GLIMMER

In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long protein coding genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Computational Biology at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. == Versions == === GLIMMER 1.0 === First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper Microbial gene identification using interpolated Markov model. Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the local composition sequence dependencies which makes GLIMMER more flexible and more powerful when compared to fixed-order Markov model. There was a comparison made between interpolated Markov model used by GLIMMER and fifth order Markov model in the paper Microbial gene identification using interpolated Markov models. "GLIMMER algorithm found 1680 genes out of 1717 annotated genes in Haemophilus influenzae where fifth order Markov model found 1574 genes. GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order Markov model found 104 genes."' === GLIMMER 2.0 === Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper Improved microbial identification with GLIMMER. This paper provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER. Interpolated context models are used instead of interpolated Markov model which gives the flexibility to select any base. In interpolated Markov model probability distribution of a base is determined from the immediate preceding bases. If the immediate preceding base is irrelevant amino acid translation, interpolated Markov model still considers the preceding base to determine the probability of given base where as interpolated context model which was used in GLIMMER 2.0 can ignore irrelevant bases. False positive predictions were increased in GLIMMER 2.0 to reduce the number of false negative predictions. Overlapped genes are also resolved in GLIMMER 2.0. Various comparisons between GLIMMER 1.0 and GLIMMER 2.0 were made in the paper Improved microbial identification with GLIMMER which shows improvement in the later version. "Sensitivity of GLIMMER 1.0 ranges from 98.4 to 99.7% with an average of 99.1% where as GLIMMER 2.0 has a sensitivity range from 98.6 to 99.8% with an average of 99.3%. GLIMMER 2.0 is very effective in finding genes of high density. The parasite Trypanosoma brucei, responsible for causing African sleeping sickness is being identified by GLIMMER 2.0" === GLIMMER 3.0 === Third version of GLIMMER, "GLIMMER 3.0" was released in 2007 and it was published in the paper Identifying bacterial genes and endosymbiont DNA with Glimmer. This paper describes several major changes made to the GLIMMER system including improved methods to identify coding regions and start codon. Scoring of ORF in GLIMMER 3.0 is done in reverse order i.e., starting from stop codon and moves back towards the start codon. Reverse scanning helps in identifying the coding portion of the gene more accurately which is contained in the context window of IMM. GLIMMER 3.0 also improves the generated training set data by comparing the long-ORF with universal amino acid distribution of widely disparate bacterial genomes."GLIMMER 3.0 has an average long-ORF output of 57% for various organisms where as GLIMMER 2.0 has an average long-ORF output of 39%." GLIMMER 3.0 reduces the rate of false positive predictions which were increased in GLIMMER 2.0 to reduce the number of false negative predictions. "GLIMMER 3.0 has a start-site prediction accuracy of 99.5% for 3'5' matches where as GLIMMER 2.0 has 99.1% for 3'5' matches. GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome." Minimum description length === Theoretical and Biological Foundation === The GLIMMER project helped introduce and popularize the use of variable length models in Computational Biology and Bioinformatics that subsequently have been applied to numerous problems such as protein classification and others. Variable length modeling was originally pioneered by information theorists and subsequently ingeniously applied and popularized in data compression (e.g. Ziv-Lempel compression). Prediction and compression are intimately linked using Minimum Description Length Principles. The basic idea is to create a dictionary of frequent words (motifs in biological sequences). The intuition is that the frequently occurring motifs are likely to be most predictive and informative. In GLIMMER the interpolated model is a mixture model of the probabilities of these relatively common motifs. Similarly to the development of HMMs in Computational Biology, the authors of GLIMMER were conceptually influenced by the previous application of another variant of interpolated Markov models to speech recognition by researchers such as Fred Jelinek (IBM) and Eric Ristad (Princeton). The learning algorithm in GLIMMER is different from these earlier approaches. == Access == GLIMMER can be downloaded from The Glimmer home page (requires