Avizo (pronounce: 'a-VEE-zo') is a general-purpose commercial software application for scientific and industrial data visualization and analysis. Avizo is developed by Thermo Fisher Scientific and was originally designed and developed by the Visualization and Data Analysis Group at Zuse Institute Berlin (ZIB) under the name Amira. Avizo was commercially released in November 2007. For the history of its development, see the Wikipedia article about Amira. == Overview == Avizo is a software application which enables users to perform interactive visualization and computation on 3D data sets. The Avizo interface is modelled on the visual programming. Users manipulate data and module components, organized in an interactive graph representation (called Pool), or in a Tree view. Data and modules can be interactively connected together, and controlled with several parameters, creating a visual processing network whose output is displayed in a 3D viewer. With this interface, complex data can be interactively explored and analyzed by applying a controlled sequence of computation and display processes resulting in a meaningful visual representation and associated derived data. == Application areas == Avizo has been designed to support different types of applications and workflows from 2D and 3D image data processing to simulations. It is a versatile and customizable visualization tool used in many fields: Scientific visualization Materials Research Tomography, Microscopy, etc. Nondestructive testing, Industrial Inspection, and Visual Inspection Computer-aided Engineering and simulation data post-processing Porous medium analysis Civil Engineering Seismic Exploration, Reservoir Engineering, Microseismic Monitoring, Borehole Imaging Geology, Digital Rock Physics (DRP), Earth Sciences Archaeology Food technology and agricultural science Physics, Chemistry Climatology, Oceanography, Environmental Studies Astrophysics == Features == Data import: 2D and 3D image stack and volume data: from microscopes (electron, optical), X-ray tomography (CT, micro-/nano-CT, synchrotron), neutron tomography and other acquisition devices (MRI, radiography, GPR) Geometric models (such as point sets, line sets, surfaces, grids) Numerical simulation data (such as Computational fluid dynamics or Finite element analysis data) Molecular data Time series and animations Seismic data Well logs 4D Multivariate Climate Models 2D/3D data visualization: Volume rendering Digital Volume Correlation Visualization of sections, through various slicing and clipping methods Isosurface rendering Polygonal meshes Scalar fields, Vector fields, Tensor representations, Flow visualization (Illuminated Streamlines, Stream Ribbons) Image processing: 2D/3D Alignment of image slices, Image registration Image filtering Mathematical Morphology (erode, dilate, open, close, tophat) Watershed Transform, Distance Transform Image segmentation 3D models reconstruction: Polygonal surface generation from segmented objects Generation of tetrahedral grids Surface reconstruction from point clouds Skeletonization (reconstruction of dendritic, porous or fracture network) Surface model simplification Quantification and analysis: Measurements and statistics Analysis spreadsheet and charting Material properties computation, based on 3D images: Absolute permeability Thermal conductivity Molecular diffusivity Electrical resistivity/formation factor 3D image-based meshing for CFD and FEA: From 3D imaging modalities (CT, micro-CT, MRI, etc.) Surface and volume meshes generation Export to FEA and CFD solvers for simulation Post-processing for simulation analysis Presentation, automation: MovieMaker, Multiscreen, Video wall, collaboration, and VR support TCL Scripting, C++ extension API Avizo is based on Open Inventor 3D graphics toolkits (FEI Visualization Sciences Group).
