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  Co-occurrence matrix

  A co-occurrence matrix or co-occurrence distribution (also referred to as : gray-level co-occurrence matrices GLCMs) is a matrix that is defined over an image to be the distribution of co-occurring pixel values (grayscale values, or colors) at a given offset. It is used as an approach to texture analysis with various applications especially in medical image analysis. == Method == Given a grey-level image I {\displaystyle I} , co-occurrence matrix computes how often pairs of pixels with a specific value and offset occur in the image. The offset, ( Δ x , Δ y ) {\displaystyle (\Delta x,\Delta y)} , is a position operator that can be applied to any pixel in the image (ignoring edge effects): for instance, ( 1 , 2 ) {\displaystyle (1,2)} could indicate "one down, two right". An image with p {\displaystyle p} different pixel values will produce a p × p {\displaystyle p\times p} co-occurrence matrix, for the given offset. The ( i , j ) th {\displaystyle (i,j)^{\text{th}}} value of the co-occurrence matrix gives the number of times in the image that the i th {\displaystyle i^{\text{th}}} and j th {\displaystyle j^{\text{th}}} pixel values occur in the relation given by the offset. For an image with p {\displaystyle p} different pixel values, the p × p {\displaystyle p\times p} co-occurrence matrix C is defined over an n × m {\displaystyle n\times m} image I {\displaystyle I} , parameterized by an offset ( Δ x , Δ y ) {\displaystyle (\Delta x,\Delta y)} , as: C Δ x , Δ y ( i , j ) = ∑ x = 1 n ∑ y = 1 m { 1 , if I ( x , y ) = i and I ( x + Δ x , y + Δ y ) = j 0 , otherwise {\displaystyle C_{\Delta x,\Delta y}(i,j)=\sum _{x=1}^{n}\sum _{y=1}^{m}{\begin{cases}1,&{\text{if }}I(x,y)=i{\text{ and }}I(x+\Delta x,y+\Delta y)=j\\0,&{\text{otherwise}}\end{cases}}} where: i {\displaystyle i} and j {\displaystyle j} are the pixel values; x {\displaystyle x} and y {\displaystyle y} are the spatial positions in the image I; the offsets ( Δ x , Δ y ) {\displaystyle (\Delta x,\Delta y)} define the spatial relation for which this matrix is calculated; and I ( x , y ) {\displaystyle I(x,y)} indicates the pixel value at pixel ( x , y ) {\displaystyle (x,y)} . The 'value' of the image originally referred to the grayscale value of the specified pixel, but could be anything, from a binary on/off value to 32-bit color and beyond. (Note that 32-bit color will yield a 232 × 232 co-occurrence matrix!) Co-occurrence matrices can also be parameterized in terms of a distance, d {\displaystyle d} , and an angle, θ {\displaystyle \theta } , instead of an offset ( Δ x , Δ y ) {\displaystyle (\Delta x,\Delta y)} . Any matrix or pair of matrices can be used to generate a co-occurrence matrix, though their most common application has been in measuring texture in images, so the typical definition, as above, assumes that the matrix is an image. It is also possible to define the matrix across two different images. Such a matrix can then be used for color mapping. == Aliases == Co-occurrence matrices are also referred to as: GLCMs (gray-level co-occurrence matrices) GLCHs (gray-level co-occurrence histograms) spatial dependence matrices == Application to image analysis == Whether considering the intensity or grayscale values of the image or various dimensions of color, the co-occurrence matrix can measure the texture of the image. Because co-occurrence matrices are typically large and sparse, various metrics of the matrix are often taken to get a more useful set of features. Features generated using this technique are usually called Haralick features, after Robert Haralick. Texture analysis is often concerned with detecting aspects of an image that are rotationally invariant. To approximate this, the co-occurrence matrices corresponding to the same relation, but rotated at various regular angles (e.g. 0, 45, 90, and 135 degrees), are often calculated and summed. Texture measures like the co-occurrence matrix, wavelet transforms, and model fitting have found application in medical image analysis in particular. == Other applications == Co-occurrence matrices are also used for words processing in natural language processing (NLP).

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  Native cloud application

  A native cloud application (NCA) is a type of computer software that natively utilizes services and infrastructure from cloud computing providers such as Amazon EC2, Force.com, or Microsoft Azure. NCAs exhibit a combined usage of the three fundamental technologies: Computational grid - loosely, e.g. MapReduce Data grids (e.g. distributed in-memory data caches) Auto-scaling on any managed infrastructure

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  Cozi

  Cozi is a family organization website and mobile app designed to streamline household management. It offers shared calendars, to-do lists, shopping lists, and messaging tools, allowing multiple users to coordinate under one account. Founded in 2005 by former Microsoft employees, Cozi has evolved through acquisitions and now operates under OurFamilyWizard. The app is available in both free and premium versions on iOS, Android, and desktop platforms. == History == Cozi was founded in 2005 by Robbie Cape and Jan Miksovsky, two former Microsoft employees who sought to simplify family logistics with technology. The company's first product, Cozi Central, was released on September 25, 2006, and included a family calendar, shopping lists, family messaging and a photo collage screensaver. The company is based in Seattle, Washington. Cozi has both a freemium version, and a paid version called Cozi Gold. Cozi Gold's additional features include Cozi Contacts, a birthday tracker, more reminders, mobile month view, and change notifications. The software can be used on desktop or mobile applications for iOS and Android. On June 5, 2011, Cozi set a Guinness World Record for the longest line of ducks in a row. The line stretched for one mile and was made up of 17,782 rubber ducks. Cozi was acquired by Time Inc. in 2014. After the Meredith Corporation acquired Time in 2018, Cozi was moved into the Parents Network division. On May 4, 2022, Cozi was acquired by OurFamilyWizard of Minneapolis, Minnesota, reporting more than 20 million registered users.