a C++ compiler). Alternatively, an online version is hosted by NCBI [1]. == How it works == GLIMMER primarily searches for long-ORFS. An open reading frame might overlap with any other open reading frame which will be resolved using the technique described in the sub section. Using these long-ORFS and following certain amino acid distribution GLIMMER generates training set data. Using these training data, GLIMMER trains all the six Markov models of coding DNA from zero to eight order and also train the model for noncoding DNA GLIMMER tries to calculate the probabilities from the data. Based on the number of observations, GLIMMER determines whether to use fixed order Markov model or interpolated Markov model. If the number of observations are greater than 400, GLIMMER uses fixed order Markov model to obtain there probabilities. If the number of observations are less than 400, GLIMMER uses interpolated Markov model which is briefly explained in the next sub section. GLIMMER obtains score for every long-ORF generated using all the six coding DNA models and also using non-coding DNA model. If the score obtained in the previous step is greater than a certain threshold then GLIMMER predicts it to be a gene. The steps explained above describes the basic functionality of GLIMMER. There are various improvements made to GLIMMER and some of them are described in the following sub-sections. === The GLIMMER system === GLIMMER system consists of two programs. First program called build-imm, which takes an input set of sequences and outputs the interpolated Markov model as follows. The probability for each base i.e., A,C,G,T for all k-mers for 0 ≤ k ≤ 8 is computed. Then, for each k-mer, GLIMMER computes weight. New sequence probability is computed as follows. where n is the length of the sequence S x {\displaystyle S_{x}} is the oligomer at position x. I M M 8 ( S x ) {\displaystyle IMM_{8}(S_{x})} , the 8 t h {\displaystyle 8^{th}} -order interpolated Markov model score is computed as "where Y k ( S x − 1 ) {\displaystyle Y_{k}(S_{x-1})} is the weight of the k-mer at position x-1 in the sequence S and P k ( S x ) {\displaystyle P_{k}(S_{x})} is the estimate obtained from the training data of the probability of the base located at position x in the k t h {\displaystyle k^{th}} -order model." The probability of base S x {\displaystyle S_{x}} given the i previous bases is computed as follows. "The value of Y i ( S x ) {\displaystyle Y_{i}(S_{x})} associated with P i ( S x ) {\displaystyle P_{i}(S_{x})} can be regarded as a measure of confidence in the accuracy of this value as an estimate of the true probability. GLIMMER uses two criteria to determine Y i ( S x ) {\displaystyle Y_{i}(S_{x})} . The first of these is simple frequency occurrence in which the number of occurrences of context string S x , i {\displaystyle S_{x,i}} in the training data exceeds a specific threshold value, then Y i ( S x ) {\displaystyle Y_{i}(S_{x})} is set to 1.0. The current default value for threshold is 400, which gives 95% confidence. When there are insufficient sample occurrences of a context string, build-imm employ additional criteria to determine Y {\displaystyle Y} value. For a

Workplace impact of artificial intelligence

The impact of artificial intelligence on workers includes both applications to improve worker safety and health, and potential hazards that must be controlled. One potential application is using AI to eliminate hazards by removing humans from hazardous situations that involve risk of stress, overwork, or musculoskeletal injuries. Predictive analytics may also be used to identify conditions that may lead to hazards such as fatigue, repetitive strain injuries, or toxic substance exposure, leading to earlier interventions. Another is to streamline workplace safety and health workflows through automating repetitive tasks, enhancing safety training programs through virtual reality, or detecting and reporting near misses. When used in the workplace, AI also presents the possibility of new hazards. These may arise from machine learning techniques leading to unpredictable behavior and inscrutability in their decision-making, or from cybersecurity and information privacy issues. Many hazards of AI are psychosocial due to its potential to cause changes in work organization. These include increased monitoring leading to micromanagement, algorithms unintentionally or intentionally mimicking undesirable human biases, and assigning blame for machine errors to the human operator instead. AI may also lead to physical hazards in the form of human–robot collisions, and ergonomic risks of control interfaces and human–machine interactions. Hazard controls include cybersecurity and information privacy measures, communication and transparency with workers about data usage, and limitations on collaborative robots. From a workplace safety