Artificial reproduction
Artificial reproduction is the re-creation of life brought about by means other than natural ones. It is new life built by human plans and projects. Examples include artificial selection, artificial insemination, in vitro fertilization, artificial womb, artificial cloning, and kinematic replication. Artificial reproduction is one aspect of artificial life. Artificial reproduction can be categorized into one of two classes according to its capacity to be self-sufficient: non-assisted reproductive technology and assisted reproductive technology. Cutting plants' stems and placing them in compost is a form of assisted artificial reproduction, xenobots are an example of a more autonomous type of reproduction, while the artificial womb presented in the movie the Matrix illustrates a non assisted hypothetical technology. The idea of artificial reproduction has led to various technologies. == Theology == Humans have aspired to create life since immemorial times. Most theologies and religions have conceived this possibility as exclusive of deities. Christian religions consider the possibility of artificial reproduction, in most cases, as heretical and sinful. == Philosophy == Although ancient Greek philosophy raised the concept that man could imitate the creative capacity of nature, classic Greeks thought that if possible, human beings would reproduce things as nature does, and vice versa, nature would do the things that man does in the same way. Aristotle, for example, wrote that if nature made tables, it would make them just as men do. In other words, Aristotle said that if nature were to create a table, such table will look like a human-made table. Correspondingly, Descartes envisioned the human body, and nature, as a machine. Cartesian philosophy does not stop seeing a perfect mirror between nature and the artificial. However, Kant revolutionized this old idea by criticizing such naturalism. Kant pedagogically wrote: "Reason, in order to be taught by nature, must approach nature with its principles in one hand, according to which the agreement among appearances can count as laws, and, in the other hand, the experiment thought out in accord with these principles—in order to be instructed by nature not like a pupil, who has recited to him whatever the teacher wants to say, but like an appointed judge who compels witnesses to answer the questions he puts to them.". Humans are not instructed by nature but rather use nature as raw material to invent. Humans find alternatives to the natural restrictions imposed by natural laws thus, nature is not necessarily mirrored. In accordance with Kant (and contrary to what Aristotle thought) Karl Marx, Alfred Whitehead, Jaques Derrida and Juan David García Bacca noticed that nature is incapable of reproducing tables; or airplanes, or submarines, or computers. If nature tried to create airplanes, it would produce birds. If nature tried to create submarines, it would get fishes. If nature tried to create computers, brains would grow. And if nature tried to create man, modern man, monkeys will be evolved. According to Whitehead, if we look for something natural in artificial life, in the most elaborate cases, if anything, only atoms remain natural. Juan David Garcia Bacca summarized, “It will not come out from wood, it will not be born, a galley; from clay, a vessel; from linen, a dress; from iron, a lever,...From natural, artificial. In the artificial, the natural is reduced to a simple raw material, even though it is perfectly specified with natural specification. The artificial is the real, positive, and original negation of the natural: of species, of genus and of essence. Thus, its ontology is superior to natural ontology. And for this very reason Marx did not attach any importance to Darwin, whose evolutionism is confined to the natural order: to changes, at most, from variety to variety, from species to species... natural. For the same reason, nature has no dialectics, even though continuous evolution and selection can occur. The dialectic cannot emerge from the natural, for deeper reasons than, using today's terms, from a bird, an airplane cannot emerge; from fish, a submarine; from ears, a telephone; from eyes, a television; from a brain, a digital computer; from feet, a car; from hands, an engine; from Euclid, Descartes; from Aristotle, Newton; from Plato, Marx.” According to García Bacca, the major difference between natural causes and artificial causes is that nature does not have plans and projects, while humans design things following plans and projects. In contrast, other influential authors such as Michael Behe have depicted the concept and promoted the idea of intelligent design, a notion that has aroused several doubts and heated controversies, as it reframe natural causes in accordance with a natural plan. Previous ideas that have also provided a positive 'sense' to natural reproduction, are orthogenesis, syntropy, orgone and morphic resonance, among others. Although, these ideas have been historically marginalized and often called pseudoscience, recently Bio-semioticians are reconsidering some of them under symbolic approaches. Current metaphysics of science actually recognizes that the artificial ways of reproduction are diverse from nature, i.e., unnatural, anti-natural or supernatural. Because