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  Discrete skeleton evolution

  Discrete Skeleton Evolution (DSE) describes an iterative approach to reducing a morphological or topological skeleton. It is a form of pruning in that it removes noisy or redundant branches (spurs) generated by the skeletonization process, while preserving information-rich "trunk" segments. The value assigned to individual branches varies from algorithm to algorithm, with the general goal being to convey the features of interest of the original contour with a few carefully chosen lines. Usually, clarity for human vision (aka. the ability to "read" some features of the original shape from the skeleton) is valued as well. DSE algorithms are distinguished by complex, recursive decision-making processes with high computational requirements. Pruning methods such as by structuring element (SE) convolution and the Hough transform are general purpose algorithms which quickly pass through an image and eliminate all branches shorter than a given threshold. DSE methods are most applicable when detail retention and contour reconstruction are valued. == Methodology == === Pre-processing === Input images will typical contain more data than is necessary to generate an initial skeleton, and thus must be reduced in some way. Reducing the resolution, converting to grayscale, and then binary by masking or thresholding are common first steps. Noise removal may occur before and/or after converting an image to binary. Morphological operations such as closing, opening, and smoothing of the binary image may also be part of pre-processing. Ideally, the binarized contour should be as noise-free as possible before the skeleton is generated. === Skeletonization === DSE techniques may be applied to an existing skeleton or incorporated as part of the skeleton growing algorithm. Suitable skeletons may be obtained using a variety of methods: Thinning algorithms, such as the Grassfire transform Voronoi diagram Medial Axis Transform or Symmetry Axis Transform Distance Mapping === Significance Measures === DSE and related methods remove entire spurious branches while leaving the main trunk intact. The intended result is typically optimized for visual clarity and retention of information, such that the original contour can be reconstructed from the fully pruned skeleton. The value of various properties must be weighted by the application, and improving the efficiency is an ongoing topic of research in computer vision and image processing. Some significance measures include: Discrete Bisector Function Contour length Bending Potential Ratio Discrete Curve Evolution === Iteration === Each branch is evaluated during a pass through the skeletonized image according to the specific algorithm being used. Low value branches are removed and the process is repeated until a desired threshold of simplicity is reached. === Reconstruction === If all points on the output skeleton are the center points of maximal disks of the image and the radius information is retained, a contour image can be reconstructed == Applications == === Handwriting and text parsing === Variability in hand-written text is an ongoing challenge, simplification makes it somewhat easier for computer vision algorithms to make judgements about intended characters. === Soft body classification (animals) === The maximal disks centered on the skeleton imply roughly spherical masses, the features of the extracted skeleton are relatively unchanged even as the soft body deforms or self-occludes. Skeleton information is one facet of determining whether two animals are the "same" some way, though it must usually be paired with another technique to effectively identify a target. === Medical uses === Investigation of organs, tissue damage and deformation caused by disease.

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  Image stitching

  Image stitching or photo stitching is the process of combining multiple photographic images with overlapping fields of view to produce a segmented panorama or high-resolution image. Commonly performed through the use of computer software, most approaches to image stitching require nearly exact overlaps between images and identical exposures to produce seamless results, although some stitching algorithms actually benefit from differently exposed images by doing high-dynamic-range imaging in regions of overlap. Some digital cameras can stitch their photos internally. == Applications == Image stitching is widely used in modern applications, such as the following: Document mosaicing Image stabilization feature in camcorders that use frame-rate image alignment High-resolution image mosaics in digital maps and satellite imagery Medical imaging Multiple-image super-resolution imaging Video stitching Object insertion == Process == The image stitching process can be divided into three main components: image registration, calibration, and blending. === Image stitching algorithms === In order to estimate image alignment, algorithms are needed to determine the appropriate mathematical model relating pixel coordinates in one image to pixel coordinates in another. Algorithms that combine direct pixel-to-pixel comparisons with gradient descent (and other optimization techniques) can be used to estimate these parameters. Distinctive features can be found in each image and then efficiently matched to rapidly establish correspondences between pairs of images. When multiple images exist in a panorama, techniques have been developed to compute a globally consistent set of alignments and to efficiently discover which images overlap one another. A final compositing surface onto which to warp or projectively transform and place all of the aligned images is needed, as are algorithms to seamlessly blend the overlapping images, even in the presence of parallax, lens distortion, scene motion, and exposure differences. === Image stitching issues === Since the illumination in two views cannot be guaranteed to be identical, stitching two images could create a visible seam. Other reasons for seams could be the background changing between two images for the same continuous foreground. Other major issues to deal with are the presence of parallax, lens distortion, scene motion, and exposure differences. In a non-ideal real-life case, the intensity varies across the whole scene, and so does the contrast and intensity across frames. Additionally, the aspect ratio of a panorama image needs to be taken into account to create a visually pleasing composite. For panoramic stitching, the ideal set of images will have a reasonable amount of overlap (at least 15–30%) to overcome lens distortion and have enough detectable features. The set of images will have consistent exposure between frames to minimize the probability of seams occurring. === Keypoint detection === Feature detection is necessary to automatically find correspondences between images. Robust correspondences are required in order to estimate the necessary transformation to align an image with the image it is being composited on. Corners, blobs, Harris corners, and differences of Gaussians of Harris corners are good features since they are repeatable and distinct. One of the first operators for interest point detection was developed by Hans Moravec in 1977 for his research involving the automatic navigation of a robot through a clustered environment. Moravec also defined the concept of "points of interest" in an image and concluded these interest points could be used to find matching regions in different images. The Moravec operator is considered to be a corner detector because it defines interest points as points where there are large intensity variations in all directions. This often is the case at corners. However, Moravec was not specifically interested in finding corners, just distinct regions in an image that could be used to register consecutive image frames. Harris and Stephens improved upon Moravec's corner detector by considering the differential of the corner score with respect to direction directly. They needed it as a processing step to build interpretations of a robot's environment based on image sequences. Like Moravec, they needed a method to match corresponding points in consecutive image frames, but were interested in tracking both corners and edges between frames. SIFT and SURF are recent key-point or interest point detector algorithms but a point to note is that SURF is patented and its commercial usage restricted. Once a feature has been detected, a descriptor method like SIFT descriptor can be applied to later match them. === Registration === Image registration involves matching features in a set of images or using direct alignment methods to search for image alignments that minimize the sum of absolute differences between overlapping pixels. When using direct alignment methods one might first calibrate one's images to get better results. Additionally, users may input a rough model of the panorama to help the feature matching stage, so that e.g. only neighboring images are searched for matching features. Since there are smaller group of features for matching, the result of the search is more accurate and execution of the comparison is faster. To estimate a robust model from the data, a common method used is known as RANSAC. The name RANSAC is an abbreviation for "RANdom SAmple Consensus". It is an iterative method for robust parameter estimation to fit mathematical models from sets of observed data points which may contain outliers. The algorithm is non-deterministic in the sense that it produces a reasonable result only with a certain probability, with this probability increasing as more iterations are performed. It being a probabilistic method means that different results will be obtained for every time the algorithm is run. The RANSAC algorithm has found many applications in computer vision, including the simultaneous solving of the correspondence problem and the estimation of the fundamental matrix related to a pair of stereo cameras. The basic assumption of the method is that the data consists of "inliers", i.e., data whose distribution can be explained by some mathematical model, and "outliers" which are data that do not fit the model. Outliers are considered points which come from noise, erroneous measurements, or simply incorrect data. For the problem of homography estimation, RANSAC works by trying to fit several models using some of the point pairs and then checking if the models were able to relate most of the points. The best model – the homography, which produces the highest number of correct matches – is then chosen as the answer for the problem; thus, if the ratio of number of outliers to data points is very low, the RANSAC outputs a decent model fitting the data. === Calibration === Image calibration aims to minimize differences between an ideal lens models and the camera-lens combination that was used, optical defects such as distortions, exposure differences between images, vignetting, camera response and chromatic aberrations. If feature detection methods were used to register images and absolute positions of the features were recorded and saved, stitching software may use the data for geometric optimization of the images in addition to placing the images on the panosphere. Panotools and its various derivative programs use this method. ==== Alignment ==== Alignment may be necessary to transform an image to match the view point of the image it is being composited with. Alignment, in simple terms, is a change in the coordinates system so that it adopts a new coordinate system which outputs image matching the required viewpoint. The types of transformations an image may go through are pure translation, pure rotation, a similarity transform which includes translation, rotation and scaling of the image which needs to be transformed, Affine or projective transform. Projective transformation is the farthest an image can transform (in the set of two dimensional planar transformations), where only visible features that are preserved in the transformed image are straight lines whereas parallelism is maintained in an affine transform. Projective transformation can be mathematically described as x ′ = H ⋅ x , {\displaystyle x'=H\cdot x,} where x {\displaystyle x} is points in the old coordinate system, x ′ {\displaystyle x'} is the corresponding points in the transformed image and H {\displaystyle H} is the homography matrix. Expressing the points x {\displaystyle x} and x ′ {\displaystyle x'} using the camera intrinsics ( K {\displaystyle K} and K ′ {\displaystyle K'} ) and its rotation and translation [ R t ] {\displaystyle [R\,t]} to the real-world coordinates X {\displaystyle X} and < m a t h > x {\displaystyle $x\}\; and\; x\; \prime \; \{\backslash displaystyle\; x\text{'}\}\; \text{'}$, we get Using the abo