and health perspective, only "weak" or "narrow" AI that is tailored to a specific task is relevant, as there are many examples that are currently in use or expected to come into use in the near future. Certain digital technologies are predicted to result in job losses. Starting in the 2020s, the adoption of modern robotics has led to net employment growth. However, many businesses anticipate that automation, or employing robots would result in job losses in the future. This is especially true for companies in Central and Eastern Europe. Other digital technologies, such as platforms or big data, are projected to have a more neutral impact on employment. A large number of tech workers have been laid off starting in 2023; many such job cuts have been attributed to artificial intelligence. == Health and safety applications == In order for any potential AI health and safety application to be adopted, it requires acceptance by both managers and workers. For example, worker acceptance may be diminished by concerns about information privacy, or from a lack of trust and acceptance of the new technology, which may arise from inadequate transparency or training. Alternatively, managers may emphasize increases in economic productivity rather than gains in worker safety and health when implementing AI-based systems. === Eliminating hazardous tasks === AI may increase the scope of work tasks where a worker can be removed from a situation that carries risk. In a sense, while traditional automation can replace the functions of a worker's body with a robot, AI effectively replaces the functions of their brain with a computer. Hazards that can be avoided include stress, overwork, musculoskeletal injuries, and boredom. This can expand the range of affected job sectors into white-collar and service sector jobs such as in medicine, finance, and information technology. === Analytics to reduce risk === Machine learning is used for people analytics to make predictions about worker behavior to assist management decision-making, such as hiring and performance assessment. These could also be used to improve worker health. The analytics may be based on inputs such as online activities, monitoring of communications, location tracking, and voice analysis and body language analysis of filmed interviews. For example, sentiment analysis may be used to spot fatigue to prevent overwork. Decision support systems have a similar ability to be used to, for example, prevent industrial disasters or make disaster response more efficient. For manual material handling workers, predictive analytics and artificial intelligence may be used to reduce musculoskeletal injury. Traditional guidelines are based on statistical averages and are geared towards anthropometrically typical humans. The analysis of large amounts of data from wearable sensors may allow real-time, personalized calculation of ergonomic risk and fatigue management, as well as better analysis of the risk associated with specific job roles. Wearable sensors may also enable earlier intervention against exposure to toxic substances than is possible with area or breathing zone testing on a periodic basis. Furthermore, the large data sets generated could improve workplace health surveillance, risk assessment, and research. === Streamlining safety and health workflows === AI has also been used to attempt to make the workplace safety and health workflow more efficient. One example is coding of workers' compensation claims, which are submitted in a prose narrative form and must manually be assigned standardized codes. AI is being investigated to perform this task faster, more cheaply, and with fewer errors. == Hazards == There are several broad aspects of AI that may give rise to specific hazards. The risks depend on implementation rather than the mere presence of AI. Systems using sub-symbolic AI such as machine learning may behave unpredictably and are more prone to inscrutability in their decision-making. This is especially true if a situation is encountered that was not part of the AI's training dataset, and is exacerbated in environments that are less structured. Undesired behavior may also arise from flaws in the system's perception (arising either from within the software or from sensor degradation), knowledge representation and reasoning, or from software bugs. They may arise from improper training, such as a user applying the same algorithm to two problems that do not have the same requirements. Machine learning applied during the design phase may have different implications than that applied at runtime. Systems using symbolic AI are less prone to unpredictable behavior. The use of AI also increases cybersecurity risks relative to platforms that do not use AI, and information privacy concerns about collected data may pose a hazard to workers. === Psychosocial === Psychosocial hazards