Biosemiotics does not focus on the function of life but on its meaning, it has a better understanding of the artificial than classic biology. == Science == Biology, being the study of cellular life, addresses reproduction in terms of growth and cellular division (i.e., binary fission, mitosis and meiosis); however, the science of artificial reproduction is not restricted by the mirroring of these natural processes.The science of artificial reproduction is actually transcending the natural forms, and natural rules, of reproduction. For example, xenobots have redefined the classical conception of reproduction. Although xenobots are made of eukariotic cells they do not reproduce by mitosis, but rather by kinematic replication. Such constructive replication does not involve growing but rather building. == Assisted reproductive technologies == Assisted reproductive technology (ART)'s purpose is to assist the development of a human embryo, commonly because of medical concerns due to fertility limitations. == Non-assisted reproductive technologies == Non-assisted reproductive technologies (NART) could have medical motivations but are mostly driven by a wider heterotopic ambition. Although, NARTs are initially designed by humans, they are programed to become independent of humans to a relative or absolute extent. James Lovelock proposed that such novelties could overcome humans. === Artificial cloning === Cloning is the cellular reproductive processes where two or more genetically identical organisms are created, either by natural or artificial means. Artificial cloning normally involves editing the genetic code, somatic cell nuclear transfer and 3D bioprinting. === Non-assisted artificial womb === A non-assisted artificial womb or artificial uterus is a device that allow for ectogenesis or extracorporeal pregnancy by growing an embryonic form outside the body of an organism (that would normally carry the embryo to term) without any human assistance. The aspect of non-assistance is the key distinction between the current artificial womb technology (AWT) in modern medical research, which still relies on human assistance. With this non-assisted hypothetical technology, a zygote or stem cells are used to create an embryo that is then incubated and monitored by artificial intelligence (AI) within a chamber composed of biocompatible material. The AI maintains the necessary conditions for the embryo to develop and thrive, proceeding to mimic organic labor and childbirth in order to best help the embryo adjust to the outside world. Ectogenesis—gestation, depicted in the science fiction movie The Matrix, is a fast approaching reality. This type of innovation presupposes that vertebrate wombs are not the only way for bearing humans or other similar forms of life. === Kinematic replication === Self-replication without binary fission, meiosis, mitosis (or any other form of cellular reproduction that involves division and growing) can be achieved. Xenobots are an example of kinematic replication. They are biobots, named after the African clawed frog (Xenopus laevis). Xenobots are cellular life forms designed by using artificial intelligence to build more of themselves by combining frog cells in a liquid medium. The term kinematic replication is usually reserved for biomolecules (e.g. DNA, RNA, prions, etc.) and artificially designed cellular forms (e.g. xenobots). === Machine constructive replication === Machine constructive replication mimics human traditional manufacturing but is entirely self-automated. Such constructive replication is a more general form of kinematic replication, which does not necessarily
Cloud-based quantum computing
Cloud-based quantum computing refers to the remote access of quantum computing resources—such as quantum emulators, simulators, or processors—via the internet. Cloud access enables users to develop, test, and execute quantum algorithms without the need for direct interaction with specialized hardware, facilitating broader participation in quantum software development and experimentation. In 2016, IBM launched the IBM Quantum Experience, one of the first publicly accessible quantum processors connected to the cloud. In early 2017, researchers at Rigetti Computing demonstrated programmable quantum cloud access through their software platform Forest, which included the pyQuil Python library. Since the early-2020s, cloud-based quantum computing has grown significantly, with multiple providers offering access to a variety of quantum hardware modalities, including superconducting qubits, trapped ions, neutral atoms, and photonic systems. Major platforms such as Amazon Braket, Azure Quantum, and qBraid aggregate quantum devices from hardware developers like IonQ, Rigetti Computing, QuEra, Pasqal, Oxford Quantum Circuits, and IBM Quantum. These platforms provide unified interfaces for users to write and execute quantum algorithms across diverse backends, often supporting open-source SDKs such as Qiskit, Cirq, and PennyLane. The proliferation of cloud-based access has played a key role in accelerating quantum education, algorithm research, and early-stage application development by lowering the barrier to experimentation with real quantum hardware. Cloud-based quantum computing has expanded access to quantum hardware and tools beyond traditional research