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  Apache Drill

  Apache Drill is an open-source software framework that supports data-intensive distributed applications for interactive analysis of large-scale datasets. Built chiefly by contributions from developers from MapR, Drill is inspired by Google's Dremel system. Drill is an Apache top-level project. Drill supports a variety of NoSQL databases and file systems, including Alluxio, HBase, MongoDB, MapR-DB, HDFS, MapR-FS, Amazon S3, Azure Blob Storage, Google Cloud Storage, Swift, NAS and local files. A single query can join data from multiple datastores. Drill's datastore-aware optimizer automatically restructures a query plan to leverage the datastore's internal processing capabilities. In addition, Drill supports data locality, if Drill and the datastore are on the same nodes. Tom Shiran is the founder of the Apache Drill Project. It was designated an Apache Software Foundation top-level project in December 2016. == Features == One explicitly stated design goal is that Drill is able to scale to 10,000 servers or more and to be able to process petabytes of data and trillions of records in seconds. Schema-free JSON document model similar to MongoDB and Elasticsearch, without requiring a formal schema to be declared Industry-standard APIs: ANSI SQL, ODBC/JDBC, RESTful APIs Extremely user and developer friendly Pluggable architecture enables connectivity to multiple datastores Version 1.9 added dynamic user-defined functions Version 1.11 added cryptographic-related functions and PCAP file format support == Back-end support == Drill is primarily focused on non-relational datastores, including Apache Hadoop text files, NoSQL, and cloud storage. A notable feature also includes in situ querying of local JSON and Apache Parquet files. Some additional datastores that it supports include: All Hadoop distributions (HDFS API 2.3+), including Apache Hadoop, MapR, CDH and Amazon EMR NoSQL: MongoDB, Apache HBase, Apache Cassandra Online Analytical Processing: Apache Kudu, Apache Druid, OpenTSDB Cloud storage: Amazon S3, Google Cloud Storage, Azure Blob Storage, Swift, IBM Cloud Object Storage Diverse data formats, including Apache Avro, Apache Parquet and JSON RDBMs storage plugins (Using JDBC to connect to MySQL, PostgreSQL, and others) A new datastore can be added by developing a storage plugin. Drill's "schema-free" JSON data model enables it to query non-relational datastores in-situ . == Front-end support == Drill itself can be queried via JDBC, ODBC, or REST through a variety of methods and languages including Python and Java. The default install includes a web interface allowing end-users to execute ANSI SQL directly and export data tables as CSV files without any programming. The dashboard library, Apache Superset, is particularly well suited for visualization of data queried with Drill.