are those that arise from the way work is designed, organized, and managed, or its economic and social contexts, rather than arising from a physical substance or object. They cause not only psychiatric and psychological outcomes such as occupational burnout, anxiety disorders, and depression, but they can also cause physical injury or illness such as cardiovascular disease or musculoskeletal injury. Many hazards of AI are psychosocial in nature due to its potential to cause changes in work organization, in terms of increasing complexity and interaction between different organizational factors. However, psychosocial risks are often overlooked by designers of advanced manufacturing systems. Einola and Khoreva explore how different organizational groups perceive and interact with AI technologies. Their research shows that successful AI integration depends on human ownership and contextual understanding. They caution against blind technological optimism and stress the importance of tailoring AI use to specific workplace ecosystems. This perspective reinforces the need for inclusive design and transparent implementation strategies. ==== Changes in work practices ==== Over-reliance on AI tools may lead to deskilling of some professions. When AI becomes a substitute for traditional peer collaboration and mentorship, there is a risk of diminishing opportunities for interpersonal skill development and team-based learning. Increased monitoring may lead to micromanagement and thus to stress and anxiety. A perception of surveillance may also lead to stress. Controls for these include consultation with worker groups, extensive testing, and attention to introduced bias. Wearable sensors, activity trackers, and augmented reality may also lead to stress from micromanagement, both for assembly line workers and gig workers. Gig workers also lack the legal protections and rights of formal workers. Newell & Marabelli argue that AI alters power dynamics and employee autonomy, requiring a more nuanced understanding of its social and organizational implications. There is also the risk of people being forced to work at a robot's pace, or to monitor robot performance at nonstandard hours. A 2025 preprint paper based on users' interactions with the AI chatbot Microsoft Copilot identified forty jobs that the author's claimed had high overlaps with the capabilities of AI. Some media outlets used this paper to report on jobs becoming obsolete. Cri

Autocommit

In the context of data management, autocommit is a mode of operation of a database connection. Each individual database interaction (i.e., each SQL statement) submitted through the database connection in autocommit mode will be executed in its own transaction that is implicitly committed. A SQL statement executed in autocommit mode cannot be rolled back. Autocommit mode incurs per-statement transaction overhead and can often lead to undesirable performance or resource utilization impact on the database. Nonetheless, in systems such as Microsoft SQL Server, as well as connection technologies such as ODBC and Microsoft OLE DB, autocommit mode is the default for all statements that change data, in order to ensure that individual statements will conform to the ACID (atomicity-consistency-isolation-durability) properties of transactions. The alternative to autocommit mode (non-autocommit) means that the SQL client application itself is responsible for ending transactions explicitly via the commit or rollback SQL commands. Non-autocommit mode enables grouping of multiple data manipulation SQL commands into a single atomic transaction. Some DBMS (e.g. MariaDB) force autocommit for every DDL statement, even in non-autocommit mode. In this case, before each DDL statement, previous DML statements in transaction are autocommitted. Each DDL statement is executed in its own new autocommit transaction.

Imieliński–Lipski algebra

In database theory, Imieliński–Lipski algebra is an extension of relational algebra onto tables with different types of null values. It is used to operate on relations with incomplete information. Imieliński–Lipski algebras are defined to satisfy precise conditions for semantically meaningful extension of the usual relational operators, such as projection, selection, union, and join, from operators on relations to operators on relations with various kinds of "null values". These conditions require that the system be safe in the sense that no incorrect conclusion is derivable by using a specified subset F of the relational operators; and that it be complete in the sense that all valid conclusions expressible by relational expressions using operators in F are in fact derivable in this system. For example, it is well known that the three-valued logic approach to deal with null values, supported treatment of nulls values by SQL is not complete, see Ullman book. To