laboratories. These platforms support educational initiatives, algorithm development, and early-stage commercial applications. == Applications == Cloud-based quantum computing is used across education, research, and software development, offering remote access to quantum systems without the need for on-site infrastructure. === Education === Quantum cloud platforms have become valuable tools in education, allowing students and instructors to engage with real quantum processors through user-friendly interfaces. Educators use these platforms to teach foundational concepts in quantum mechanics and quantum computing, as well as to demonstrate and implement quantum algorithms in a classroom or laboratory setting. === Scientific Research === Cloud-based access to quantum hardware has enabled researchers to conduct experiments in quantum information, test quantum algorithms, and compare quantum hardware platforms. Experiments such as testing Bell's theorem or evaluating quantum teleportation protocols have been performed on publicly available quantum processors. === Software Development and Prototyping === Developers use cloud-based platforms to prototype quantum software applications across fields such as optimization, machine learning, and chemistry. These platforms offer SDKs and APIs that integrate classical and quantum workflows, enabling experimentation with quantum algorithms in real-world or simulated environments. === Public Engagement and Games === Quantum cloud tools have also been used to create educational games and interactive applications aimed at increasing public understanding of quantum concepts. These efforts help bridge the gap between theoretical content and intuitive learning. == Existing platforms == qBraid Lab by qBraid is a cloud-based platform for quantum computing. It provides software tools for researchers and developers in quantum, as well as access to quantum hardware. qBraid provides cloud based access to Microsoft Azure Quantum and Amazon Braket devices including IQM, QuEra, Pasqal, Rigetti, IonQ, QIR simulators, Amazon Braket simulators, and the NEC Vector Annealer, as of August 2025. qBraid's base version is free, where unlimited hardware and simulator access is available with the purchase of credits. Quandela Cloud by Quandela is the platform to access first cloud-accessible European photonic quantum computer. The computer is interfaced using the Perceval scripting language, with tutorials and documentation available online for free. Xanadu Quantum Cloud by Xanadu is a platform with cloud-based access to three fully programmable photonic quantum computers. Forest by Rigetti Computing is a tool suite for cloud-based quantum computing. It includes a programming language, development tools and example algorithms. LIQUi> by Microsoft is a software architecture and tool suite for quantum computing. It includes a programming language, example optimization and scheduling algorithms, and quantum simulators. Q#, a quantum programming language by Microsoft on the .NET Framework seen as a successor to LIQUi|>. IBM Quantum Platform by IBM, providing access to quantum hardware as well as HPC simulators. These can be accessed programmatically using the Python-based Qiskit framework, or via graphical interface with the IBM Q Experience GUI. Both are based on the OpenQASM standard for representing quantum operations. There is also a tutorial and online community. Quantum in the Cloud by The University of Bristol, which consists of a quantum simulator and a four qubit optical quantum system. Quantum Playground by Google is an educational resource which features a simulator with a simple interface, and a scripting language and 3D quantum state visualization. Quantum in the Cloud is an experimental quantum cloud platform for access to a four-qubit nuclear magnetic resonance-NMRCloudQ computer, managed by Tsinghua University. Quantum Inspire by Qutech is the first platform in Europe providing cloud-based quantum computing to two hardware chips. Next to a 5-qubit transmon processor, Quantum Inspire is the first platform in the world to provide online access to a fully programmable 2-qubit electron spin quantum processor. Amazon Braket is a cloud-based quantum computing platform hosted by AWS which, as of June 2025, provides access to quantum computers built by IonQ, Rigetti, IQM, and QuEra. Braket also provides a quantum algorithm development environment and simulator. Forge by QC Ware is a cloud-based quantum computing platform that provides access to D-Wave hardware, as well as Google and IBM simulators. The platform offers a 30-day free trial, including one minute of quantum computing time. Quantum-as-a-Service by Scaleway is a cloud-based platform created in 2022 to access to real quantum hardware from IQM Quantum Computers, Alpine Quantum Technologies, Quandela and Pasqal. It also include access to GPU-powered emulators such as Aer, Qsim and Quandela proprietary emulation.
Color science
Color science is the scientific study of color including lighting and optics; measurement of light and color; the physiology, psychophysics, and modeling of color vision; and color reproduction. It is the modern extension of traditional color theory. == Organizations == International Commission on Illumination (CIE) Illuminating Engineering Society (IES) Inter-Society Color Council (ISCC) Society for Imaging Science and Technology (IS&T) International Colour Association (AIC) Optica, formerly the Optical Society of America (OSA) The Colour Group Society of Dyers and Colourists (SDC) American Association of Textile Chemists and Colorists (AATCC) Association for Research in Vision and Ophthalmology (ARVO) ACM SIGGRAPH Vision Sciences Society (VSS) Council for Optical Radiation Measurements (CORM) == Journals == The preeminent scholarly journal publishing research papers in color science is Color Research and Application, started in 1975 by founding editor-in-chief Fred Billmeyer, along with Gunter Wyszecki, Michael Pointer and Rolf Kuehni, as a successor to the Journal of Colour (1964–1974). Previously most color science work had been split between journals with broader or partially overlapping focus such as the Journal of the Optical Society of America (JOSA), Photographic Science and Engineering (1957–1984), and the Journal of the Society of Dyers and Colourists (renamed Coloration Technology in 2001). Other journals where color science papers are published include the Journal of Imaging Science & Technology, the Journal of Perceptual Imaging, the Journal of the International Colour Association (JAIC), the Journal of the Color Science Association of Japan, Applied Optics, and the Journal of Vision. == Conferences == Congress of the International Color Association IS&T Color and Imaging Conference (CIC) SIGGRAPH International Symposium for Color Science and Art == Selected books == Berns, Roy S. (2019). Billmeyer and Saltzman's Principles of Color Technology (4th ed.). Wiley. doi:10.1002/9781119367314. 3rd ed. (2000). Daw, Nigel (2012). How Vision Works: The Physiological Mechanisms Behind What We See. Oxford. doi:10.1093/acprof:oso/9780199751617.001.0001. Elliot, Andrew J.; Fairchild, Mark D.; Franklin, Anna, eds. (2015). Handbook of Color Psychology. Cambridge. doi:10.1017/CBO9781107337930. Fairchild, Mark D. (2013). Color Appearance Models (3rd ed.). Wiley. doi:10.1002/9781118653128. Author's website. 2nd ed. (2005). Hunt, Robert W. G. (2004). The Reproduction of Colour (6th ed.). Wiley. doi:10.1002/0470024275. Kuehni, Rolf G. (2012). Color: An Introduction to Practice and Principles (3rd ed.). Wiley. doi:10.1002/9781118533567. 1st ed. (1997). Luo, Ming R., ed. (2016). Encyclopedia of Color Science and Technology. Springer. doi:10.1007/978-1-4419-8071-7. MacAdam, David L., ed. (1970). Sources of Color Science. MIT Press. Reinhard, Erik; Khan, Erum Arif; Akyuz, Ahmet Oguz; Johnson, Garrett (2008). Color Imaging: Fundamentals and Applications. CRC Press. doi:10.1201/b10637. Schanda, János, ed. (2007). Colorimetry: Understanding the CIE System. Wiley. doi:10.1002/9780470175637. Shamey, Renzo; Kuehni, Rolf G. (2020). Pioneers of Color Science. Springer. doi:10.1007/978-3-319-30811-1. Wyszecki, Günter; Stiles, Walter S. (1982). Color Science: Concepts and Methods, Quantitative Data and Formulae (2nd ed.). Wiley.
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
XLNet
The XLNet was an autoregressive Transformer designed as an improvement over BERT, with 340M parameters and trained on 33 billion words. It was released on 19 June 2019, under the Apache 2.0 license. It achieved state-of-the-art results on a variety of natural language processing tasks, including language modeling, question answering, and natural language inference. == Architecture == The main idea of XLNet is to model language autoregressively like the GPT models, but allow for all possible permutations of a sentence. Concretely, consider the following sentence:My dog is cute.In standard autoregressive language modeling, the model would be tasked with predicting the probability of each word, conditioned on the previous words as its context: We factorize the joint probability of a sequence of words x 1 , … , x T {\displaystyle x_{1},\ldots ,x_{T}} using the chain rule: Pr ( x 1 , … , x T ) = Pr ( x 1 ) Pr ( x 2 | x 1 ) Pr ( x 3 | x 1 , x 2 ) … Pr ( x T | x 1 , … , x T − 1 ) . {\displaystyle \Pr(x_{1},\ldots ,x_{T})=\Pr(x_{1})\Pr(x_{2}|x_{1})\Pr(x_{3}|x_{1},x_{2})\ldots \Pr(x_{T}|x_{1},\ldots ,x_{T-1}).} For example, the sentence "My dog is cute" is factorized as: Pr ( My , dog , is , cute ) = Pr ( My ) Pr ( dog | My ) Pr ( is | My , dog ) Pr ( cute | My , dog , is ) . {\displaystyle \Pr({\text{My}},{\text{dog}},{\text{is}},{\text{cute}})=\Pr({\text{My}})\Pr({\text{dog}}|{\text{My}})\Pr({\text{is}}|{\text{My}},{\text{dog}})\Pr({\text{cute}}|{\text{My}},{\text{dog}},{\text{is}}).} Schematically, we can write it as
Tertiary review
In software engineering, a tertiary review is a systematic review of systematic reviews. It is also referred to as a tertiary study in the software engineering literature. However, Umbrella review is the term more commonly used in medicine. Kitchenham et al. suggest that methodologically there is no difference between a systematic review and a tertiary review. However, as the software engineering community has started performing tertiary reviews new concerns unique to tertiary reviews have surfaced. These include the challenge of quality assessment of systematic reviews, search validation and the additional risk of double counting. == Examples of Tertiary reviews in software engineering literature == Test quality Machine Learning Test-driven development