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  Carrier cloud

  In cloud computing, a carrier cloud is a class of cloud that integrates wide area networks (WAN) and other attributes of communications service providers’ carrier-grade networks to enable the deployment of highly-complex applications in the cloud. In contrast, classic cloud computing focuses on the data center and does not address the network connecting data centers and cloud users. This may result in unpredictable response times and security issues when business-critical data are transferred over the Internet. == History == The advent of virtualization technology, cost-effective computing hardware, and ubiquitous Internet connectivity have enabled the first wave of cloud services starting in the early years of the 21st century. But many businesses and other organizations hesitated to move to more demanding applications, from on-premises dedicated hardware to private or public clouds. As a response, communications service providers started in the 2010/2011 time frame to develop carrier clouds that address perceived weaknesses in existing cloud services. Cited weaknesses vary but often include possible downtime, security issues, high cost of custom software and data transfer, inflexibility of some cloud apps, poor customer and nonfulfillment of service level agreements (SLAs). == Characteristics == To enable the deployment of time-sensitive and business critical applications in the cloud, the carrier cloud is designed to match or even exceed the characteristics of on-premises deployments. Therefore, the carrier cloud is characterized by some or all of the following items: Configurable, elastic network performance: Typical cloud computing solutions use the best effort of the public Internet to connect cloud users and data centers. This approach provides instant connectivity but does not offer control over network capacities, latencies, and jitter. Carrier clouds address these gaps with content delivery networks and/or dedicated virtual private networks (VPN) at OSI layers 1 (optical wavelengths), 2 (data link layer), and 3 (network layer). These VPNs can be configured to offer the desired performance parameters and exhibit the same type of elasticity for the network that regular clouds provide for servers and storage. To achieve the requested performance parameters, such as low latency, cloud applications can be (automatically) allocated to distributed data centers that are close enough to the cloud users. Automatic resource placement: For a cloud with multiple data centers, information about both the data center and the connecting network is relevant for a decision of where to place cloud images and storage volumes. For this decision, carrier clouds can obtain relevant information about the network, e.g., using the Application-Layer Traffic Optimization (ALTO) protocol. High level of security and governance: Cloud application providers are subject to general and domain specific security, privacy, and governance requirements and regulations, such as the European Data Protection Directive and the U.S. Health Insurance Portability and Accountability Act. For added security, the wide area network of the carrier cloud can provide segregated encrypted or unencrypted network links that are not accessible from the general Internet. At the data center, the carrier cloud provides e.g. virtual private servers, management processes, logs, and documentation to fulfill security and governance rules. Location control: Fundamentally, cloud users should not be concerned with the geographic location of their cloud resources. However, privacy and other regulations may mandate that certain types of data must not be sent outside a national jurisdiction or other geographical region. Open APIs: Carrier clouds provide graphical user interfaces and Web application programming interfaces that allow cloud application providers to set up, manage, and monitor both, the data center and the WAN, of their cloud services. == Architecture == Carrier clouds encompass data centers at different network tiers and wide area networks that connect multiple data centers to each other as well as to the cloud users. Links between data centers are used for failover, overflow, backup, and geographic diversity. Carrier clouds can be set up as public, private, or hybrid clouds. The carrier cloud federates these cloud entities by using a single management system to orchestrate, manage, and monitor data center and network resources as a single system.

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  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

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  Smart object

  A smart object is an object that enhances the interaction with not only people but also with other smart objects. Also known as smart connected products or smart connected things (SCoT), they are products, assets and other things embedded with processors, sensors, software and connectivity that allow data to be exchanged between the product and its environment, manufacturer, operator/user, and other products and systems. Connectivity also enables some capabilities of the product to exist outside the physical device, in what is known as the product cloud. The data collected from these products can be then analysed to inform decision-making, enable operational efficiencies and continuously improve the performance of the product. It can not only refer to interaction with physical world objects but also to interaction with virtual (computing environment) objects. A smart physical object may be created either as an artifact or manufactured product or by embedding electronic tags such as RFID tags or sensors into non-smart physical objects. Smart virtual objects are created as software objects that are intrinsic when creating and operating a virtual or cyber world simulation or game. The concept of a smart object has several origins and uses, see History. There are also several overlapping terms, see also smart device, tangible object or tangible user interface and Thing as in the Internet of things. == History == In the early 1990s, Mark Weiser, from whom the term ubiquitous computing originated, referred to a vision "When almost every object either contains a computer or can have a tab attached to it, obtaining information will be trivial", Although Weiser did not specifically refer to an object as being smart, his early work did imply that smart physical objects are smart in the sense that they act as digital information sources. Hiroshi Ishii and Brygg Ullmer refer to tangible objects in terms of tangibles bits or tangible user interfaces that enable users to "grasp & manipulate" bits in the center of users' attention by coupling the bits with everyday physical objects and architectural surfaces. The