show this, let T be: Take SQL query Q SQL query Q will return empty set (no results) under 3-valued semantics currently adopted by all variants of SQL. This is the case because in SQL, NULL is never equal to any constant – in this case, neither to “Spring” nor “Fall” nor “Winter” (if there is Winter semester in this school). NULL='Spring' will evaluate to MAYBE and so will NULL='Fall'. The disjunction MAYBE OR MAYBE evaluates to MAYBE (not TRUE). Thus Igor will not be part of the answer (and of course neither will Rohit). But Igor should be returned as the answer. Indeed, regardless what semester Igor took the Networks class (no matter what was the unknown value of NULL), the selection condition will be true. This “Igor” will be missed by SQL and the SQL answer would be incomplete according to completeness requirements specified in Tomasz Imieliński, Witold Lipski, 'Incomplete Information in Relational Databases'. It is also argued there that 3-valued logic (TRUE, FALSE, MAYBE) can never provide guarantee of complete answer for tables with incomplete information. Three algebras which satisfy conditions of safety and completeness are defined as Imielinski–Lipski algebras: the Codd-Tables algebra, the V-tables algebra and the Conditional tables (C-tables) algebra. == Codd-tables algebra == Codd-tables algebra is based on the usual Codd's single NULL values. The table T above is an example of Codd-table. Codd-table algebra supports projection and positive selections only. It is also demonstrated in [IL84 that it is not possible to correctly extend more relational operators over Codd-Tables. For example, such basic operation as join is not extendable over Codd-tables. It is not possible to define selections with Boolean conditions involving negation and preserve completeness. For example, queries like the above query Q cannot be supported. In order to be able to extend more relational operators, more expressive form of null value representation is needed in tables which are called V-table. == V-tables algebra == V-tables algebra is based on many different ("marked") null values or variables allowed to appear in a table. V-tables allow to show that a value may be unknown but the same for different tuples. For example, in the table below Gaurav and Igor order the same (but unknown) beer in two unknown bars (which may, or may not be different – but remain unknown). Gaurav and Jane frequent the same unknown bar (Y1). Thus, instead one NULL value, we use indexed variables, or Skolem constants . V-tables algebra is shown to correctly support projection, positive selection (with no negation occurring in the selection condition), union, and renaming of attributes, which allows for processing arbitrary conjunctive queries. A very desirable property enjoyed by the V-table algebra is that all relational operators on tables are performed in exactly the same way as in the case of the usual relations. === Conditional tables (c-tables) algebra === Example of conditional table (c-table) is shown below. It has additional column “con” which is a Boolean condition involving variables, null values – same as in V-tables. over the following table c-table Conditional tables algebra, mainly of theoretical interest, supports projection, selection, union, join, and renaming. Under closed-world assumption, it can also handle the operator of difference, thus it can support all relational operators. == History == Imieliński–Lipski algebras were introduced by Tomasz Imieliński and Witold Lipski Jr. in Incomplete Information in Relational Databases.

Supertoroid

In geometry and computer graphics, a supertoroid or supertorus is usually understood to be a family of doughnut-like surfaces (technically, a topological torus) whose shape is defined by mathematical formulas similar to those that define the superellipsoids. The plural of "supertorus" is either supertori or supertoruses. The family was described and named by Alan Barr in 1994. Barr's supertoroids have been fairly popular in computer graphics as a convenient model for many objects, such as smooth frames for rectangular things. One quarter of a supertoroid can provide a smooth and seamless 90-degree joint between two superquadric cylinders. However, they are not algebraic surfaces (except in special cases). == Formulas == Alan Barr's supertoroids are defined by parametric equations similar to the trigonometric equations of the torus, except that the sine and cosine terms are raised to arbitrary powers. Namely, the generic point P(u, v) of the surface is given by P ( u , v ) = ( X ( u , v ) Y ( u , v ) Z ( u , v ) ) = ( ( a + C u s ) C v t ( b + C u s ) S v t S u s ) {\displaystyle P(u,v)=\left({\begin{array}{c}X(u,v)\\Y(u,v)\\Z(u,v)\end{array}}\right)=\left({\begin{array}{c}(a+C_{u}^{s})C_{v}^{t}\\(b+C_{u}^{s})S_{v}^{t}\\S_{u}^{s}\end{array}}\right)} where C θ ε = sgn ⁡ ( cos ⁡ θ ) | cos ⁡ θ | ε , S θ ε = sgn ⁡ ( sin ⁡ θ ) | sin ⁡ θ | ε , {\displaystyle {\begin{aligned}C_{\theta }^{\varepsilon }&=\operatorname {sgn} (\cos \theta )\,\left|\,\cos \theta \,\right|^{\varepsilon },\\S_{\theta }^{\varepsilon }&=\operatorname {sgn} (\sin \theta )\ \left|\,\sin \theta \ \right|^{\varepsilon },\end{aligned}}} sgn is the sign function, and the parameters u, v range from 0 to 360 degrees (0 to 2π radians). In these formulas, the parameter s > 0 controls the "squareness" of the vertical sections, t > 0 controls the squareness of the horizontal sections, and a, b ≥ 1 are the major radii in the x and y directions. With s = t = 1 and a = b = R one obtains the ordinary torus with major radius R and minor radius 1, with the center at the origin and rotational symmetry about the z-axis. In general, the supertorus defined as above spans the intervals: − ( a + 1 ) ≤ x ≤ + ( a + 1 ) − ( b + 1 ) ≤ y ≤ + ( b + 1 ) − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}-(a+1)&\leq &x&\leq &+(a+1)\\[4pt]-(b+1)&\leq &y&\leq &+(b+1)\\[4pt]-1&\leq &z&\leq &+1\end{array}}} The whole shape is symmetric about the planes x = 0, y = 0, and z = 0. The hole runs in the z direction and spans the intervals − ( a − 1 ) ≤ x ≤ + ( a − 1 ) − ( b − 1 ) ≤ y ≤ + ( b − 1 ) − ∞ ≤ z ≤ + ∞ {\displaystyle {\begin{array}{rcccl}-(a-1)&\leq &x&\leq &+(a-1)\\[4pt]-(b-1)&\leq &y&\leq &+(b-1)\\[4pt]-\infty &\leq &z&\leq &+\infty \end{array}}} A curve of constant u on this surface is a horizontal Lamé curve with exponent ⁠ 2 t , {\displaystyle {\tfrac {2}{t}},} ⁠ scaled in x and y and displaced in z. A curve of constant v, projected on the plane x = 0 or y = 0, is a Lamé curve with exponent ⁠ 2 s , {\displaystyle {\tfrac {2}{s}},} ⁠ scaled and horizontally shifted. If v = 0, the curve is planar and spans the intervals: a − 1 ≤ x ≤ a + 1 − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}a-1&\leq &x&\leq &a+1\\[4pt]-1&\leq &z&\leq &+1\end{array}}} and similarly if v = 90°, 180°, 270°. The curve is also planar if a = b. In general, if a ≠ b and v is not a multiple of 90 degrees, the curve of constant v will not be planar; and, conversely, a vertical plane section of the supertorus will not be a Lamé curve. The basic supertoroid shape defined above is often modified by non-uniform scaling to yield supertoroids of specific width, length, and vertical thickness. == Plotting code == The following GNU Octave code generates plots of a supertorus:

Amira (software)

Amira (ah-MEER-ah) is a software platform for visualization, processing, and analysis of 3D and 4D data. It is being actively developed by Thermo Fisher Scientific in collaboration with the Zuse Institute Berlin (ZIB), and commercially distributed by Thermo Fisher Scientific — together with its sister software Avizo. == Overview == Amira is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. It is used by researchers and engineers in academia and industry. It is a tool for processing, analysis and visualization of data from various modalities; e.g. micro-CT, PET, Ultrasound. It is used in many fields, such as microscopy in biology and materials science, molecular biology, quantum physics, astrophysics, computational fluid dynamics (CFD), finite element modeling (FEM), non-destructive testing (NDT), and many more. One of the key features, besides data visualization, is Amira's set of tools for image segmentation and geometry reconstruction. This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis, density analysis, shape analysis, or the generation of 3D computer models for visualization, numerical simulations, or rapid prototyping or 3D printing. Other key Amira features are multi-planar and volume visualization, image registration, filament tracing, cell separation and analysis, tetrahedral mesh generation, fiber-tracking from diffusion tensor imaging (DTI) data, skeletonization, spatial graph analysis, and stereoscopic rendering of 3D data over multiple displays and immersive virtual reality environments, including CAVEs. As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge. == History == === 1993–1998: Research software === Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department's mission is to help solve computationally and scientifically challenging tasks in medicine, biology, engineering and materials science. