientific computer. The TRANSAC S-2000 mainframe computer system was first produced in 1958, and a family of compatible machines, with increasing performance, was released over the next several years. However, the mainframe computer market was dominated by IBM. Other companies could not deploy resources for development, customer support and marketing on the scale that IBM could afford, making competition in this segment difficult after the introduction of the IBM 360 family. Philco went bankrupt and was purchased in 1961 by Ford Motor Company, but the computer division carried on until the Philco division of Ford exited the computer business in 1963. The Ford company maintained one Philco mainframe in use until 1981. == The surface-barrier transistor == The surface-barrier transistor developed by Philco in 1953 had a much higher frequency response than the original point-contact transistors. The transistor was made of a thin crystal of germanium, which was electrolytically etched with pits on either side forming a very thin base region, on the order of 5 micrometers. Philco's process for etching was United States patent number 2,885,571. Philco surface-barrier transistors were used in TX-0, and in early models of what would become the DEC PDP product line. Although relatively fast, the small size of the devices limited their power to circuits operating at a few tens of milliwatts. == Military and government == Between 1955 and 1957, Philco built transistor computers for use in aircraft, models C-1000, C-1100, and C-1102, intended for airborne real-time applications. By 1957, the C-1102 had been used by a civilian sector customer. The BASICPAC AN/TYK 6V (first delivery in 1961), COMPAC AN/TYK 4V (not completed), and LOGICPAC systems were built for the US Army as transportable computer systems for use with their Fieldata concept of integrated information management. BASICPAC was a transistorized computer with up to 28,672 words of 38-bit core memory (including sign and parity), available in several configurations from a minimum system, to a truck-borne mobile version, to a fully expanded system. Basic clock periods was 1 microsecond (which gives a clock rate of 1 MHz), with 12 microsecond memory access and a fixed-point multiplication taking 242 microseconds. Input/output was by paper tape reader and punch, or through a teletypewriter. With additional hardware, magnetic tape storage was also available, with up to seven I/O devices. The instruction set had 31 basic operation codes and nine opcodes for I/O === CXPQ === Philco was contracted by the US Navy to build the CXPQ computer. One model was completed and installed at the David Taylor Model Basin. This design was later adapted to become the commercial TRANSAC S-2000. Only one CXPQ was built. The CXPQ is a 48-bit transistorized computer. === SOLO === In 1955, the National Security Agency through the US Navy contracted with Philco to produce a computer suitable for use as a workstation, with an architecture based on the vacuum-tube computer system called Atlas II already in use at the NSA, and similar to the commercial UNIVAC 1103. At the time, Philco was the largest producer of surface barrier transistors, which were the only type available with the speed and quantities required for a computer. The SOLO prototype was delivered in 1958, but required extensive debugging at NSA. Difficulties were encountered with core memory and power supplies. SOLO used paper tape and teleprinter machines for input and output. SOLO cost about $1 million US, and contained 8,000 transistors. While the system was extensively used for training, testing, research and development, no additional units were ordered. SOLO was removed from active service in 1963. The design of the SOLO became commercialized as Philco's TRANSAC Model S-1000. == Commercial == === S-1000 === The TRANSAC S-1000 was a scientific computer with a 36-bit word length and 4096 words of core memory. It was packaged in a container about the size of a large office desk, and used only 1.2 kilowatts, much less than vacuum-tube-based computers of similar capacity. In a 1961 survey, about 15 S-1000 computer installations had been identified. It weighed about 1,650 pounds (750 kg). === S-2000 === The TRANSAC S-2000 was a large mainframe system intended for both business and scientific work. It had a 48-bit word length and supported calculations in fixed point, floating point and binary-coded decimal formats. The original S-2000 "TRANSAC" (Transistor Automatic Computer) released in 1958 was later designated Model 210; it was used internally at Philco. Similar to the Control Data Corporation Model 1604, it was a 48-bit fully transistorized computer. Three succeeding models were released in the series, all compatible with the software of the original model. The Model 211 was introduced in 1960, using micro-alloy diffused field-effect transistors, requiring significant redesign of circuits compared to the original. The TRANSAC S-2000/Philco 210/211 weighed about 2,000 pounds (910 kg). By 1964, eighteen Model 210, eighteen Model 211 and seven Model 212 systems had been sold. After Philco was purchased by Ford Motor Company, the Model 212 was introduced in 1962 and released in 1963. It had 65,535 words of 48-bit memory. Initially made with 6-microsecond core memory, it had better performance than the IBM 7094 transistor computer. It was later upgraded in 1964 to 2-microsecond core memory, which gave the machine floating-point performance greater than the IBM 7030 Stretch computer. A Model 213 was announced in 1964 but never built. By that time competition from IBM had made the Philco computer operations no longer profitable for Ford, and the division was closed down. The Model 212 could carry out a floating-point multiplication in 22 microseconds. Each word contained two 24-bit instructions with 16 bits of address information and eight bits for the opcode. There were 225 different valid opcodes in the Model 212; invalid opcodes were detected and halted the machine. The CPU had an accumulator register of 48 bits, three general-purpose registers of 24 bits, and 32 index registers of 15 bits. Main memory size ranged from 4K words to 64K words. Only the first model had a magnetic drum memory; later editions used tape drives. The Model 212 weighed about 6,500 pounds (3.3 short tons; 2.9 t). Software for the S-2000 initially consisted of TAC (Translator-Assembler-Compiler), and ALTAC, a FORTRAN II-like language with some differences from the IBM 704 FORTRAN implementation. A COBOL compiler was also available, targeted at business applications. The Philco 2400 was the input/output system for the S-2000. Operations such as reading cards or printing were carried out through magnetic tapes, thereby offloading the S-2000 from relatively slow input/output processing. The 2400 had a 24-bit word length and could be supplied with 4K to 32K characters (1K to 8K words) of core memory, rated at 3-microsecond cycle time. The instruction set was aimed at character I/O use. The idea of base registers, implemented in Philco computers, influenced the design of IBM/360. The last Philco TRANSAC S-2000 Model 212 was taken out of service in December 1981, after 19 years of service at Ford.