smart object concept was introduced by Marcelo Kallman and Daniel Thalmann as an object that can describe its own possible interactions. The main focus here is to model interactions of smart virtual objects with virtual humans, agents, in virtual worlds. The opposite approach to smart objects is 'plain' objects that do not provide this information. The additional information provided by this concept enables far more general interaction schemes, and can greatly simplify the planner of an artificial intelligence agent. In contrast to smart virtual objects used in virtual worlds, Lev Manovich focuses on physical space filled with electronic and visual information. Here, "smart objects" are described as "objects connected to the Net; objects that can sense their users and display smart behaviour". More recently in the early 2010s, smart objects are being proposed as a key enabler for the vision of the Internet of things. The combination of the Internet and emerging technologies such as near field communications, real-time localization, and embedded sensors enables everyday objects to be transformed into smart objects that can understand and react to their environment. Such objects are building blocks for the Internet of things and enable novel computing applications. In 2018, one of the world's first smart houses was built in Klaukkala, Finland in the form of a five-floor apartment block, using the Kone Residential Flow solution created by KONE, allowing even a smartphone to act as a home key. == Characteristics == Although we can view interaction with physical smart object in the physical world as distinct from interaction with virtual smart objects in a virtual simulated world, these can be related. Poslad considers the progression of: how humans use models of smart objects situated in the physical world to enhance human to physical world interaction; versus how smart physical objects situated in the physical world can model human interaction in order to lessen the need for human to physical world interaction; versus how virtual smart objects by modelling both physical world objects and modelling humans as objects and their subsequent interactions can form a predominantly smart virtual object environment. === Smart physical objects === The concept smart for a smart physical object simply means that it is active, digital, networked, can operate to some extent autonomously, is reconfigurable and has local control of the resources it needs such as energy, data storage, etc. Note, a smart object does not necessarily need to be intelligent as in exhibiting a strong essence of artificial intelligence—although it can be designed to also be intelligent. Physical world smart objects can be described in terms of three properties: Awareness: is a smart object's ability to understand (that is, sense, interpret, and react to) events and human activities occurring in the physical world. Representation: refers to a smart object's application and programming model—in particular, programming abstractions. Interaction: denotes the object's ability to converse with the user in terms of input, output, control, and feedback. Based upon these properties, these have been classified into three types: Activity-Aware Smart Objects: Are objects that can record information about work activities and its own use. Policy-Aware Smart Objects: Are objects that are activity-aware Objects can interpret events and activities with respect to predefined organizational policies. Process-Aware Smart Objects: Processes play a fundamental role in industrial work management and operation. A process is a collection of related activities or tasks that are ordered according to their position in time and space. === Smart virtual objects === For the virtual object in a virtual world case, an object is called smart when it has the ability to describe its possible interactions. This focuses on constructing a virtual world using only virtual objects that contain their own interaction information. There are four basic elements to constructing such a smart virtual object framework. Object properties: physical properties and a text description Interaction information: position of handles, buttons, grips, and the like Object behavior: different behaviors based on state variables Agent behaviors: description of the behavior an agent should follow when using the object Some versions of smart objects also include animation information in the object information, but this is not considered to be an efficient approach, since this can make objects inappropriately oversized. === Categorization === The terms smart, connected product or smart product can be confusing as it is used to cover a broad range of different products, ranging from smart home appliances (e.g., smart bathroom scales or smart light bulbs) to smart cars (e.g., Tesla). While these products share certain similarities, they often differ substantially in their capabilities. Raff et al. developed a conceptual framework that distinguishes different smart products based on their capabilities, which features 4 types of smart product archetypes (in ascending order of "smartness"). Digital Connected Responsive Intelligent == Advantages == Smart, connected products have three primary components: Physical – made up of the product's mechanical and electrical parts. Smart – made up of sensors, microprocessors, data storage, controls, software, and an embedded operating system with enhanced user interface. Connectivity – made up of ports, antennae, and protocols enabling wired/wireless connections that serve two purposes, it allows data to be exchanged with the product and enables some functions of the product to exist outside the physical device. Each component expands the capabilities of one another resulting in "a virtuous cycle of value improvement". First, the smart components of a product amplify the value and capabilities of the physical components. Then, connectivity amplifies the value and capabilities of the smart components. These improvements include: Monitoring of the product's conditions, its external environment, and its operations and usage. Control of various product functions to better respond to changes in its environment, as well as to personalize the user experience. Optimization of the product's overall operations based on actual performance data, and reduction of downtimes through predictive maintenance and remote service. Autonomous product operation, including learning from their environment, adapting to users' preferences and self-diagnosing and service. === The Internet of things (IoT) === The Internet of things is the network of physical objects that contain embedded technology to communicate and sense or interact with their internal states or the external environment. The phrase "Internet of things" reflects the gro