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE, IRIS Explorer, and Advanced Visualization Studio (AVS), but was not satisfied with these products' interactivity, flexibility, and ease-of-use for non-computer scientists. Therefore, the development of a new software system was started in a research project within a medically oriented, multi-disciplinary collaborative research center. Based on experiences that Tobias Höllerer had gained in late 1993 with the new graphics library IRIS Inventor, it was decided to utilize that library. The development of the medical planning system was performed by Detlev Stalling, who later became the chief software architect of Amira. The new software was called "HyperPlan", highlighting its initial target application – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. The software was based on libraries such as OpenGL (originally IRIS GL), Open Inventor (originally IRIS Inventor), and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit. The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in medical image computing, medical visualization, neurobiology, confocal microscopy, flow visualization, molecular analytics and computational astrophysics. === 1998–today: Commercially supported product === The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB's primary mission was algorithmic research. Therefore, the spin-off company Indeed – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff. In Feb 1998 the HyperPlan software was given the new, application-neutral name "Amira". This name is not an acronym, but was chosen for being pronounceable in different languages and providing a suitable connotation, namely "to look at" or "to wonder at", from the Latin verb "admirare" (to admire), which reflects a basic situation in data visualization. A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths. Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years. In 2003 both Indeed – Visual Concepts GmbH, as well as TGS, Inc. were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury's newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences. In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. This brought the two software sisters Amira and Avizo back into one hand. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. In 2016 FEI has been bought by Thermo Fisher Scientific and became part of its Materials & Structural Analysis division in early 2017. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. In the meantime, the number of scientific articles using the Amira / Avizo software, is in the order of 10 thousands. == Amira options == === Microscopy option === Specific readers for microscopy data Image deconvolution Exploration of 3D imagery obtained from virtually any microscope Extraction and editing of filament networks from microscopy images === DICOM reader === Import of clinical and preclinical data in DICOM format === Mesh option === Generation of 3D finite element (FE) meshes from segmented image data Support for many state-of-the-art FE solver formats High-quality visualization of simulation mesh-based results, using scalar, vector, and tensor field display modules === Skeletonization option === Reconstruction and analysis of neural and vascular networks Visualization of skeletonized networks Length and diameter quantification of network segments Ordering of segments in a tree graph Skeletonization of very large image stacks === Molecular option === Advanced tools for the visualization of molecule models Hardware-accelerated volume rendering Powerful molecule editor Specific tools for complex molecular visualization === Developer option === Creation of new custom components for visualizing or data processing Implementation of new file readers or writers C++ programming language Development wizard for getting started quickly === Neuro option === Medical image analysis for DTI and brain perfusion Fiber tracking supporting several stream-line based algorithms Fiber separation into fiber bundles based on user defined source and destination regions Computation of tensor fields, diffusion weighted maps Eigenvalue decomposition of tensor fields Computation of mean transit time, cerebral blood flow, and cerebral blood volume === VR option === Visualization of data on large tiled displays

Cybernetic Serendipity

Cybernetic Serendipity was an exhibition of cybernetic art curated by Jasia Reichardt, shown at the Institute of Contemporary Arts, London, England, from 2 August to 20 October 1968, and then toured across the United States. Two stops in the United States were the Corcoran Annex (Corcoran Gallery of Art), Washington, D.C., from 16 July to 31 August 1969, and the newly opened Exploratorium in San Francisco, from 1 November to 18 December 1969. == Content == One part of the exhibition was concerned with algorithms and devices for generating music. Some exhibits were pamphlets describing the algorithms, whilst others showed musical notation produced by computers. Devices made musical effects and played tapes of sounds made by computers. Peter Zinovieff lent part of his studio equipment - visitors could sing or whistle a tune into a microphone and his equipment would improvise a piece of music based on the tune. Another part described computer projects such as Gustav Metzger's self-destructive Five Screens With Computer, a design for a new hospital, a computer programmed structure, and dance choreography. The machines and installations were a very noticeable part of the exhibition. Gordon Pask produced a collection of large mobiles (Colloquy of Mobiles (1968)) with interacting parts that let the viewers join in the conversation. Many machines formed kinetic environments or displayed moving images. Bruce Lacey contributed his radio-controlled robots and a light-sensitive owl. Nam June Paik was represented by Robot K-456 and televisions with distorted images. Jean Tinguely provided two of his painting machines. Edward Ihnatowicz's biomorphic hydraulic ear (Sound Activated Mobile (SAM, 1968)) turned toward sounds and John Billingsley's Albert 1967 turned to face light. Wen-Ying Tsai presented his interactive cybernetic sculptures of vibrating stainless-steel rods, stroboscopic light, and audio feedback control. Several artists exhibited machines that drew patterns that the visitor could take away, or involved visitors in games. Cartoonist Rowland Emett designed the mechanical computer Forget-me-not, which was commissioned by Honeywell. Another section explored the computer's ability to produce text - both essays and poetry. Different programs produced Haiku, children's stories, and essays. One of the first computer-generated poems, by Alison Knowles and James Tenney, was included in the exhibition and catalogue. Computer-generated movies were represented by John Whitney's Permutations and a Bell Labs movie on their technology for producing movies. Some samples included images of tesseracts rotating in four dimensions, a satellite orbiting the Earth, and an animated data structure. Computer graphics were also represented, including pictures produced on cathode ray oscilloscopes and digital plotters. There was a variety of posters and graphics demonstrating the power of computers to do complex (and apparently random) calculations. Other graphics showed a simulated Mondrian and the iconic decreasing squares spiral that appeared on the exhibition's poster and book. The Boeing Company exhibited their use of wireframe graphics. The innovative computer-generated sculpture, Quad 1, was displayed at the Cybernetic Serendipity exhibit. Created by the American abstract expressionist sculptor, Robert Mallary, in 1968, Quad 1 is widely believed to be the world's first Computer Aided Design sculpture. Keith Albarn & Partners contributed to the design of the exhibition. Reflecting the prominence of music in the show, a ten-track album Cybernetic Serendipity Music was released by the ICA to accompany the show. Artists featured included Iannis Xenakis, John Cage, and Peter Zinovieff, a detail of whose graphic score for 'Four Sacred April Rounds’ (1968) was used as the cover artwork. == Attendance == Time magazine noted that there had been 40,000 visitors to the London exhibition. Other reports suggested visitor numbers were as high as 44,000 to 60,000. However, the ICA did not accurately count visitors. == After-effects == The exhibition provided the energy for the formation of British Computer Arts Society which continued to explore the interaction between science, technology and art, and put on exhibitions (for example Event One at the Royal College of Art). Several pieces were purchased by the Exploratorium in 1971, some of which are on display to this day. In 2014 the ICA held a retrospective exhibition Cybernetic Serendipity: A Documentation which included documents, installation photographs, press reviews and publications and a series of discussions in one of which Peter Zinovieff took part. To coincide with the exhibition, Cybernetic Serendipity Music was re-released as a limited-edition vinyl LP by The Vinyl Factory. The Victoria and Albert Museum marked the 50th anniversary with an exhibition in 2018 entitled "Chance and Control: Art in the Age of Computers". The V&A exhibition included many works by artists who featured in the original ICA show, plus related ephemera. "Chance and Control" subsequently toured to Chester Visual Arts and Firstsite, Colchester. In 2020, The Centre Pompidou exhibited the replica of Gordon Pask's 1968 Colloquy of Mobiles, reproduced by Paul Pangaro and TJ McLeish in 2018. In 2022 the Australian National University's School of Cybernetics launched the school by presenting an exhibition Australian Cybernetic: a point through time. The exhibition included works from Cybernetic Serendipity (1968), Australia ‘75: Festival of Creative Arts and Science (1975), and contemporary pieces curated by the School of Cybernetics. In describing Reichardt's Cybernetic Serendipity exhibition the school stated that it "represented points of expanding the cybernetic imagination" and was a "ground-breaking" "glimpse of a future in which computers were entangled with people and cultures, and through this she fashioned a blueprint for the future of computing that has since inspired generations".