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  GNU Binutils

  The GNU Binary Utilities, or binutils, is a collection of programming tools maintained by the GNU Project for working with executable code including assembly, linking and many other development operations. The tools are originally from Cygnus Solutions. The tools are typically used along with other GNU tools such as GNU Compiler Collection, and the GNU Debugger. == Tools == The tools include: == elfutils == Ulrich Drepper wrote elfutils, to partially replace GNU Binutils, purely for Linux and with support only for ELF and DWARF. It distributes three libraries with it for programmatic access.

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  Focus recovery based on the linear canonical transform

  For digital image processing, the Focus recovery from a defocused image is an ill-posed problem since it loses the component of high frequency. Most of the methods for focus recovery are based on depth estimation theory. The Linear canonical transform (LCT) gives a scalable kernel to fit many well-known optical effects. Using LCTs to approximate an optical system for imaging and inverting this system, theoretically permits recovery of a defocused image. == Depth of field and perceptual focus == In photography, depth of field (DOF) means an effective focal length. It is usually used for stressing an object and deemphasizing the background (and/or the foreground). The important measure related to DOF is the lens aperture. Decreasing the diameter of aperture increases focus and lowers resolution and vice versa. == The Huygens–Fresnel principle and DOF == The Huygens–Fresnel principle describes diffraction of wave propagation between two fields. It belongs to Fourier optics rather than geometric optics. The disturbance of diffraction depends on two circumstance parameters, the size of aperture and the interfiled distance. Consider a source field and a destination field, field 1 and field 0, respectively. P1(x1,y1) is the position in the source field, P0(x0,y0) is the position in the destination field. The Huygens–Fresnel principle gives the diffraction formula for two fields U(x0,y0), U(x1,y1) as following: U ( x 0 , y 0 ) = 1 j λ ∫ ∫ U ( x 1 , y 1 ) e j k r 01 r 01 cos ⁡ θ d x 1 d y 1 {\displaystyle \mathbf {U} (x_{0},y_{0})={\frac {1}{j\lambda }}\int \!\int \mathbf {U} (x_{1},y_{1}){\frac {e^{jkr_{01}}}{r_{01}}}\cos \theta dx_{1}dy_{1}} where θ denotes the angle between r 01 {\displaystyle r_{01}} and z {\displaystyle z} . Replace cos θ by r 01 z {\displaystyle {\frac {r_{01}}{z}}} and r 01 {\displaystyle r_{01}} by [ ( x 0 − x 1 ) 2 + ( y 0 − y 1 ) 2 + z 2 ] 1 / 2 {\displaystyle [(x_{0}-x_{1})^{2}+(y_{0}-y_{1})^{2}+z^{2}]^{1/2}} we get U ( x 0 , y 0 ) = 1 j λ z ∫ ∫ U ( x 1 , y 1 ) exp ⁡ ( j k z [ 1 + ( x 0 − x 1 z ) 2 + ( y 0 − y 1 z ) 2 ] 1 / 2 ) 1 + ( x 0 − x 1 z ) 2 + ( y 0 − y 1 z ) 2 d x 1 d y 1 {\displaystyle \mathbf {U} (x_{0},y_{0})={\frac {1}{j\lambda z}}\int \!\int \mathbf {U} (x_{1},y_{1}){\frac {\exp(jkz[1+({\frac {x_{0}-x_{1}}{z}})^{2}+({\frac {y_{0}-y_{1}}{z}})^{2}]^{1/2})}{1+({\frac {x_{0}-x_{1}}{z}})^{2}+({\frac {y_{0}-y_{1}}{z}})^{2}}}dx_{1}dy_{1}} The further distance z or the smaller aperture (x1,y1) causes a greater diffraction. A larger DOF can lead to a more effective focused wave distribution. This seems to be a conflict. Here are the notations: Diffraction In a real imaging environment, the depths of objects comparing to the aperture are usually not enough to lead to serious diffraction. However, a long enough depth of the object can truly blurs the image. Effective Focus Small aperture, small blurring radius, few wave information. Loses details in comparing to a large aperture. In conclusion, diffraction explains a micro behavior whereas DOF shows a macro behavior. Both of them are related to aperture size. == Linear canonical transform == As the meaning of "canonical", the linear canonical transform (LCT) is a scalable transform that connects to many important kernels such as the Fresnel transform, Fraunhofer transform and the fractional Fourier transform. It can be easily controlled by its four parameters, a, b, c, d (3 degrees of freedom). The definition: L M ( f ( u ) ) = ∫ L M ( u , u ′ ) f ( u ′ ) d u ′ {\displaystyle L_{M}(f(u))=\int L_{M}(u,u')f(u')du'} where L M ( u , u ′ ) = { 1 b e − j π / 4 e [ j π ( d b u 2 ) − 2 1 b u u ′ + a b u ′ 2 ] , if b ≠ 0 d e j 2 c d u 2 δ ( u ′ − d u ) , if b = 0 {\displaystyle L_{M}(u,u')={\begin{cases}{\sqrt {\frac {1}{b}}}e^{-j\pi /4}e^{[j\pi ({\frac {d}{b}}u^{2})-2{\frac {1}{b}}uu'+{\frac {a}{b}}u'^{2}]},&{\mbox{if }}b\neq 0\\{\sqrt {d}}e^{{\frac {j}{2}}cdu^{2}}\delta (u'-du),&{\mbox{if }}b=0\end{cases}}} Consider a general imaging system with object distance z0, focal length of the thin lens f and an imaging distance z1. The effect of the propagation in freespace acts as nearly a chirp convolution, that is, the formula of diffraction. Besides, the effect of the propagation in thin lens acts as a chirp multiplication. The parameters are all simplified as paraxial approximations while meeting the freespace propagation. It does not consider aperture size. From the properties of the LCT, it is possible to obtain those 4 parameters for this optical system as: [ 1 − z 1 f λ z 0 − λ z 0 z 1 f + λ z 1 − 1 λ f 1 − z 0 f ] {\displaystyle {\begin{bmatrix}1-{\frac {z_{1}}{f}}\quad &\lambda z_{0}-{\frac {\lambda z_{0}z_{1}}{f}}+\lambda z_{1}\\-{\frac {1}{\lambda f}}\quad &1-{\frac {z_{0}}{f}}\end{bmatrix}}} Once the values of z1, z0 and f are known, the LCT can simulate any optical system.

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  CAMeL-View TestRig

  CAMeL-View is a software application, which is used for the model based design of mechatronic systems (multi-body simulation, block diagrams, pneumatic systems, hydraulic systems, general simulation, linear analysis and Hardware-in-the-Loop). CAMeL-View enables object-oriented model creation of mechatronic systems through the use of graphic blocks. The basic elements of multi-body system dynamics, control technology, hydraulics and hardware connectivity support the modeling process. The user’s proprietary C-Code can also be integrated into the models, which allows CAMeL-View TestRig to be implemented in all phases of the model based design process ( modeling, physical testing and prototyping), and lends itself especially well to mechatronic system design. The model’s structure is described and displayed with the help of directional connectors. Physical connections (such as mechanical or hydraulic linkages) as well as input and output connections (signal flow) are also available. The input of equations is done via mathematical expressions, e.g. the input of constitutive differential equations in vector and matrix form. Based on the model’s structure, the descriptive equations are converted into non-linear state space representations and converted into executable C-Code. CAMeL-View supports the simulation process with a configurable “experiment environment” (for simulator and instrumentation components) which allows the user to apply simulation models to supported targets (MPC5200, TriCore, X86, etc.) without the need for additional software tools for Hardware-in-the-Loop applications. In addition, the generation of so-called S-Functions for use in Simulink and the generation of ANSI C-Code for use in stand-alone simulators is also supported. A particularly noteworthy feature in CAMeL-View TestRig is the way in which the descriptive equations for multi-body system models are created. All multi-body simulation formalisms used for code generation create their equations in the form of typical explicit differential equations (ODE). This is especially important in Hardware-in-the-Loop applications where the calculation of simulation results within a specific, defined time frame must be assured. Only then is it possible to implement complex multi-body simulation models for Hardware-in-the-Loop applications under stringent real-time conditions. These constraints cannot be met when using DAE-based methods. Additional Toolboxes are available for linear analysis (Eigenvalues, pole-zero analysis, frequency response, etc.) of VRML-based animation. Development of CAMeL-View began in 1991 in the Paderborn Mechatronic Laboratory of Professor Dr. Ing. J. Lückel. The software was based on predecessors that had been developed there since 1986. The name stands for Computer Aided Mechatronic Laboratory – Virtual Engineering Workbench and describes the basic intent of one of the specific demands placed on development engineers in the computer lab.

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  KE Software

  KE Software is a formerly Australian-owned computer software company based in Manchester, United Kingdom, which specialises in collection management programs for museums, galleries and archives. The Axiell Group acquired the firm in 2014. == History == KE Software had its origins in investigations into electronic systems for managing natural science collections conducted in the late 1970s under a joint program of the University of Melbourne, the then National Museum of Victoria and the Australian Museum, which led to the development of the Titan Database in 1984. Much of the credit for the development of the project was due to the work of Martin Hallett of the Museum of Victoria which evolved into Textpress, and by 2000, the KE EMu database program. KE Software was bought by Axiell in 2014 and the team merged with the Axiell staff. Axiell continues to sell and support EMu. == Products == The firm has two main products: the Ke EMu Electronic Museum management system, a collections management system for museums; and Vitalware Vital Records Management System. The first version of Ke EMu was launched in 1997 and uses the Texpress database engine with client/server architecture on a Windows or Unix/Linux server. Ke Emu is consistent with the Dublin Core / Darwin Core standards for archive and museum catalogue metadata. "The company’s clients include the three largest museums in the world.: == KE EMu == KE EMu is considered one of the more effective and purpose-designed museum cataloguing programs. particularly in the creation of public interfaces to museum catalogue data. KE EMu was further developed in 1997 as a multilingual platform, which has been utilised in bilingual institutions such as the Canadian Museum of Civilisation. Subsequently this evolved into Texpress and KE EMu (standing for Electronic MUseum) in 2000, which is "now used across the world in natural science museums with huge collections'". KE EMu is used by a large number of museums and galleries around the world, including the Smithsonian Anthropological Collection, American Museum of Natural HistoryVancouver Art Gallery, New York Botanical Garden, the University of Chicago Research Archives, the University of Pennsylvania Museum in Philadelphia, the National Museum of Australia, the Australian Museum, Museum of Victoria, University of Melbourne Archives, and the Alexander Turnbull Library, National Library of New Zealand. There are over 300 clients, and more than 5000 users of the EMu software worldwide. The program has been described as providing "...comprehensive museum management (collection management plus other administrative needs for a museum), workflow and project management, flexible metadata, various stats and metrics, and comprehensive web interface with support for mobile devices and kiosks" == KE Vitalware == The firm's vitalware software is used by a number of governments and commercial organisations for managing and accessing large data sets, such as the birth records of the Trinidad and Tobago Registrar General, the Government of Anguilla, Ministry for Infrastructure, Communications, Utility and Housing, and the Mississippi Department of Information Technology Services. == Further development == A specialist tracking component for KE EMu has been developed by Forbes Hawkins of Museum Victoria. This enables locations to be barcoded, and data to be updated as items are moved around the stores, or between venues, display, laboratories and other locations. This system has been considered by Museums around the world. The company has been working with Australian government agencies to digitize birth deaths and marriage registers in order to cross match identity data. The program has also been used for managing the Australian Plant Disease Database and the Australian Plant Pest Database as the program "...has several features that have proven to be invaluable for a plant disease database".

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  Software development process

  A software development process prescribes a process for developing software. It typically divides an overall effort into smaller steps or sub-processes that are intended to ensure high-quality results. The process may describe specific deliverables – artifacts to be created and completed. Although not strictly limited to it, software development process often refers to the high-level process that governs the development of a software system from its beginning to its end of life – known as a methodology, model or framework. The system development life cycle (SDLC) describes the typical phases that a development effort goes through from the beginning to the end of life for a system – including a software system. A methodology prescribes how engineers go about their work in order to move the system through its life cycle. A methodology is a classification of processes or a blueprint for a process that is devised for the SDLC. For example, many processes can be classified as a spiral model. Software process and software quality are closely interrelated; some unexpected facets and effects have been observed in practice. == Methodology == The SDLC drives the definition of a methodology in that a methodology must address the phases of the SDLC. Generally, a methodology is designed to result in a high-quality system that meets or exceeds expectations (requirements) and is delivered on time and within budget even though computer systems can be complex and integrate disparate components. Various methodologies have been devised, including waterfall, spiral, agile, rapid prototyping, incremental, and synchronize and stabilize. A major difference between methodologies is the degree to which the phases are sequential vs. iterative. Agile methodologies, such as XP and scrum, focus on lightweight processes that allow for rapid changes. Iterative methodologies, such as Rational Unified Process and dynamic systems development method, focus on stabilizing project scope and iteratively expanding or improving products. Sequential or big-design-up-front (BDUF) models, such as waterfall, focus on complete and correct planning to guide larger projects and limit risks to successful and predictable results. Anamorphic development is guided by project scope and adaptive iterations. In scrum, for example, one could say a single user story goes through all the phases of the SDLC within a two-week sprint. By contrast the waterfall methodology, where every business requirement is translated into feature/functional descriptions which are then all implemented typically over a period of months or longer. A project can include both a project life cycle (PLC) and an SDLC, which describe different activities. According to Taylor (2004), "the project life cycle encompasses all the activities of the project, while the systems development life cycle focuses on realizing the product requirements". === History === The term SDLC is often used as an abbreviated version of SDLC methodology. Further, some use SDLC and traditional SDLC to mean the waterfall methodology. According to Elliott (2004), SDLC "originated in the 1960s, to develop large scale functional business systems in an age of large scale business conglomerates. Information systems activities revolved around heavy data processing and number crunching routines". The structured systems analysis and design method (SSADM) was produced for the UK government Office of Government Commerce in the 1980s. Ever since, according to Elliott (2004), "the traditional life cycle approaches to systems development have been increasingly replaced with alternative approaches and frameworks, which attempted to overcome some of the inherent deficiencies of the traditional SDLC". The main idea of the SDLC has been "to pursue the development of information systems in a very deliberate, structured and methodical way, requiring each stage of the life cycle––from the inception of the idea to delivery of the final system––to be carried out rigidly and sequentially" within the context of the framework being applied. Other methodologies were devised later: 1970s Structured programming since 1969 Cap Gemini SDM, originally from PANDATA, the first English translation was published in 1974. SDM stands for System Development Methodology 1980s Structured systems analysis and design method (SSADM) from 1980 onwards Information Requirement Analysis/Soft systems methodology 1990s Object-oriented programming (OOP) developed in the early 1960s and became a dominant programming approach during the mid-1990s Rapid application development (RAD), since 1991 Dynamic systems development method (DSDM), since 1994 Scrum, since 1995 Team software process, since 1998 Rational Unified Process (RUP), maintained by IBM since 1998 Extreme programming, since 1999 2000s Agile Unified Process (AUP) maintained since 2005 by Scott Ambler Disciplined agile delivery (DAD) Supersedes AUP 2010s Scaled Agile Framework (SAFe) Large-Scale Scrum (LeSS) DevOps Since DSDM in 1994, all of the methodologies on the above list except RUP have been agile methodologies - yet many organizations, especially governments, still use pre-agile processes (often waterfall or similar). === Examples === The following are notable methodologies somewhat ordered by popularity. Agile Agile software development refers to a group of frameworks based on iterative development, where requirements and solutions evolve via collaboration between self-organizing cross-functional teams. The term was coined in the year 2001 when the Agile Manifesto was formulated. Waterfall The waterfall model is a sequential development approach, in which development flows one-way (like a waterfall) through the SDLC phases. Spiral In 1988, Barry Boehm published a software system development spiral model, which combines key aspects of the waterfall model and rapid prototyping, in an effort to combine advantages of top-down and bottom-up concepts. It emphases a key area many felt had been neglected by other methodologies: deliberate iterative risk analysis, particularly suited to large-scale complex systems. Incremental Various methods combine linear and iterative methodologies, with the primary objective of reducing inherent project risk by breaking a project into smaller segments and providing more ease-of-change during the development process. Prototyping Software prototyping is about creating prototypes, i.e. incomplete versions of the software program being developed. Rapid Rapid application development (RAD) is a methodology which favors iterative development and the rapid construction of prototypes instead of large amounts of up-front planning. The "planning" of software developed using RAD is interleaved with writing the software itself. The lack of extensive pre-planning generally allows software to be written much faster and makes it easier to change requirements. Shape Up Shape Up is a software development approach introduced by Basecamp in 2018. It is a set of principles and techniques that Basecamp developed internally to overcome the problem of projects dragging on with no clear end. Its primary target audience is remote teams. Shape Up has no estimation and velocity tracking, backlogs, or sprints, unlike waterfall, agile, or scrum. Instead, those concepts are replaced with appetite, betting, and cycles. As of 2022, besides Basecamp, notable organizations that have adopted Shape Up include UserVoice and Block. Chaos Chaos model has one main rule: always resolve the most important issue first. Incremental funding Incremental funding methodology - an iterative approach. Lightweight Lightweight methodology - a general term for methods that only have a few rules and practices. Structured systems analysis and design Structured systems analysis and design method - a specific version of waterfall. Slow programming As part of the larger slow movement, emphasizes careful and gradual work without (or minimal) time pressures. Slow programming aims to avoid bugs and overly quick release schedules. V-Model V-Model (software development) - an extension of the waterfall model. Unified Process Unified Process (UP) is an iterative software development methodology framework, based on Unified Modeling Language (UML). UP organizes the development of software into four phases, each consisting of one or more executable iterations of the software at that stage of development: inception, elaboration, construction, and guidelines. === Comparison === The waterfall model describes the SDLC phases such that each builds on the result of the previous one. Not every project requires that the phases be sequential. For relatively simple projects, phases may be combined or overlapping. Alternative methodologies to waterfall are described and compared below. == Process meta-models == Some process models are abstract descriptions for evaluating, comparing, and improving the specific process adopted by an organization. ISO/IEC 12207 ISO/IEC 12207 i

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  BioBIKE

  BioBike(nee. BioLingua ) is a cloud-based, through-the-web programmable (Paas) symbolic biocomputing and bioinformatics platform that aims to make computational biology, and especially intelligent biocomputing (that is, the application of Artificial Intelligence to computational biology) accessible to research scientists who are not expert programmers. == Unique capabilities == BioBIKE is an integrated symbolic biocomputing and bioinformatics platform, built from the start as an entirely (what is now called) cloud-based architecture where all computing is done in remote servers, and all user access is accomplished through web browsers. BioBIKE has a built-in frame system in which all objects, data, and knowledge are represented. This enables code written either in the native Lisp, in the visual programming language, or systems of rules expressed in the SNARK theorem prover to access the whole of biological knowledge in an integrated manner. For its time (released in 2002) it was unique in permitting users to create fully functional biocomputing programs that run on the back-end servers entirely through the web browser UI. (In modern terms it was one of the first PaaS (Platform as a Service) systems, predating even Salesforce in this capability.) Initially this programming was carried out in raw Lisp, but Jeff Elhai's team at VCU, with NSF funding, created an entirely graphical programming environment on top of BioBIKE based upon the Boxer-style programming environments. Being a multi-headed, multi-threaded, multi-user, multi-tenancy cloud-based system, BioBIKE users were able to directly work together through their web browsers, remotely sharing the same listener and memory space. This permitted a unique sort of collaboration, discussed in Shrager (2007). A specialized offshoot of BioBIKE called "BioDeducta" includes SRI's SNARK theorem prover, offering unique "deductive biocomputing" capabilities. == Implementation == BioBIKE is open-source software implemented using the Lisp programming language. Continuing development takes place by the BioBIKE team centered at Virginia Commonwealth University . == History == BioBIKE was originally called "BioLingua", and was developed by Jeff Shrager at The Carnegie Inst. of Washington Dept. of Plant Biology, and JP Massar with funding from NASA's Astrobiology Division. Shrager and Massar wanted to create a web-based, multi-user Lisp Machine, specialized for bioinformatics. Other early contributors to the project included Mike Travers, and Jeff Elhai of VCU. Elhai obtained continuing funding from the National Science Foundation for the project, which was renamed BioBIKE. Elhai and colleagues added BioBIKE's unique visual programming language. Shrager, meanwhile, collaborated with Richard Waldinger at SRI to build SRI's (SNARK) theorem prover into BioBIKE, creating a deductive biocomputing system, called BioDeducta. == Instances == There used to be a number of BioBIKE verticals in different biological domains, including viral pathogens, cyanobacteria and other bacteria, Arabidopsis thaliana, and several others described in the references.

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